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Conserved domains on  [gi|19114289|ref|NP_593377|]
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major poly(A) binding protein Pabp/Pab1 [Schizosaccharomyces pombe]

Protein Classification

polyadenylate-binding protein( domain architecture ID 11492860)

polyadenylate-binding protein binds the poly(A) tail of mRNA

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
80-642 0e+00

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 709.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRD 159
Cdd:TIGR01628   1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   160 PSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVY 239
Cdd:TIGR01628  81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   240 VGHHVSRRERQSkveALKANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVD 319
Cdd:TIGR01628 161 VGRFIKKHEREA---APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   320 ELNDKEY----KGKKLYVGRAQKKHEREEELRKRYEQMKLEKMNKYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKI 395
Cdd:TIGR01628 238 EMNGKKIglakEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   396 MTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEVRRSQLEAQiqaRNQFRLQqqvAAAAGIPAVQ 475
Cdd:TIGR01628 318 MLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ---FMQLQPR---MRQLPMGSPM 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   476 YGATG-PLIYGPGG---YPIPAAVNGRGMPMvpghngPMPMYPGMPTQfPAGGPAPGYPGMNARGPVPAQGRPMMMP--- 548
Cdd:TIGR01628 392 GGAMGqPPYYGQGPqqqFNGQPLGWPRMSMM------PTPMGPGGPLR-PNGLAPMNAVRAPSRNAQNAAQKPPMQPvmy 464
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   549 ----GSVPSAGPAEAEAVPAVPGMPERFTAADLAAVPEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELL 624
Cdd:TIGR01628 465 ppnyQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELLHLL 544
                         570
                  ....*....|....*...
gi 19114289   625 EDDSALNERVNEAIGVLQ 642
Cdd:TIGR01628 545 ESPELLKSKVDEALEVLK 562
Epiglycanin_TR super family cl20301
Tandem-repeating region of mucin, epiglycanin-like; The unusual mucin, epiglycanin, is ...
20-79 4.48e-03

Tandem-repeating region of mucin, epiglycanin-like; The unusual mucin, epiglycanin, is membrane-bound at the C-terminus but has a long region of this tandem-repeat at the N-terminus. It was the first mucin identified to be associated with the malignant behaviour of carcinoma cells. Mouse Muc21/epiglycanin is thought to be a highly glycosylated molecule, which makes it likely that its function is dependent on its glycoforms. Cells expressing Muc21 are significantly less adherent to each other and to extracellular matrix components than control cells, and this loss of adhesion is mediated by the TR portion of Muc21. This family also now contains the repeat that was the C. elegans protein of unknown function (DUF801).


The actual alignment was detected with superfamily member pfam05647:

Pssm-ID: 461702 [Multi-domain]  Cd Length: 68  Bit Score: 36.15  E-value: 4.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289    20 TNNE-AVESSTKEESSNTPSTETQPEKKAEEPEAAAEPSESTSTPTNASSVATPSGTAPTS 79
Cdd:pfam05647   1 SSTEsSTTSSGASTTSNTGSSTTSGGTSTTSNTGSSTTSSGTSTATNTGSSETSSGSSTTS 61
 
Name Accession Description Interval E-value
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
80-642 0e+00

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 709.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRD 159
Cdd:TIGR01628   1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   160 PSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVY 239
Cdd:TIGR01628  81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   240 VGHHVSRRERQSkveALKANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVD 319
Cdd:TIGR01628 161 VGRFIKKHEREA---APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   320 ELNDKEY----KGKKLYVGRAQKKHEREEELRKRYEQMKLEKMNKYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKI 395
Cdd:TIGR01628 238 EMNGKKIglakEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   396 MTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEVRRSQLEAQiqaRNQFRLQqqvAAAAGIPAVQ 475
Cdd:TIGR01628 318 MLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ---FMQLQPR---MRQLPMGSPM 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   476 YGATG-PLIYGPGG---YPIPAAVNGRGMPMvpghngPMPMYPGMPTQfPAGGPAPGYPGMNARGPVPAQGRPMMMP--- 548
Cdd:TIGR01628 392 GGAMGqPPYYGQGPqqqFNGQPLGWPRMSMM------PTPMGPGGPLR-PNGLAPMNAVRAPSRNAQNAAQKPPMQPvmy 464
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   549 ----GSVPSAGPAEAEAVPAVPGMPERFTAADLAAVPEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELL 624
Cdd:TIGR01628 465 ppnyQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELLHLL 544
                         570
                  ....*....|....*...
gi 19114289   625 EDDSALNERVNEAIGVLQ 642
Cdd:TIGR01628 545 ESPELLKSKVDEALEVLK 562
RRM1_I_PABPs cd12378
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily ...
81-160 8.07e-57

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409812 [Multi-domain]  Cd Length: 80  Bit Score: 186.30  E-value: 8.07e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRDP 160
Cdd:cd12378   1 SLYVGDLHPDVTEAMLYEKFSPAGPVLSIRVCRDAVTRRSLGYAYVNFQQPADAERALDTLNFDVIKGKPIRIMWSQRDP 80
PABP pfam00658
Poly-adenylate binding protein, unique domain; The region featured in this family is found ...
576-641 1.53e-28

Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family.


Pssm-ID: 459893 [Multi-domain]  Cd Length: 66  Bit Score: 108.33  E-value: 1.53e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289   576 DLAAVPEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELLEDDSALNERVNEAIGVL 641
Cdd:pfam00658   1 ALANASPEQQKQMLGERLYPLVQAIQPELAGKITGMLLEMDNSELLHLLEDPEALKEKVDEALEVL 66
PolyA smart00517
C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs ...
581-644 1.98e-28

C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein; Involved in homodimerisation (either directly or indirectly)


Pssm-ID: 197769 [Multi-domain]  Cd Length: 64  Bit Score: 108.14  E-value: 1.98e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289    581 PEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELLEDDSALNERVNEAIGVLQEF 644
Cdd:smart00517   1 PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEVLKSH 64
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
262-342 1.06e-22

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 92.47  E-value: 1.06e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKKH 340
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDReTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                ..
gi 19114289 341 ER 342
Cdd:COG0724  83 ER 84
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
360-442 5.46e-12

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 63.90  E-value: 5.46e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  360 KYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:PLN03134  31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDrETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110

                 ....
gi 19114289  439 AQRK 442
Cdd:PLN03134 111 ANDR 114
Epiglycanin_TR pfam05647
Tandem-repeating region of mucin, epiglycanin-like; The unusual mucin, epiglycanin, is ...
20-79 4.48e-03

Tandem-repeating region of mucin, epiglycanin-like; The unusual mucin, epiglycanin, is membrane-bound at the C-terminus but has a long region of this tandem-repeat at the N-terminus. It was the first mucin identified to be associated with the malignant behaviour of carcinoma cells. Mouse Muc21/epiglycanin is thought to be a highly glycosylated molecule, which makes it likely that its function is dependent on its glycoforms. Cells expressing Muc21 are significantly less adherent to each other and to extracellular matrix components than control cells, and this loss of adhesion is mediated by the TR portion of Muc21. This family also now contains the repeat that was the C. elegans protein of unknown function (DUF801).


Pssm-ID: 461702 [Multi-domain]  Cd Length: 68  Bit Score: 36.15  E-value: 4.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289    20 TNNE-AVESSTKEESSNTPSTETQPEKKAEEPEAAAEPSESTSTPTNASSVATPSGTAPTS 79
Cdd:pfam05647   1 SSTEsSTTSSGASTTSNTGSSTTSGGTSTTSNTGSSTTSSGTSTATNTGSSETSSGSSTTS 61
 
Name Accession Description Interval E-value
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
80-642 0e+00

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 709.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRD 159
Cdd:TIGR01628   1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   160 PSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVY 239
Cdd:TIGR01628  81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   240 VGHHVSRRERQSkveALKANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVD 319
Cdd:TIGR01628 161 VGRFIKKHEREA---APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   320 ELNDKEY----KGKKLYVGRAQKKHEREEELRKRYEQMKLEKMNKYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKI 395
Cdd:TIGR01628 238 EMNGKKIglakEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   396 MTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEVRRSQLEAQiqaRNQFRLQqqvAAAAGIPAVQ 475
Cdd:TIGR01628 318 MLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQ---FMQLQPR---MRQLPMGSPM 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   476 YGATG-PLIYGPGG---YPIPAAVNGRGMPMvpghngPMPMYPGMPTQfPAGGPAPGYPGMNARGPVPAQGRPMMMP--- 548
Cdd:TIGR01628 392 GGAMGqPPYYGQGPqqqFNGQPLGWPRMSMM------PTPMGPGGPLR-PNGLAPMNAVRAPSRNAQNAAQKPPMQPvmy 464
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   549 ----GSVPSAGPAEAEAVPAVPGMPERFTAADLAAVPEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELL 624
Cdd:TIGR01628 465 ppnyQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQVLGERLFPLVEAIEPALAAKITGMLLEMDNSELLHLL 544
                         570
                  ....*....|....*...
gi 19114289   625 EDDSALNERVNEAIGVLQ 642
Cdd:TIGR01628 545 ESPELLKSKVDEALEVLK 562
RRM1_I_PABPs cd12378
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily ...
81-160 8.07e-57

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409812 [Multi-domain]  Cd Length: 80  Bit Score: 186.30  E-value: 8.07e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRDP 160
Cdd:cd12378   1 SLYVGDLHPDVTEAMLYEKFSPAGPVLSIRVCRDAVTRRSLGYAYVNFQQPADAERALDTLNFDVIKGKPIRIMWSQRDP 80
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
363-441 2.64e-51

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 171.69  E-value: 2.64e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12381   1 GVNLYVKNLDDTIDDEKLREEFSPFGTITSAKVMTDEGGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
166-242 1.09e-49

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 167.37  E-value: 1.09e-49
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 166 GTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12379   1 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAERAIEKVNGMLLNGKKVFVGR 77
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
260-339 7.63e-43

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 148.86  E-value: 7.63e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 260 FTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12380   1 FTNVYVKNFGEDVDDDELKELFEKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYVGRAQKK 80
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
365-442 4.80e-34

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 124.21  E-value: 4.80e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12380   3 NVYVKNFGEDVDDDELKELFEKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYVGRAQKK 80
PABP pfam00658
Poly-adenylate binding protein, unique domain; The region featured in this family is found ...
576-641 1.53e-28

Poly-adenylate binding protein, unique domain; The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family.


Pssm-ID: 459893 [Multi-domain]  Cd Length: 66  Bit Score: 108.33  E-value: 1.53e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289   576 DLAAVPEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELLEDDSALNERVNEAIGVL 641
Cdd:pfam00658   1 ALANASPEQQKQMLGERLYPLVQAIQPELAGKITGMLLEMDNSELLHLLEDPEALKEKVDEALEVL 66
PolyA smart00517
C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs ...
581-644 1.98e-28

C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein; Involved in homodimerisation (either directly or indirectly)


Pssm-ID: 197769 [Multi-domain]  Cd Length: 64  Bit Score: 108.14  E-value: 1.98e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289    581 PEESRKQVLGELLYPKVFVREEKLSGKITGMLLEMPNSELLELLEDDSALNERVNEAIGVLQEF 644
Cdd:smart00517   1 PPQEQKQALGERLYPKVQALEPELAGKITGMLLEMDNSELLHLLESPELLRAKVDEALEVLKSH 64
RRM1_PES4_MIP6 cd21601
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
81-163 5.51e-27

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410180 [Multi-domain]  Cd Length: 80  Bit Score: 104.35  E-value: 5.51e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMwsqrdP 160
Cdd:cd21601   2 ALFIGDLDKDVTEEMLRDIFSKYKSLVSVKICLDSETKKSLGYGYLNFSDKEDAEKAIEEFNYTPIFGKEVRIM-----P 76

                ...
gi 19114289 161 SLR 163
Cdd:cd21601  77 SLR 79
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
78-445 7.68e-27

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 112.34  E-value: 7.68e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:TIGR01661   2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   158 rdPSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGmllndk 236
Cdd:TIGR01661  82 --PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVtGLSKGVGFIRFDKRDEADRAIKTLNG------ 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   237 kvyvghhvsrRERQSKVEALKANFTNvyikNLDTEITEQEFSDLFgqfgEITSLSLVKDQNDKPRGFGFVNYANHECAQK 316
Cdd:TIGR01661 154 ----------TTPSGCTEPITVKFAN----NPSSSNSKGLLSQLE----AVQNPQTTRVPLSTILTAAGIGPMHHAAARF 215
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   317 AVDELNDKEYKGKKLYVGRAQKKHEREeelrkRYEQMKLEKM------------NKYQGVNLFIKNLQDEVDDERLKAEF 384
Cdd:TIGR01661 216 RPSAGDFTAVLAHQQQQHAVAQQHAAQ-----RASPPATDGQtaglaagaqisaSDGAGYCIFVYNLSPDTDETVLWQLF 290
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289   385 SAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEVR 445
Cdd:TIGR01661 291 GPFGAVQNVKIIRDLTtNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAYR 352
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
261-531 2.10e-24

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 105.02  E-value: 2.10e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAqkk 339
Cdd:TIGR01661   4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKvTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA--- 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   340 hereeelRKRYEQMKlekmnkyqGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEAN 418
Cdd:TIGR01661  81 -------RPSSDSIK--------GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNvTGLSKGVGFIRFDKRDEAD 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   419 KAVTEMNQRMLAG--KPLYVALA-----QRKEVRRSQLEAQIQARNQFRLQQQVAAAAGIPAVQYGATGpLIYGPGGYPI 491
Cdd:TIGR01661 146 RAIKTLNGTTPSGctEPITVKFAnnpssSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAAR-FRPSAGDFTA 224
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 19114289   492 PAAVNGRGMPMVPGHNGP---MPMYPGMPTQFPAGGPAPGYPG 531
Cdd:TIGR01661 225 VLAHQQQQHAVAQQHAAQrasPPATDGQTAGLAAGAQISASDG 267
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
262-338 7.65e-24

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 95.42  E-value: 7.65e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd12381   3 NLYVKNLDDTIDDEKLREEFSPFGTITSAKVMTDEGGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
263-332 1.43e-23

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 94.22  E-value: 1.43e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLY 332
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
363-437 3.82e-23

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 93.41  E-value: 3.82e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 363 GV-NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12379   1 GVgNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAERAIEKVNGMLLNGKKVFVG 76
RRM smart00360
RNA recognition motif;
262-333 5.33e-23

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 92.66  E-value: 5.33e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289    262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
263-333 8.83e-23

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 92.35  E-value: 8.83e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
262-342 1.06e-22

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 92.47  E-value: 1.06e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKKH 340
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDReTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                ..
gi 19114289 341 ER 342
Cdd:COG0724  83 ER 84
RRM smart00360
RNA recognition motif;
365-436 1.87e-22

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 91.12  E-value: 1.87e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289    365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
366-436 2.58e-22

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 90.81  E-value: 2.58e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM2_SF3B4 cd12335
RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
169-242 3.86e-22

RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409772 [Multi-domain]  Cd Length: 83  Bit Score: 90.88  E-value: 3.86e-22
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKIL-SCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12335   3 NLFIGNLDPEVDEKLLYDTFSAFGVILqTPKIMRDPdTGNSKGFGFVSFDSFEASDAAIEAMNGQYLCNRPITVSY 78
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
363-446 4.32e-22

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 90.54  E-value: 4.32e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:COG0724   1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDrETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARP 80

                ....*
gi 19114289 442 KEVRR 446
Cdd:COG0724  81 REERP 85
RRM smart00360
RNA recognition motif;
81-153 8.30e-22

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 89.58  E-value: 8.30e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289     81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
365-439 5.51e-21

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 87.22  E-value: 5.51e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDrETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
81-432 6.78e-21

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 96.53  E-value: 6.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRIMWSQRDP 160
Cdd:TIGR01622 116 TVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSRRSKGVGYVEFYDVDSVQAAL-ALTGQKLLGIPVIVQLSEAEK 194
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   161 SLRKMGTGNV-------------FIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIE 226
Cdd:TIGR01622 195 NRAARAATETsghhpnsipfhrlYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDpETGRSKGYGFIQFRDAEQAKEALE 274
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   227 HVNGMLLNDKKVYVGHHVSRRERQSKVEA------LKANFTNvyiKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKp 300
Cdd:TIGR01622 275 KMNGFELAGRPIKVGLGNDFTPESDANLAqrfqdqDGSAFSG---AGLNTPARSQLMRKLARDNEKGTGGLAIPGTDVG- 350
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   301 rGFGFVNYAnhecAQKAVDELNDKEYKGKKLYVGRAQKKHEREEELRKRY----EQMKLEKM---NKYQGVNlFIKNLQD 373
Cdd:TIGR01622 351 -GVNMNNYS----RDGLMRKLAPTDEPPAVIPETQILKPKAETSFVPVNVnlasRCLVLSNMfdpATEEEPN-WDKEIED 424
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289   374 EVDDerlkaEFSAFGTITSakIMTDEQgKSKGFGFVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:TIGR01622 425 DVRE-----ECSKYGGVVH--IYVDDK-NSAGDIYLKFDSVQAAEAAIKALNGRYFGGK 475
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
365-449 7.32e-21

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 87.42  E-value: 7.32e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEV--DDERLKAEFSAFGTITSAKIMT-DEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd21622   5 NLFVKNLDDTVitNKEDLEQLFSPFGQIVSSYLATyPGTGISKGFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYAER 84

                ....*...
gi 19114289 442 KEVRRSQL 449
Cdd:cd21622  85 KEDREKRL 92
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
170-240 7.63e-21

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 86.57  E-value: 7.63e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
169-241 1.10e-20

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 86.56  E-value: 1.10e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd12381   3 NLYVKNLDDTIDDEKLREEFSPFGTITSAKVMTDEGGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVA 75
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
170-239 1.32e-20

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 85.75  E-value: 1.32e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVY 239
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM smart00360
RNA recognition motif;
169-240 6.26e-20

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 84.18  E-value: 6.26e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289    169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDkETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
245-553 1.01e-19

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 92.67  E-value: 1.01e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   245 SRRERQSKVEALKANFT-------NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQK 316
Cdd:TIGR01622  92 SRREKPRARDGTPEPLTederdrrTVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSrRSKGVGYVEFYDVDSVQA 171
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   317 AVdELNDKEYKGKKLYVGRAQKKHEREEELRKryeQMKLEKMNKYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIM 396
Cdd:TIGR01622 172 AL-ALTGQKLLGIPVIVQLSEAEKNRAARAAT---ETSGHHPNSIPFHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQ 247
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   397 TD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEVRRSQLEAQIQArnQFRLQQQVAAAAGIPA-- 473
Cdd:TIGR01622 248 KDpETGRSKGYGFIQFRDAEQAKEALEKMNGFELAGRPIKVGLGNDFTPESDANLAQRFQ--DQDGSAFSGAGLNTPArs 325
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   474 --VQYGATGPlIYGPGGYPIPAAvNGRGMPMvPGHNGPMPMYPGMPTQFPaggpapgypgmNARGPVPAQGRPMMMPGSV 551
Cdd:TIGR01622 326 qlMRKLARDN-EKGTGGLAIPGT-DVGGVNM-NNYSRDGLMRKLAPTDEP-----------PAVIPETQILKPKAETSFV 391

                  ..
gi 19114289   552 PS 553
Cdd:TIGR01622 392 PV 393
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
262-335 1.43e-19

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 83.01  E-value: 1.43e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGR 335
Cdd:cd12379   4 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAERAIEKVNGMLLNGKKVFVGR 77
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
82-152 5.82e-19

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 81.13  E-value: 5.82e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289    82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCR 152
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDE-TGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
366-435 1.51e-18

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 79.97  E-value: 1.51e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLY 435
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM2_SF3B4 cd12335
RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
363-443 3.20e-18

RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409772 [Multi-domain]  Cd Length: 83  Bit Score: 79.71  E-value: 3.20e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTI-TSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12335   1 GANLFIGNLDPEVDEKLLYDTFSAFGVIlQTPKIMRDPDtGNSKGFGFVSFDSFEASDAAIEAMNGQYLCNRPITVSYAF 80

                ...
gi 19114289 441 RKE 443
Cdd:cd12335  81 KKD 83
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
366-436 4.99e-18

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 78.81  E-value: 4.99e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12362   1 LFVYHLPNEFTDQDLYQLFAPFGNVVSAKVFVDKNtGRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
366-439 5.10e-18

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 78.76  E-value: 5.10e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12565   3 IIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKDGKSRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
82-154 9.17e-18

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 77.71  E-value: 9.17e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIM 154
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDR-DGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
365-439 1.21e-17

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 77.86  E-value: 1.21e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRGsGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
169-323 3.09e-17

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 83.53  E-value: 3.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHhvsrr 247
Cdd:TIGR01659 109 NLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDyKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY----- 183
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289   248 eRQSKVEALKAnfTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELND 323
Cdd:TIGR01659 184 -ARPGGESIKD--TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKlTGTPRGVAFVRFNKREEAQEAISALNN 257
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
366-432 3.37e-17

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 76.28  E-value: 3.37e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:cd12353   2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKDTQtGKSKGYGFVSFVKKEDAENAIQGMNGQWLGGR 69
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
363-434 7.13e-17

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 75.61  E-value: 7.13e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12619   1 HFNIFVGDLSPEVTDAALFNAFSDFPSCSDARVMWDQKtGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPI 73
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
366-442 1.39e-16

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 74.96  E-value: 1.39e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNVGPAIRK 81
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
79-153 2.58e-16

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 74.36  E-value: 2.58e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:COG0724   1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
170-240 2.76e-16

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 73.81  E-value: 2.76e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12362   1 LFVYHLPNEFTDQDLYQLFAPFGNVVSAKVFVDKNTGRsKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
74-232 4.03e-16

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 80.06  E-value: 4.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    74 GTAPTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRpcRI 153
Cdd:TIGR01659 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK--RL 179
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   154 MWSQRDPSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGML 232
Cdd:TIGR01659 180 KVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLtGTPRGVAFVRFNKREEAQEAISALNNVI 259
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
262-333 5.20e-16

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 72.97  E-value: 5.20e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDRETgRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVV 73
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
366-439 6.58e-16

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 72.58  E-value: 6.58e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12414   2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
170-242 9.42e-16

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 72.65  E-value: 9.42e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNVGP 77
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
231-602 1.18e-15

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 80.50  E-value: 1.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   231 MLLNDKKVYVGHHVSRRERQSKVEALKANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYA 309
Cdd:TIGR01645  78 VLLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPaTGKHKGFAFVEYE 157
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   310 NHECAQKAVDELNDKEYKGKKLYVGRAQKKHEREEELRKRYEQMKleKMNKyqgvnLFIKNLQDEVDDERLKAEFSAFGT 389
Cdd:TIGR01645 158 VPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAK--KFNR-----IYVASVHPDLSETDIKSVFEAFGE 230
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   390 ITSAKIMTDEQG-KSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV--------ALAQ---------RKEVRRSQLEA 451
Cdd:TIGR01645 231 IVKCQLARAPTGrGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVgkcvtppdALLQpatvsaipaAAAVAAAAATA 310
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   452 QIQARNQFRLQQQVAAAAGIPAVQYGA------TGPLIYGPGGYPIPAAVNGRGMPMV--PG-HNGPMPMYP---GMPTQ 519
Cdd:TIGR01645 311 KIMAAEAVAGAAVLGPRAQSPATPSSSlptdigNKAVVSSAKKEAEEVPPLPQAAPAVvkPGpMEIPTPVPPpglAIPSL 390
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   520 FPAGG---PAPGYPGMNA--RGPVPAQGRPMMMPGSV-------PSAGPAEAEAVPAVPGMPErfTAADLAAVPEESRKQ 587
Cdd:TIGR01645 391 VAPPGlvaPTEINPSFLAspRKKMKREKLPVTFGALDdtlawkePSKEDQTSEDGKMLAIMGE--AAAALALEPKKKKKE 468
                         410
                  ....*....|....*
gi 19114289   588 VLGELLYPKVFVREE 602
Cdd:TIGR01645 469 KEGEELQPKLVMNSE 483
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
81-156 1.56e-15

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 71.76  E-value: 1.56e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12619   3 NIFVGDLSPEVTDAALFNAFSDFPSCSDARVMWDQKTGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPIRCNWA 78
RRM2_SECp43_like cd12345
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
81-153 1.80e-15

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409781 [Multi-domain]  Cd Length: 80  Bit Score: 71.53  E-value: 1.80e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGP-VASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12345   3 SLFVGDLAPDVTDYQLYETFSARYPsVRGAKVVMDPVTGRSKGYGFVRFGDESEQDRALTEMQGVYLGSRPIRV 76
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
257-512 2.63e-15

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 77.75  E-value: 2.63e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   257 KANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGR 335
Cdd:TIGR01659 104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDyKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY 183
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   336 AqkkhereeelRKRYEQMKlekmnkyqGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTP 414
Cdd:TIGR01659 184 A----------RPGGESIK--------DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKlTGTPRGVAFVRFNKR 245
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   415 EEANKAVTEMNQRMLAG--KPLYVALAqrkevrrsqleaqiqarnqfrlQQQVAAAAGIPAVQYGATGPLIYGPGGYPIP 492
Cdd:TIGR01659 246 EEAQEAISALNNVIPEGgsQPLTVRLA----------------------EEHGKAKAHHYMSQMGHGNMGNMGHGNMGMA 303
                         250       260
                  ....*....|....*....|
gi 19114289   493 AAVNGrGMPMVPGHNGPMPM 512
Cdd:TIGR01659 304 GGSGM-NPPNPPAFMGMNNM 322
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
82-153 2.81e-15

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 70.71  E-value: 2.81e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12334   1 VYVGNLDEKVTEELLWELFIQAGPVVNVHMPKDRVTQQHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
RRM2_hnRNPM_like cd12386
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
366-436 3.72e-15

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409820 [Multi-domain]  Cd Length: 74  Bit Score: 70.47  E-value: 3.72e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12386   1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIREDKDGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRV 71
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
262-333 6.68e-15

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 70.02  E-value: 6.68e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLV----KDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12355   1 RLWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLfhktGPLKGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVV 76
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
82-153 6.99e-15

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 69.96  E-value: 6.99e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12284   1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQKDPETGRSKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKV 72
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
263-339 7.01e-15

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 69.95  E-value: 7.01e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNVGPAIRK 81
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
263-339 1.12e-14

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 69.16  E-value: 1.12e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12413   2 LFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKGkDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
263-336 1.21e-14

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 69.08  E-value: 1.21e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12398   3 VFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDRETgKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
265-327 1.28e-14

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 69.07  E-value: 1.28e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYK 327
Cdd:cd12408   4 VTNLSEDATEEDLRELFRPFGPISRVYLAKDKEtGQSKGFAFVTFETREDAERAIEKLNGFGYD 67
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
366-439 1.38e-14

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 69.19  E-value: 1.38e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12284   1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQKDpETGRSKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKVGHV 75
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
366-441 1.71e-14

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 68.97  E-value: 1.71e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12382   4 LFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDrETNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQATK 80
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
169-240 2.01e-14

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 68.97  E-value: 2.01e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDrETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
366-421 3.19e-14

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 67.93  E-value: 3.19e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12325   1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKDPAtGRSRGFGFVTFKDPSSVDAVL 57
RRM2_SECp43_like cd12345
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
366-439 3.41e-14

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409781 [Multi-domain]  Cd Length: 80  Bit Score: 68.06  E-value: 3.41e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSA-FGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12345   4 LFVGDLAPDVTDYQLYETFSArYPSVRGAKVVMDPVtGRSKGYGFVRFGDESEQDRALTEMQGVYLGSRPIRVSPA 79
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
169-249 4.78e-14

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 68.16  E-value: 4.78e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 169 NVFIKNLD-PAIDNKA-LHDTFSAFGKILSCKVA-VDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVS 245
Cdd:cd21622   5 NLFVKNLDdTVITNKEdLEQLFSPFGQIVSSYLAtYPGTGISKGFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYAER 84

                ....
gi 19114289 246 RRER 249
Cdd:cd21622  85 KEDR 88
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
82-245 6.17e-14

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 75.11  E-value: 6.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRDPS 161
Cdd:TIGR01645 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQ 189
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   162 LRKM---------GTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGM 231
Cdd:TIGR01645 190 AQPIidmvqeeakKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARApTGRGHKGYGFIEYNNLQSQSEAIASMNLF 269
                         170
                  ....*....|....
gi 19114289   232 LLNDKKVYVGHHVS 245
Cdd:TIGR01645 270 DLGGQYLRVGKCVT 283
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
82-156 7.72e-14

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 66.66  E-value: 7.72e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12352   1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMITE--HGGNDPYCFVEFYEHNHAAAALQAMNGRKILGKEVKVNWA 73
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
261-336 8.57e-14

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 66.82  E-value: 8.57e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12565   1 SRIIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKDGKSRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
82-153 9.19e-14

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 66.66  E-value: 9.19e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
82-155 1.00e-13

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 66.65  E-value: 1.00e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12353   2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKDTQTGKSKGYGFVSFVKKEDAENAIQGMNGQWLGGRNIRTNW 75
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
262-346 1.33e-13

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 66.62  E-value: 1.33e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 262 NVYIKNLDTEI--TEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd21622   5 NLFVKNLDDTVitNKEDLEQLFSPFGQIVSSYLATYPGTGiSKGFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYAER 84

                ....*...
gi 19114289 339 KHEREEEL 346
Cdd:cd21622  85 KEDREKRL 92
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
154-336 1.50e-13

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 73.95  E-value: 1.50e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   154 MWSQRDPSLRKMGtgNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGML 232
Cdd:TIGR01645  96 RQQQRQQALAIMC--RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPAtGKHKGFAFVEYEVPEAAQLALEQMNGQM 173
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   233 LNDKKVYVGHHVSRRERQSKVEALKAN---FTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNY 308
Cdd:TIGR01645 174 LGGRNIKVGRPSNMPQAQPIIDMVQEEakkFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTgRGHKGYGFIEY 253
                         170       180
                  ....*....|....*....|....*...
gi 19114289   309 ANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:TIGR01645 254 NNLQSQSEAIASMNLFDLGGQYLRVGKC 281
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
81-142 1.52e-13

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 65.99  E-value: 1.52e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12408   1 TIRVTNLSEDATEEDLRELFRPFGPISRVYLAKDKETGQSKGFAFVTFETREDAERAIEKLN 62
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
366-426 1.93e-13

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 65.80  E-value: 1.93e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQ 426
Cdd:cd12564   3 LIVKNLPSSITEDRLRKLFSAFGTITDVQLKYTKDGKFRRFGFVGFKSEEEAQKALKHFNN 63
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
366-442 2.23e-13

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 65.69  E-value: 2.23e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12413   2 LFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKgKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
68-333 2.49e-13

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 71.90  E-value: 2.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    68 SVATPSGTAPTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIK 147
Cdd:TIGR01661  78 SYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPS 157
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   148 GrpcrimwsQRDPSLRKmgtgnvFIKNldPAIDN-KALHDTFSAFGKILSCKVAVDELGNAKGYGFVHfdsvesANAAIE 226
Cdd:TIGR01661 158 G--------CTEPITVK------FANN--PSSSNsKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMH------HAAARF 215
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   227 HVNGMLLND--KKVYVGHHVSRRERQSKVEALKAN------------------FTNVYIKNLDTEITEQEFSDLFGQFGE 286
Cdd:TIGR01661 216 RPSAGDFTAvlAHQQQQHAVAQQHAAQRASPPATDgqtaglaagaqisasdgaGYCIFVYNLSPDTDETVLWQLFGPFGA 295
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 19114289   287 ITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:TIGR01661 296 VQNVKIIRDlTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
263-333 3.34e-13

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 64.97  E-value: 3.34e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ----NDKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12298   3 IRVRNLDFELDEEALRGIFEKFGEIESINIPKKQknrkGRHNNGFAFVTFEDADSAESAL-QLNGTLLDNRKISV 76
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
82-153 3.39e-13

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 64.91  E-value: 3.39e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDR-SGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKV 73
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
82-153 3.83e-13

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 64.88  E-value: 3.83e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd21608   2 LYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVV 73
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
81-154 4.55e-13

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 64.44  E-value: 4.55e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRIM 154
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRETGIGKGFGYVLFKDKDSVDLAL-KLNGSKLRGRKLRVK 73
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
366-442 4.80e-13

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 64.79  E-value: 4.80e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12674   3 LFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDpETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKPR 80
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
265-333 4.85e-13

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 64.50  E-value: 4.85e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12414   4 VRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAV 72
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
366-439 4.86e-13

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 64.55  E-value: 4.86e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12347   1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIPLDYEtEKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA 75
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
366-436 5.90e-13

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 64.46  E-value: 5.90e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12399   1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDrETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
82-156 7.93e-13

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 63.99  E-value: 7.93e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDK-NSKGVNYGFVEYYDRRSAEIAIQTLNGRQIFGQEIKVNWA 74
RRM2_SECp43 cd12612
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); ...
366-442 9.41e-13

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region.


Pssm-ID: 410024 [Multi-domain]  Cd Length: 82  Bit Score: 63.93  E-value: 9.41e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSA-FGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEM-NQRMLAGKPLYVALAQRK 442
Cdd:cd12612   4 LFVGDLTPEVDDGMLYEFFLKrYPSCKGAKVVLDQLGNSRGYGFVRFSDENEQKRALTECqGASGLGGKPIRLSVAIPK 82
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
169-240 1.04e-12

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 63.73  E-value: 1.04e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDrETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVV 73
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
82-142 1.07e-12

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 63.58  E-value: 1.07e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12650   3 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPSDAEKAINTLN 63
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
365-436 1.07e-12

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 63.43  E-value: 1.07e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKG-FGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12417   1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSARTPGSRcYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
264-334 1.18e-12

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 63.41  E-value: 1.18e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd12284   2 YVGSLHFNITEDMLRGIFEPFGKIEFVQLQKDPeTGRSKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKVG 73
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
263-336 1.22e-12

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 63.31  E-value: 1.22e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12399   1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDrETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNEA 75
RRM2_PES4_MIP6 cd21602
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
169-246 1.23e-12

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410181 [Multi-domain]  Cd Length: 76  Bit Score: 63.59  E-value: 1.23e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 169 NVFIKNL---DPAIDNKALHDTFSAFGKILSCKvavdeLGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVS 245
Cdd:cd21602   1 NVFFSNLpleNPRLTTRVFYDTFKKYGKILSCK-----LDRRKNIGFVYFENDKAARKVIKEYNNKEFFGNKILCGLHFD 75

                .
gi 19114289 246 R 246
Cdd:cd21602  76 K 76
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
170-233 1.32e-12

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 63.18  E-value: 1.32e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12353   2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKDtQTGKSKGYGFVSFVKKEDAENAIQGMNGQWL 66
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
261-334 1.43e-12

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 63.47  E-value: 1.43e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLV----KDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd12223   2 TNLYVGNLPPSVTEEVLLREFGRFGPLASVKIMwprtEEERRRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLG 79
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
263-333 1.68e-12

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 63.03  E-value: 1.68e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12251   4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD-------YAFVHFEERDDAVKAMEEMNGKELEGSEIEV 67
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
366-434 1.76e-12

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 63.07  E-value: 1.76e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12383   9 IFCGDLGNEVTDEVLARAFSKYPSFQKAKVIRDkRTGKSKGYGFVSFKDPNDYLKALREMNGKYVGNRPI 78
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
366-439 1.90e-12

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 63.00  E-value: 1.90e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQR------MLAGKPLYVAL 438
Cdd:cd12415   3 VFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDkDTGHSKGTAFVQFKTKESADKCIEAANDEsedgglVLDGRKLIVSL 82

                .
gi 19114289 439 A 439
Cdd:cd12415  83 A 83
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
366-442 1.95e-12

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 62.88  E-value: 1.95e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12449   3 LFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDrETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQAGKS 80
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
265-333 2.47e-12

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 62.71  E-value: 2.47e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12564   5 VKNLPSSITEDRLRKLFSAFGTITDVQLKYTKDGKFRRFGFVGFKSEEEAQKALKHFNNSFIDTSRITV 73
RRM1_MSSP cd12243
RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...
169-231 2.48e-12

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409689 [Multi-domain]  Cd Length: 71  Bit Score: 62.33  E-value: 2.48e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGM 231
Cdd:cd12243   2 NVYIRGLPPNTTDEDLLLLCQSFGKIISTKAIIDKqTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
81-151 2.55e-12

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 63.87  E-value: 2.55e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTL---IKGRPC 151
Cdd:cd21615  20 TLFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDKETGKSRGYAFIVFKSESDAKNAFKEGNGLRglkINDRTC 93
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
81-156 2.65e-12

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 62.45  E-value: 2.65e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
66-194 2.80e-12

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 69.56  E-value: 2.80e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    66 ASSVATPSGTAPTSAS---LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:TIGR01622 198 ARAATETSGHHPNSIPfhrLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALEKMN 277
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 19114289   143 YTLIKGRPCRImwsqrdpslrkmGTGNVFIKNLDPAIDNKALHDTFSAFGKI 194
Cdd:TIGR01622 278 GFELAGRPIKV------------GLGNDFTPESDANLAQRFQDQDGSAFSGA 317
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
366-437 2.92e-12

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 62.36  E-value: 2.92e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12316   2 LFVRNLPFTATEDELRELFEAFGKISEVHIPLDKQtKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHVL 74
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
170-595 2.98e-12

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 69.64  E-value: 2.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEhvngmLLNDKKVYVGHHVSrrer 249
Cdd:TIGR01648  61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVK-----LLNNYEIRPGRLLG---- 131
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   250 qskVEALKANfTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND---KPRGFGFVNYANHECAQKAVDELNDKEY 326
Cdd:TIGR01648 132 ---VCISVDN-CRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAAdkkKNRGFAFVEYESHRAAAMARRKLMPGRI 207
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   327 K--GKKLYVGRAQKKHEREEELrkryeqMKLEKMnkyqgvnLFIKNLQDEVDDERLKAEFSAF--GTITSAKimtdeqgK 402
Cdd:TIGR01648 208 QlwGHVIAVDWAEPEEEVDEDV------MAKVKI-------LYVRNLMTTTTEEIIEKSFSEFkpGKVERVK-------K 267
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   403 SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAqrKEVRRSQLEAQIQARNQFRLQQQvaAAAGIPAVQYGATGPL 482
Cdd:TIGR01648 268 IRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA--KPVDKKSYVRYTRGTGGRGKERQ--AARQSLGQVYDPASRS 343
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   483 IYGPGGYPIPAAVNGRGMPMVPGH-----NGPMPMYPGMPTQFPAGGPAPGY---------------------PGMNARG 536
Cdd:TIGR01648 344 LAYEDYYYHPPYAPSLHFPRMPGPirgrgRGGAPSRAAGGRGYPPYGYEAYYgdyygyhdyrgkyedkyygydPGMELTP 423
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289   537 PVPAQGRPmmmPGSVpsagpaeaeAVPAVPGMPERFTAADLAAVPEESRKQVLGELLYP 595
Cdd:TIGR01648 424 MNPVRGKP---GGRG---------GRPAIPPPRGRKNGAPPPAIGQDGRQLFLYKITIP 470
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
263-339 3.18e-12

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 62.50  E-value: 3.18e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12449   3 LFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDrETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQAGKS 80
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
267-333 3.30e-12

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 62.25  E-value: 3.30e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 267 NLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12363   8 GLSLYTTERDLREVFSRYGPIEKVQVVYDqQTGRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRV 75
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
365-439 3.32e-12

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 62.42  E-value: 3.32e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12649   2 NLIVNYLPQDLTDREFRALFRAIGPVNTCKIVRDKKtGYSYGFGFVDFTSEEDAQRAIKTLNGLQLQNKRLKVAYA 77
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
261-338 3.49e-12

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 62.42  E-value: 3.49e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd12382   2 GKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDReTNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQATK 80
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
263-432 3.81e-12

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 69.15  E-value: 3.81e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA----- 336
Cdd:TIGR01642 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATgLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAcvgan 377
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   337 QKKHEREE------ELRKRYEQMKLEKMNKYQGVnLFIKNL--QDEVDD--------ERLKAEFSAFGTITSAKIMTDEQ 400
Cdd:TIGR01642 378 QATIDTSNgmapvtLLAKALSQSILQIGGKPTKV-VQLTNLvtGDDLMDdeeyeeiyEDVKTEFSKYGPLINIVIPRPNG 456
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 19114289   401 GKSKGFG----FVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:TIGR01642 457 DRNSTPGvgkvFLEYADVRSAEKAMEGMNGRKFNDR 492
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
366-438 4.92e-12

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 61.83  E-value: 4.92e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKVEL 75
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
360-442 5.46e-12

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 63.90  E-value: 5.46e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  360 KYQGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:PLN03134  31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDrETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110

                 ....
gi 19114289  439 AQRK 442
Cdd:PLN03134 111 ANDR 114
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
367-436 7.08e-12

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 61.09  E-value: 7.08e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 367 FIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTeMNQRMLAGKPLYV 436
Cdd:cd12391   3 FVSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKGKSKGYCYVEFKDEESAQKALK-LDRQPVEGRPMFV 71
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
365-438 7.76e-12

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 61.18  E-value: 7.76e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQG-KSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12377   1 CIFVYNLAPDADESLLWQLFGPFGAVQNVKIIRDFTTnKCKGYGFVTMTNYDEAAVAIASLNGYRLGGRVLQVSF 75
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
366-439 8.24e-12

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 60.99  E-value: 8.24e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12398   3 VFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDrETGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast ...
81-153 8.34e-12

RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 410025 [Multi-domain]  Cd Length: 80  Bit Score: 61.37  E-value: 8.34e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGP-VASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12613   3 SIFVGDLSPTTNESDLVSLFQSRFPsCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGKYCQGRPLRI 76
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
366-442 9.50e-12

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 60.88  E-value: 9.50e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVtEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12450   2 LFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDrDDGRSKGFGHVEFASAESAQKAL-EKSGQDLGGREIRLDLANER 78
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
81-158 9.98e-12

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 60.94  E-value: 9.98e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQR 158
Cdd:cd12674   2 TLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKP 79
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
263-333 1.22e-11

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 60.67  E-value: 1.22e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKV 73
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
262-336 1.25e-11

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 60.99  E-value: 1.25e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12671   8 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDrETGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRVDNA 83
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
261-339 1.52e-11

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 60.56  E-value: 1.52e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12674   1 TTLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDpETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKPR 80
RRM3_Bruno_like cd12640
RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar ...
362-436 1.87e-11

RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 241084 [Multi-domain]  Cd Length: 79  Bit Score: 60.40  E-value: 1.87e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12640   3 EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNlSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRLKV 78
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
161-240 2.05e-11

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 62.36  E-value: 2.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  161 SLRKMGTgNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVY 239
Cdd:PLN03134  29 SLRLMST-KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDrETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR 107

                 .
gi 19114289  240 V 240
Cdd:PLN03134 108 V 108
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
263-333 2.08e-11

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 59.94  E-value: 2.08e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12362   1 LFVYHLPNEFTDQDLYQLFAPFGNVVSAKVFVDKNTGrSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKV 72
RRM1_MSSP cd12243
RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...
365-431 2.13e-11

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409689 [Multi-domain]  Cd Length: 71  Bit Score: 59.63  E-value: 2.13e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAG 431
Cdd:cd12243   2 NVYIRGLPPNTTDEDLLLLCQSFGKIISTKAIIDKQtNKCKGYGFVDFDSPEAALKAIEGLNGRGVQA 69
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
81-156 2.32e-11

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 59.84  E-value: 2.32e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12398   2 SVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDRETGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
263-339 2.37e-11

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 60.03  E-value: 2.37e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKaVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12330   2 IFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDHDtGRSRGFGFVTFDSESAVEK-VLSKGFHELGGKKVEVKRATPK 78
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
81-154 2.51e-11

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 59.55  E-value: 2.51e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRIM 154
Cdd:cd12283   1 TVFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDRNSRRSKGVAYVEFYDVESVPLAL-ALTGQRLLGQPIMVQ 73
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
263-333 2.71e-11

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 59.54  E-value: 2.71e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12347   1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIPLDyETEKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIRV 72
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
365-439 2.89e-11

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 59.73  E-value: 2.89e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12375   1 NLIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKItGQSLGYGFVNYRDPNDARKAINTLNGLDLENKRLKVSYA 76
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
79-156 3.16e-11

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 59.61  E-value: 3.16e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVC--RDAVTR-RSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12223   1 TTNLYVGNLPPSVTEEVLLREFGRFGPLASVKIMwpRTEEERrRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLGW 80

                .
gi 19114289 156 S 156
Cdd:cd12223  81 G 81
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
366-439 3.33e-11

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 59.61  E-value: 3.33e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12371   3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDpETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRVGRA 77
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
82-575 4.47e-11

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 65.79  E-value: 4.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDaVTRRSLGYAYVNFHNMEDGEKALDELN-YTLIKGRPCRIMWSQRDP 160
Cdd:TIGR01648  61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNnYEIRPGRLLGVCISVDNC 139
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   161 SLrkmgtgnvFIKNLDpaiDNKALHDTFSAFGKILSCKVAV-------DELGNaKGYGFVHFDSVESANAAIEHvngmLL 233
Cdd:TIGR01648 140 RL--------FVGGIP---KNKKREEILEEFSKVTEGVVDVivyhsaaDKKKN-RGFAFVEYESHRAAAMARRK----LM 203
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   234 NDKKVYVGHHVSRRERQSKVEALKANFTNV---YIKNLDTEITEQEFSDLFGQFGEiTSLSLVKdqndKPRGFGFVNYAN 310
Cdd:TIGR01648 204 PGRIQLWGHVIAVDWAEPEEEVDEDVMAKVkilYVRNLMTTTTEEIIEKSFSEFKP-GKVERVK----KIRDYAFVHFED 278
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   311 HECAQKAVDELNDKEYKGKKLYVGRAQKKherEEELRKRYEQMKLEKMNKYQGVNlfiknlqdevddERLKAEFSAFGTI 390
Cdd:TIGR01648 279 REDAVKAMDELNGKELEGSEIEVTLAKPV---DKKSYVRYTRGTGGRGKERQAAR------------QSLGQVYDPASRS 343
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   391 TSAKIMTDEQGKSKGFGFVCyTTPEEANKAVTEMNQRMLA--GKPLYVALAQRKEVRRSQLE--------------AQIQ 454
Cdd:TIGR01648 344 LAYEDYYYHPPYAPSLHFPR-MPGPIRGRGRGGAPSRAAGgrGYPPYGYEAYYGDYYGYHDYrgkyedkyygydpgMELT 422
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   455 ARNQFRLQQQVAAAAGIPAVQYGATgpliygpGGYPIPaAVNGRGMPMVPGHNGPMPMYPGMPTQFPAGGPAPGYPGMNA 534
Cdd:TIGR01648 423 PMNPVRGKPGGRGGRPAIPPPRGRK-------NGAPPP-AIGQDGRQLFLYKITIPAGYSQRPAPHPLGPPRGSAFVRGA 494
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*...
gi 19114289   535 RG-PVPAQGRPMMMPGS-----VPSAGPAEAEAVP-AVPGMPERFTAA 575
Cdd:TIGR01648 495 RGgPAQYQQRGRGSRTSrgngrGGTAGGKRKAFDGyAQPDATARQTNN 542
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
81-154 4.83e-11

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 59.14  E-value: 4.83e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIM 154
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVE 74
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
81-153 4.84e-11

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 58.85  E-value: 4.84e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTrRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12336   3 TLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNG-KPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRI 74
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
170-240 5.32e-11

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 58.77  E-value: 5.32e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12347   1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIPLDyETEKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIRV 72
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
262-335 5.49e-11

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 58.99  E-value: 5.49e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNdkprgFGFVNYANHECAQKAVDELN-DKEYKGKKLYVGR 335
Cdd:cd12523   5 NVYLGNLPESITEEELREDLEKFGPIDQIKIVKEKN-----IAFVHFLSIANAIKVVTTLPlNPKWAKRRIYYGK 74
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
263-333 5.59e-11

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410185 [Multi-domain]  Cd Length: 75  Bit Score: 58.91  E-value: 5.59e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd21606   4 VFIANLPYSINWQALKDMFKECGDVLRADVELDYNGRSRGFGTVIYATEEEMHRAIDTFNGYELEGRVLEV 74
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
170-240 6.94e-11

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 58.78  E-value: 6.94e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFikNLDPAIDNKALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12363   6 VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQqTGRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRV 75
RRM2_hnRNPM cd12659
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
366-438 7.35e-11

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410060 [Multi-domain]  Cd Length: 76  Bit Score: 58.52  E-value: 7.35e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12659   3 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVKM 75
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
262-336 7.76e-11

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 58.19  E-value: 7.76e-11
                        10        20        30        40        50        60        70
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gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12375   1 NLIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKITgQSLGYGFVNYRDPNDARKAINTLNGLDLENKRLKVSYA 76
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
82-149 8.58e-11

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 58.00  E-value: 8.58e-11
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12347   1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQIPLDYETEKHRGFAFVEFEEAEDAAAAIDNMNESELFGR 68
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
82-153 8.87e-11

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 58.26  E-value: 8.87e-11
                        10        20        30        40        50        60        70
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12449   3 LFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRV 74
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
82-142 9.71e-11

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 58.19  E-value: 9.71e-11
                        10        20        30        40        50        60
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12375   2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKITGQSLGYGFVNYRDPNDARKAINTLN 62
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
366-421 1.01e-10

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 58.31  E-value: 1.01e-10
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12579   2 LFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKDtGKKRGFGFVYFEDHDSADKAA 58
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
263-333 1.02e-10

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 58.12  E-value: 1.02e-10
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12316   2 LFVRNLPFTATEDELRELFEAFGKISEVHIPLDkQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
170-240 1.06e-10

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 57.62  E-value: 1.06e-10
                        10        20        30        40        50        60        70
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12343   2 IFVGNLPDAATSEELRALFEKYGKVTECDIV-------KNYAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
261-337 1.08e-10

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 58.20  E-value: 1.08e-10
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12770   2 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKiTGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 79
RRM1_PES4_MIP6 cd21601
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
364-432 1.15e-10

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410180 [Multi-domain]  Cd Length: 80  Bit Score: 58.13  E-value: 1.15e-10
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gi 19114289 364 VNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:cd21601   1 TALFIGDLDKDVTEEMLRDIFSKYKSLVSVKICLDsETKKSLGYGYLNFSDKEDAEKAIEEFNYTPIFGK 70
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
366-439 1.18e-10

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 57.64  E-value: 1.18e-10
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeqgkskgFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12251   4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD-------YAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLA 70
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
366-421 1.20e-10

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 57.66  E-value: 1.20e-10
                        10        20        30        40        50
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12328   2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIVTDKEtGKKRGFAFVTFDDHDSVDKIV 58
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
260-322 1.24e-10

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 59.25  E-value: 1.24e-10
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gi 19114289 260 FTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd21615  18 YKTLFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDKEtGKSRGYAFIVFKSESDAKNAFKEGN 81
RRM3_CELF1_2 cd12638
RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and ...
362-447 1.27e-10

RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins; This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3.


Pssm-ID: 241082 [Multi-domain]  Cd Length: 92  Bit Score: 58.15  E-value: 1.27e-10
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gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12638   6 EGANLFIYHLPQEFGDQDILQMFMPFGNVVSAKVFIDKQTNlSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKR 85

                ....*..
gi 19114289 441 RKEVRRS 447
Cdd:cd12638  86 SKNDSKP 92
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
81-159 1.29e-10

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 58.15  E-value: 1.29e-10
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRD 159
Cdd:cd12312   2 SLFVRNVADDTRPDDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFAQGD 80
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
188-241 1.31e-10

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 57.68  E-value: 1.31e-10
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gi 19114289 188 FSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd12371  21 FEAFGKIKSCSLAPDpETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRVG 75
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
261-331 1.44e-10

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 57.29  E-value: 1.44e-10
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQndkprGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12354   1 TTVYVGNITKGLTEALLQQTFSPFGQILEVRVFPDK-----GYAFIRFDSHEAATHAIVSVNGTIINGQAV 66
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
365-434 1.54e-10

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 57.71  E-value: 1.54e-10
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gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12618   4 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDmATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 74
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
366-442 1.57e-10

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 57.72  E-value: 1.57e-10
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTpEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12330   2 IFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDhDTGRSRGFGFVTFDS-ESAVEKVLSKGFHELGGKKVEVKRATPK 78
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
82-155 1.60e-10

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 57.71  E-value: 1.60e-10
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12618   5 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW 78
RRM1_hnRNPM_like cd12385
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
263-333 1.80e-10

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409819 [Multi-domain]  Cd Length: 76  Bit Score: 57.43  E-value: 1.80e-10
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gi 19114289 263 VYIKNLDTEITEQEFSDLF-GQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12385   2 VFISNIPYDYKWQDLKDLFrEKVGEVTYVELFKDENGKSRGCGIVEFKDLESVQKALETMNRYELKGRKLVV 73
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
262-333 1.82e-10

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 57.33  E-value: 1.82e-10
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gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12377   1 CIFVYNLAPDADESLLWQLFGPFGAVQNVKIIRDFTtNKCKGYGFVTMTNYDEAAVAIASLNGYRLGGRVLQV 73
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast ...
366-439 1.99e-10

RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 410025 [Multi-domain]  Cd Length: 80  Bit Score: 57.52  E-value: 1.99e-10
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gi 19114289 366 LFIKNLQDEVDDERLKAEF-SAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12613   4 IFVGDLSPTTNESDLVSLFqSRFPSCKSAKIMTDPVtGVSRGYGFVRFSDENDQQRALIEMQGKYCQGRPLRISYA 79
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
169-240 2.13e-10

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 56.88  E-value: 2.13e-10
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gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12417   1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSaRTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
RRM1_MSSP cd12243
RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...
261-328 2.17e-10

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409689 [Multi-domain]  Cd Length: 71  Bit Score: 56.93  E-value: 2.17e-10
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12243   1 TNVYIRGLPPNTTDEDLLLLCQSFGKIISTKAIIDKQTnKCKGYGFVDFDSPEAALKAIEGLNGRGVQA 69
RRM3_CELF3_4_5_6 cd12639
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
362-436 2.58e-10

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 241083 [Multi-domain]  Cd Length: 79  Bit Score: 57.17  E-value: 2.58e-10
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gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12639   3 EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRaTNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV 78
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
263-333 2.96e-10

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 56.47  E-value: 2.96e-10
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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12391   2 VFVSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKGKSKGYCYVEFKDEESAQKAL-KLDRQPVEGRPMFV 71
RRM2_PES4_MIP6 cd21602
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
262-334 3.00e-10

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410181 [Multi-domain]  Cd Length: 76  Bit Score: 56.65  E-value: 3.00e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 262 NVYIKNLDTE---ITEQEFSDLFGQFGEITSLSLvkdqnDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd21602   1 NVFFSNLPLEnprLTTRVFYDTFKKYGKILSCKL-----DRRKNIGFVYFENDKAARKVIKEYNNKEFFGNKILCG 71
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
261-336 3.36e-10

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 56.64  E-value: 3.36e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPR-GFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12650   1 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSlGYGFVNYVDPSDAEKAINTLNGLRLQNKTIKVSYA 77
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
81-155 3.44e-10

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 56.54  E-value: 3.44e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGP-VASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKG--RPCRIMW 155
Cdd:cd12344   1 TLWMGDLEPWMDEAYISSCFAKTGEeVVSVKIIRNKQTGKSAGYCFVEFATQEAAEQALEHLNGKPIPNtqQRFRLNW 78
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
171-240 3.51e-10

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 56.25  E-value: 3.51e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKvavdeLGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12340   3 FVRPFPPDTSESAIREIFSPYGPVKEVK-----MLSDSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67
RRM_RBM7 cd12592
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily ...
81-153 3.68e-10

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.


Pssm-ID: 410005 [Multi-domain]  Cd Length: 75  Bit Score: 56.37  E-value: 3.68e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLgYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12592   3 TLFVGNLDTKVTEELLFELFLQAGPVIKVKIPKDKDGKPKQ-FAFVNFKHEVSVPYAMNLLNGIKLYGRPLKI 74
RRM2_TIAR cd12617
RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup ...
82-158 3.75e-10

RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410029 [Multi-domain]  Cd Length: 80  Bit Score: 56.54  E-value: 3.75e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQR 158
Cdd:cd12617   4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATR 80
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
261-322 3.77e-10

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 56.44  E-value: 3.77e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12651   3 TNLYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKlTGRPRGVAFVRYDKREEAQAAISALN 65
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
366-425 3.87e-10

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 56.23  E-value: 3.87e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12384   3 IFVGGLPYHTTDDSLREYFEQFGEIEEAVVITDRQtGKSRGYGFVTMADREAAERACKDPN 63
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
366-434 4.03e-10

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 56.47  E-value: 4.03e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMT----DEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12318   3 LFVKNLNFKTTEEALKKHFEKCGPIRSVTIAKkkdpKGPLLSMGYGFVEFKSPEAAQKALKQLQGTVLDGHAL 75
RRM2_TIAR cd12617
RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup ...
365-441 4.13e-10

RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410029 [Multi-domain]  Cd Length: 80  Bit Score: 56.54  E-value: 4.13e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12617   3 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDmATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATR 80
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
263-333 4.21e-10

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 56.57  E-value: 4.21e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12392   5 LFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISV 75
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
263-333 4.92e-10

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 56.00  E-value: 4.92e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKP---RGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd21619   4 IYVGNIDMTINEDALEKIFSRYGQVESVRRPPIHTDKAdrtTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
262-335 5.02e-10

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 56.25  E-value: 5.02e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKE--YKGKKLYVGR 335
Cdd:cd12262   5 NVYVGNLDDSLTEEEIRGILEKYGEIESIKILKE-----KNCAFVNYLNIANAIKAVQELPIKNpkFKKVRINYGK 75
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
365-437 5.25e-10

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 56.15  E-value: 5.25e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIM---TDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12223   3 NLYVGNLPPSVTEEVLLREFGRFGPLASVKIMwprTEEErRRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLG 79
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
263-340 5.47e-10

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 56.13  E-value: 5.47e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSL------SLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVgra 336
Cdd:cd12409   2 VYISNLSYSTTEEELEELLKDYKPVSVLipsytvRGFRSRKHRPLGIAYAEFSSVEEAEKVVKDLNGKVFKGRKLFV--- 78

                ....
gi 19114289 337 qKKH 340
Cdd:cd12409  79 -KLH 81
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
261-337 5.51e-10

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 56.28  E-value: 5.51e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12772   5 TNLIVNYLPQNMTQEEFKSLFGSIGDIESCKLVRDKiTGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 82
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
261-333 5.66e-10

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 55.75  E-value: 5.66e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNdkprgFGFVNYANHECAQKAVDELNDKEY-KGKKLYV 333
Cdd:cd12224   2 TTLYVGGLGDKITEKDLRDHFYQFGEIRSITVVARQQ-----CAFVQFTTRQAAERAAERTFNKLIiKGRRLKV 70
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
170-240 5.71e-10

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 56.06  E-value: 5.71e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVaVDELGNAK--GYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12413   2 LFVRNLPYDTTDEQLEELFSDVGPVKRCFV-VKDKGKDKcrGFGYVTFALAEDAQRALEEVKGKKFGGRKIKV 73
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
263-333 5.95e-10

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 56.06  E-value: 5.95e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12411  12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDkKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
365-439 6.09e-10

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 55.87  E-value: 6.09e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12650   2 NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDkVTGQSLGYGFVNYVDPSDAEKAINTLNGLRLQNKTIKVSYA 77
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
169-238 6.31e-10

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 55.96  E-value: 6.31e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12619   3 NIFVGDLSPEVTDAALFNAFSDFPSCSDARVMWDqKTGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPI 73
RRM1_RBM19_MRD1 cd12315
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple ...
261-333 6.52e-10

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409754 [Multi-domain]  Cd Length: 81  Bit Score: 56.01  E-value: 6.52e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQF-----GEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12315   1 SRLIVKNLPLSLDEDQFRRLFSQKckdigLTITDCKLLTKSGGVSRRFGFVGFKDEEDAQKAKEFFNGTYFRTSKVTV 78
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
366-438 7.27e-10

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 55.80  E-value: 7.27e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12392   5 LFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAI 77
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
87-156 7.37e-10

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 55.70  E-value: 7.37e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  87 LDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12363   9 LSLYTTERDLREVFSRYGPIEKVQVVYDQQTGRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRVDYS 78
RRM2_SF3B4 cd12335
RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
262-339 7.53e-10

RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409772 [Multi-domain]  Cd Length: 83  Bit Score: 55.83  E-value: 7.53e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEI-TSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12335   3 NLFIGNLDPEVDEKLLYDTFSAFGVIlQTPKIMRDPDTGnSKGFGFVSFDSFEASDAAIEAMNGQYLCNRPITVSYAFKK 82
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
366-439 8.90e-10

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 55.48  E-value: 8.90e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12407   3 LHVSNIPFRFRDPDLRQMFGQFGTILDVEIIFNERG-SKGFGFVTFANSADADRAREKLNGTVVEGRKIEVNNA 75
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
263-339 9.43e-10

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 55.66  E-value: 9.43e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12673   5 IFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDRAGVSKGYGFITFETQEDAQKILQEAEKLNYKDKKLNIGPAIRK 81
RRM2_MYEF2 cd12660
RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This ...
366-438 9.70e-10

RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410061 [Multi-domain]  Cd Length: 76  Bit Score: 55.41  E-value: 9.70e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12660   3 IFVANLDFKVGWKKLKEVFSMAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRPMHVKM 75
RRM3_Bruno_like cd12640
RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar ...
169-240 1.01e-09

RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 241084 [Multi-domain]  Cd Length: 79  Bit Score: 55.39  E-value: 1.01e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12640   6 NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNlSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRLKV 78
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
261-337 1.08e-09

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 55.50  E-value: 1.08e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12771   5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKiTGQSLGYGFVNYIEPKDAEKAINTLNGLRLQTKTIKVSYAR 82
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
170-240 1.11e-09

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 54.87  E-value: 1.11e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12565   3 IIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKDGKSRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISV 73
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
82-153 1.26e-09

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 54.83  E-value: 1.26e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12399   1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
263-331 1.28e-09

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 54.56  E-value: 1.28e-09
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gi 19114289 263 VYIKNLDTE-ITEQEFSDLFGQFGEITSLSLVKdqndkprGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12341   3 IFVGNLPTDqMTKEDLEEIFSKYGKILGISLHK-------GYGFVQFDNEEDARAAVAGENGRTIKGQRL 65
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
261-328 1.29e-09

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 54.94  E-value: 1.29e-09
                        10        20        30        40        50        60
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12376   1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQlTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEG 69
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
366-438 1.29e-09

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 54.96  E-value: 1.29e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKI-----MTDEQgKSKGFGFVCYTTPEEANKAVtEMNQRMLAGKPLYVAL 438
Cdd:cd12298   3 IRVRNLDFELDEEALRGIFEKFGEIESINIpkkqkNRKGR-HNNGFAFVTFEDADSAESAL-QLNGTLLDNRKISVSL 78
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
82-142 1.36e-09

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 55.10  E-value: 1.36e-09
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                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12649   3 LIVNYLPQDLTDREFRALFRAIGPVNTCKIVRDKKTGYSYGFGFVDFTSEEDAQRAIKTLN 63
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
172-240 1.37e-09

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 54.63  E-value: 1.37e-09
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gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12564   5 VKNLPSSITEDRLRKLFSAFGTITDVQLKYTKDGKFRRFGFVGFKSEEEAQKALKHFNNSFIDTSRITV 73
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
368-425 1.44e-09

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 54.82  E-value: 1.44e-09
                        10        20        30        40        50
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gi 19114289 368 IKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12408   4 VTNLSEDATEEDLRELFRPFGPISRVYLAKDkETGQSKGFAFVTFETREDAERAIEKLN 62
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
263-329 1.53e-09

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 54.70  E-value: 1.53e-09
                        10        20        30        40        50        60
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGK 329
Cdd:cd12353   2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKDtQTGKSKGYGFVSFVKKEDAENAIQGMNGQWLGGR 69
RRM2_hnRNPM_like cd12386
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
170-240 1.62e-09

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409820 [Multi-domain]  Cd Length: 74  Bit Score: 54.67  E-value: 1.62e-09
                        10        20        30        40        50        60        70
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12386   1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIREDKDGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRV 71
RRM1_HuR cd12769
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup ...
81-157 1.64e-09

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410162 [Multi-domain]  Cd Length: 82  Bit Score: 54.66  E-value: 1.64e-09
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12769   4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
78-157 1.65e-09

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 54.73  E-value: 1.65e-09
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gi 19114289  78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12771   3 SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIEPKDAEKAINTLNGLRLQTKTIKVSYAR 82
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
263-336 1.74e-09

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 54.91  E-value: 1.74e-09
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDK------EYKGKKLYVGR 335
Cdd:cd12415   3 VFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDkDTGHSKGTAFVQFKTKESADKCIEAANDEsedgglVLDGRKLIVSL 82

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gi 19114289 336 A 336
Cdd:cd12415  83 A 83
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
264-333 1.81e-09

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 54.22  E-value: 1.81e-09
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gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12332   5 FVGNLPNDITEEEFKELFQKYGEVSEVFLNKG-----KGFGFIRLDTRANAEAAKAELDGTPRKGRQLRV 69
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
82-158 1.85e-09

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 54.58  E-value: 1.85e-09
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQR 158
Cdd:cd12381   4 LYVKNLDDTIDDEKLREEFSPFGTITSAKVMTDE-GGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQR 79
RRM1_HuR cd12769
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup ...
261-337 1.88e-09

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410162 [Multi-domain]  Cd Length: 82  Bit Score: 54.66  E-value: 1.88e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12769   3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKvAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
366-434 2.12e-09

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 54.37  E-value: 2.12e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12397   1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMATFEdSGKCKGFAFVDFKEIESATNAVKGPINHSLNGRDL 70
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
263-333 2.17e-09

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 54.34  E-value: 2.17e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDrETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM2_MSSP cd12244
RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) ...
169-233 2.18e-09

RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409690 [Multi-domain]  Cd Length: 82  Bit Score: 54.30  E-value: 2.18e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12244   2 NLYISNLPLDMDEQDLENMLKPFGQVISTRILRDSKGQSRGVGFARMESREKCEDVISKFNGKVL 66
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
268-320 2.20e-09

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 54.07  E-value: 2.20e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 19114289 268 LDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDE 320
Cdd:cd12325   6 LSWETTEESLREYFSKYGEVVDCVVMKDPATGrSRGFGFVTFKDPSSVDAVLAA 59
RRM1_HuR cd12769
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup ...
362-440 2.38e-09

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410162 [Multi-domain]  Cd Length: 82  Bit Score: 54.27  E-value: 2.38e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12769   1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKvAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
366-427 2.40e-09

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 54.37  E-value: 2.40e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAvteMNQR 427
Cdd:cd12578   2 LFIGGLSYETTDDSLRNHFEQWGEITDVVVMKDPATKrSRGFGFVTYSSASEVDAA---MNAR 61
RRM2_p54nrb_like cd12333
RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
172-229 2.40e-09

RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409770 [Multi-domain]  Cd Length: 80  Bit Score: 54.24  E-value: 2.40e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVN 229
Cdd:cd12333   4 VKNLSPYVSNELLEQAFSQFGDVERAVVIVDDRGRSTGEGIVEFSRKPGAQAALKRCS 61
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
170-238 2.44e-09

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 53.79  E-value: 2.44e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPA-IDNKALHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12341   3 IFVGNLPTDqMTKEDLEEIFSKYGKILGISLH-------KGYGFVQFDNEEDARAAVAGENGRTIKGQRL 65
RRM3_CELF3_4_5_6 cd12639
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
169-240 2.44e-09

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 241083 [Multi-domain]  Cd Length: 79  Bit Score: 54.09  E-value: 2.44e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12639   6 NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNqSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV 78
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
82-153 2.62e-09

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 54.16  E-value: 2.62e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12680   3 LLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDR-SGRSLGTAEVVFERRADALKAMKQYNGVPLDGRPMKI 73
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
263-331 2.72e-09

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 53.83  E-value: 2.72e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12393   4 VYVSNLPFSLTNNDLHQIFSKYGKVVKVTILKDKETrKSKGVAFVLFLDRESAHNAVRAMNNKELFGRTL 73
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
90-156 3.83e-09

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 53.71  E-value: 3.83e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  90 SVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12414  10 KCTEDDLKKLFSKFGKVLEVTIPKKP-DGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
366-438 3.86e-09

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 53.17  E-value: 3.86e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEqgkskGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12340   2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDS-----NFAFVEFEELEDAIRAKDSVHGRVLNNEPLYVTY 69
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
263-336 3.93e-09

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 53.59  E-value: 3.93e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQTLNGRQIFGQEIKVNWA 74
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
82-153 3.94e-09

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 53.43  E-value: 3.94e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12311   1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRV 72
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
81-154 4.06e-09

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410071 [Multi-domain]  Cd Length: 77  Bit Score: 53.60  E-value: 4.06e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIM 154
Cdd:cd12670   1 CVFVGNLAFEAEEEGLWRYFGKCGAIESVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLNEKPTMKGRKLRVS 74
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
170-236 4.24e-09

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410185 [Multi-domain]  Cd Length: 75  Bit Score: 53.52  E-value: 4.24e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDK 236
Cdd:cd21606   4 VFIANLPYSINWQALKDMFKECGDVLRADVELDYNGRSRGFGTVIYATEEEMHRAIDTFNGYELEGR 70
RRM2_SECp43 cd12612
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); ...
170-230 4.25e-09

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region.


Pssm-ID: 410024 [Multi-domain]  Cd Length: 82  Bit Score: 53.53  E-value: 4.25e-09
                        10        20        30        40        50        60
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSA-FGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12612   4 LFVGDLTPEVDDGMLYEFFLKrYPSCKGAKVVLDQLGNSRGYGFVRFSDENEQKRALTECQG 65
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
82-153 4.61e-09

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 53.44  E-value: 4.61e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12383   9 IFCGDLGNEVTDEVLARAFSKYPSFQKAKVIRDKRTGKSKGYGFVSFKDPNDYLKALREMNGKYVGNRPIKL 80
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
366-440 4.74e-09

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 53.58  E-value: 4.74e-09
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDRYtGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITE 77
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
81-151 5.09e-09

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 53.00  E-value: 5.09e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTrRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPC 151
Cdd:cd12391   1 TVFVSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKG-KSKGYCYVEFKDEESAQKAL-KLDRQPVEGRPM 69
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
82-154 5.10e-09

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 53.78  E-value: 5.10e-09
                        10        20        30        40        50        60        70
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRpcRIM 154
Cdd:cd12236   4 LFVARLSYDTTESKLRREFEKYGPIKRVRLVRDKKTGKSRGYAFIEFEHERDMKAAYKHADGKKIDGR--RVL 74
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
169-240 5.41e-09

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 53.43  E-value: 5.41e-09
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gi 19114289 169 NV-FIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12235   4 NVlFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDkKTGDSLQYAFIEFETKESCEEAYFKMDNVLIDDRRIHV 77
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
82-150 5.74e-09

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 53.33  E-value: 5.74e-09
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12380   4 VYVKNFGEDVDDDELKELFEKYGKITSAKVMKDD-SGKSKGFGFVNFENHEAAQKAVEELNGKELNGKK 71
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
81-157 5.75e-09

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 53.19  E-value: 5.75e-09
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12770   3 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 79
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
172-240 6.01e-09

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 52.94  E-value: 6.01e-09
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gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12414   4 VRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAV 72
RRM5_MRD1 cd12570
RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 ...
261-331 6.05e-09

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241014 [Multi-domain]  Cd Length: 76  Bit Score: 52.90  E-value: 6.05e-09
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12570   1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRL 71
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
263-333 6.09e-09

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 53.02  E-value: 6.09e-09
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKdqndKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12373   2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVAR----NPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRV 68
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
170-240 6.18e-09

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 52.80  E-value: 6.18e-09
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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDrETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM_RBM25 cd12446
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...
364-436 6.40e-09

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.


Pssm-ID: 409880 [Multi-domain]  Cd Length: 83  Bit Score: 53.30  E-value: 6.40e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 364 VNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12446   1 TTVFVGNIPDDVSDDFIRQLLEKCGKVLSWKRVQDPSGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLV 73
RRM_NCBP2 cd12240
RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
82-155 6.43e-09

RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins; This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC.


Pssm-ID: 409686 [Multi-domain]  Cd Length: 78  Bit Score: 52.96  E-value: 6.43e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12240   1 LYVGNLSFYTTEEQIYELFSKCGDIKRIIMGLDKFKKTPCGFCFVEYYSREDAENAVKYLNGTKLDDRIIRVDW 74
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
263-336 6.58e-09

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 53.06  E-value: 6.58e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12371   3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDpETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRVGRA 77
RRM1_RBM19_MRD1 cd12315
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple ...
366-425 6.67e-09

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409754 [Multi-domain]  Cd Length: 81  Bit Score: 52.93  E-value: 6.67e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAF-----GTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12315   3 LIVKNLPLSLDEDQFRRLFSQKckdigLTITDCKLLTKSGGVSRRFGFVGFKDEEDAQKAKEFFN 67
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
263-338 7.65e-09

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 52.81  E-value: 7.65e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDrYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITEK 78
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
265-333 7.68e-09

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 52.70  E-value: 7.68e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVK-DQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12389   4 VTNLPLSFTEEQFEELVRPYGNVERCFLVYsEVTGESKGYGFVEYTSKESAIRAKNQLHGRQIGGRALQV 73
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
263-333 7.95e-09

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 52.68  E-value: 7.95e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKdQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd21605   4 IFVGNLPFDCTWEDLKDHFSQVGEVIRADIVT-SRGRHRGMGTVEFTNKEDVDRAISKFDHTMFMGREIFV 73
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
366-436 8.05e-09

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 52.41  E-value: 8.05e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDrETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPIRL 72
RRM4_MRD1 cd12319
RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 ...
364-441 8.13e-09

RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409758 [Multi-domain]  Cd Length: 84  Bit Score: 52.87  E-value: 8.13e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 364 VNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD----EQGK--SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12319   1 ATLFVKNLNFSTTNQHLTDVFKHLDGFVFARVKTKpdpkRPGKtlSMGFGFVGFKTKEQAQAALKAMDGFVLDGHKLEVK 80

                ....
gi 19114289 438 LAQR 441
Cdd:cd12319  81 FSHR 84
RRM_RBM25 cd12446
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...
261-333 8.67e-09

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.


Pssm-ID: 409880 [Multi-domain]  Cd Length: 83  Bit Score: 52.91  E-value: 8.67e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12446   1 TTVFVGNIPDDVSDDFIRQLLEKCGKVLSWKRVQDPSGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLV 73
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
363-436 9.28e-09

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410185 [Multi-domain]  Cd Length: 75  Bit Score: 52.36  E-value: 9.28e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd21606   1 GYEVFIANLPYSINWQALKDMFKECGDVLRADVELDYNGRSRGFGTVIYATEEEMHRAIDTFNGYELEGRVLEV 74
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
168-242 9.28e-09

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 52.48  E-value: 9.28e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12449   1 GKLFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDrETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQ 76
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
366-439 9.86e-09

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 52.41  E-value: 9.86e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNL-----QDEVDDErLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAvTEMNQRMLAGKPLYVALA 439
Cdd:cd12451   2 IFVKGFdaslgEDTIRDE-LREHFGECGEVTNVRIPTDrETGELKGFAYIEFSTKEAKEKA-LELNGSDIAGGNLVVDEA 79
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
78-157 1.06e-08

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 52.81  E-value: 1.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12772   3 SKTNLIVNYLPQNMTQEEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 82
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
261-336 1.09e-08

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 52.40  E-value: 1.09e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12649   1 TNLIVNYLPQDLTDREFRALFRAIGPVNTCKIVRDkKTGYSYGFGFVDFTSEEDAQRAIKTLNGLQLQNKRLKVAYA 77
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
366-432 1.10e-08

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 52.11  E-value: 1.10e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEmnQRMLAGK 432
Cdd:cd12577   1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIMKDSAtGRSRGFGFLTFEDPSSVNEVMKK--EHVLDGK 66
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
82-157 1.13e-08

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 52.42  E-value: 1.13e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDRYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITE 77
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
172-230 1.13e-08

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 52.13  E-value: 1.13e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12408   4 VTNLSEDATEEDLRELFRPFGPISRVYLAKDkETGQSKGFAFVTFETREDAERAIEKLNG 63
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
87-156 1.16e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 52.65  E-value: 1.16e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  87 LDPSVTEAMLFELFNSIG--PVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTL----IKGRPCRIMWS 156
Cdd:cd12313  10 LDVLTTEEDILSALQAHAdlPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLLppfkIDGRVVSVSYA 85
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
170-240 1.20e-08

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 52.05  E-value: 1.20e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
169-240 1.24e-08

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 52.05  E-value: 1.24e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDrGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINV 73
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
366-442 1.27e-08

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 52.19  E-value: 1.27e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12673   5 IFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDRAGVSKGYGFITFETQEDAQKILQEAEKLNYKDKKLNIGPAIRK 81
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
261-341 1.30e-08

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 52.09  E-value: 1.30e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPrGFGFVNYANHECAQKAVDELNDKEYKGKKLYVgraQKKH 340
Cdd:cd12454   4 LSIFVGQLDPKTTDSELFRRFSKYGKIVDCKLIKRPEPVN-AFAFLRFESEEAAEAAVEEENHSEFLNKQIRV---QKRE 79

                .
gi 19114289 341 E 341
Cdd:cd12454  80 L 80
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
265-336 1.30e-08

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 51.85  E-value: 1.30e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12320   5 VKNVPFEATRKEIRELFSPFGQLKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
363-474 1.36e-08

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 52.81  E-value: 1.36e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAvtemnqrmLAGKPlyvALAQR 441
Cdd:cd12676   1 GRTLFVRNLPFDATEDELYSHFSQFGPLKYARVVKDpATGRSKGTAFVKFKNKEDADNC--------LSAAP---EAQST 69
                        90       100       110
                ....*....|....*....|....*....|....*
gi 19114289 442 KEVRRSQLEAQIQARN--QFRLQQQVAAAagIPAV 474
Cdd:cd12676  70 SLLEKYSLEQDITDDVsaKFTLDGRVLQV--TPAV 102
RRM1_hnRNPA1 cd12761
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) ...
366-422 1.45e-08

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.


Pssm-ID: 410154 [Multi-domain]  Cd Length: 81  Bit Score: 51.98  E-value: 1.45e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVT 422
Cdd:cd12761   5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKrSRGFGFVTYATVEEVDAAMN 62
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
170-240 1.46e-08

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 52.09  E-value: 1.46e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVaVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12454   6 IFVGQLDPKTTDSELFRRFSKYGKIVDCKL-IKRPEPVNAFAFLRFESEEAAEAAVEEENHSEFLNKQIRV 75
RRM_RBM25 cd12446
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...
170-240 1.48e-08

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.


Pssm-ID: 409880 [Multi-domain]  Cd Length: 83  Bit Score: 52.14  E-value: 1.48e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12446   3 VFVGNIPDDVSDDFIRQLLEKCGKVLSWKRVQDPSGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLV 73
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
170-240 1.49e-08

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 53.08  E-value: 1.49e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGML---LNDKKVYV 240
Cdd:cd21615  21 LFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDkETGKSRGYAFIVFKSESDAKNAFKEGNGLRglkINDRTCIV 95
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
81-150 1.50e-08

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 51.92  E-value: 1.50e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRP 150
Cdd:cd12306   1 SIYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFTGQPKGFAYIEFVDKSSVENAL-LLNESEFRGRQ 69
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
169-240 1.55e-08

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 52.03  E-value: 1.55e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12375   1 NLIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKItGQSLGYGFVNYRDPNDARKAINTLNGLDLENKRLKV 73
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
79-153 1.56e-08

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 52.03  E-value: 1.56e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  79 SASLYVGELDPSVTEAML----FELFNSIGPVASIRVCRDavtRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12453   2 SACLFVASLSSARSDEELcaavTNHFSKWGELLNVKVLKD---WSNRPYAFVQYTNTEDAKNALVNGHNTLLDGRHLRV 77
RRM2_MSSP1 cd12473
RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
169-233 1.57e-08

RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409903 [Multi-domain]  Cd Length: 85  Bit Score: 51.97  E-value: 1.57e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12473   2 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHFNGKFI 66
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
365-436 1.62e-08

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 52.13  E-value: 1.62e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12671   8 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDrETGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRV 80
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
365-440 1.72e-08

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 52.04  E-value: 1.72e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12771   6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKiTGQSLGYGFVNYIEPKDAEKAINTLNGLRLQTKTIKVSYAR 82
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
263-333 1.78e-08

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 51.34  E-value: 1.78e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12395   2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDrETGIGKGFGYVLFKDKDSVDLAL-KLNGSKLRGRKLRV 72
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
263-339 1.86e-08

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 51.63  E-value: 1.86e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12450   2 LFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRDDgRSKGFGHVEFASAESAQKAL-EKSGQDLGGREIRLDLANER 78
RRM2_Bruno_like cd12636
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar ...
366-439 1.87e-08

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 410044 [Multi-domain]  Cd Length: 81  Bit Score: 51.80  E-value: 1.87e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQ-RMLAG--KPLYVALA 439
Cdd:cd12636   4 LFVGMLSKKCNESDVRIMFSPYGSIEECTVLRDQNGKSRGCAFVTFTSRQCAVNAIKAMHHsQTMEGcsSPLVVKFA 80
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
366-436 1.94e-08

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409983 [Multi-domain]  Cd Length: 79  Bit Score: 51.62  E-value: 1.94e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQG-KSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12567   5 LFVRNLPYTCTEEDLEKLFSKYGPLSEVHFPIDSLTkKPKGFAFVTYMIPEHAVKAYAELDGTVFQGRLLHL 76
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
82-155 1.97e-08

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 51.53  E-value: 1.97e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVA--SIRVCRDAVTR-RSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12355   2 LWIGNLDPRLTEYHLLKLLSKYGKIKkfDFLFHKTGPLKgQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRW 78
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
169-238 2.01e-08

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 51.51  E-value: 2.01e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12354   2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPD-----KGYAFIRFDSHEAATHAIVSVNGTIINGQAV 66
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
365-439 2.02e-08

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 51.53  E-value: 2.02e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIM----TDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12355   1 RLWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLfhktGPLKGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWA 79
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
80-155 2.05e-08

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 51.13  E-value: 2.05e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12354   1 TTVYVGNITKGLTEALLQQTFSPFGQILEVRVFPDK------GYAFIRFDSHEAATHAIVSVNGTIINGQAVKCSW 70
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
170-229 2.06e-08

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 51.83  E-value: 2.06e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVN 229
Cdd:cd12415   3 VFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDkDTGHSKGTAFVQFKTKESADKCIEAAN 63
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
366-437 2.34e-08

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 51.37  E-value: 2.34e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSA---KIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd21619   4 IYVGNIDMTINEDALEKIFSRYGQVESVrrpPIHTDKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVVR 78
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
82-157 2.41e-08

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 51.50  E-value: 2.41e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12235   6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKESCEEAYFKMDNVLIDDRRIHVDFSQ 81
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
264-336 2.48e-08

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 51.25  E-value: 2.48e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ--NDKprgFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12352   2 YVGNLDRQVTEDLILQLFSQIGPCKSCKMITEHggNDP---YCFVEFYEHNHAAAALQAMNGRKILGKEVKVNWA 73
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
263-333 2.49e-08

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 51.46  E-value: 2.49e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12324   9 IFVTGVHEEAQEEDIHDKFAEFGEIKNLHLNLDrRTGFVKGYALVEYETKKEAQAAIEGLNGKELLGQTISV 80
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
367-436 2.53e-08

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 50.96  E-value: 2.53e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 367 FIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVtEMNQRMLAGKPLYV 436
Cdd:cd12395   3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDrETGIGKGFGYVLFKDKDSVDLAL-KLNGSKLRGRKLRV 72
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
81-138 2.54e-08

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 52.04  E-value: 2.54e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKAL 138
Cdd:cd12676   3 TLFVRNLPFDATEDELYSHFSQFGPLKYARVVKDPATGRSKGTAFVKFKNKEDADNCL 60
RRM2_MSSP cd12244
RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) ...
365-439 2.58e-08

RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409690 [Multi-domain]  Cd Length: 82  Bit Score: 51.22  E-value: 2.58e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRML-----AGKPLYVALA 439
Cdd:cd12244   2 NLYISNLPLDMDEQDLENMLKPFGQVISTRILRDSKGQSRGVGFARMESREKCEDVISKFNGKVLktpsaSGEPLLVKFA 81
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
82-149 2.61e-08

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 51.19  E-value: 2.61e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12316   2 LFVRNLPFTATEDELRELFEAFGKISEVHIPLDKQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGR 69
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
77-159 2.67e-08

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 51.98  E-value: 2.67e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  77 PTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12559   3 PPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFA 82

                ...
gi 19114289 157 QRD 159
Cdd:cd12559  83 QGD 85
RRM_RBM11 cd12593
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily ...
366-436 2.69e-08

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 410006 [Multi-domain]  Cd Length: 75  Bit Score: 50.95  E-value: 2.69e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12593   4 VFVGNLHSNVNEEILYELFLQAGPLTKVTIAKDKEGKPKSFGFVCFKHAESVPYAIALLNGIRLYGRPIKL 74
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
263-318 2.84e-08

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 51.12  E-value: 2.84e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAV 318
Cdd:cd12328   2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIVTDkETGKKRGFAFVTFDDHDSVDKIV 58
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
81-149 2.86e-08

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 51.13  E-value: 2.86e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSlgYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd21603   2 AIFVKNLPLDTNNDEILDFFSKVGPIKSVFTSPKYKYNSL--WAFVTYKKGSDTEKAIKLLNGTLFKGR 68
RRM2_PSRP2 cd21610
RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
170-240 2.86e-08

RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). PSRP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410189 [Multi-domain]  Cd Length: 79  Bit Score: 51.08  E-value: 2.86e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVA-VDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd21610   5 VYVGNLAKTVTNELLKDFFSEKGKVLGAKVQrTPGTSKSNGFGFVSFSSEEDVEAAIQALNNSVLEGQKIRV 76
RRM2_PSRP2 cd21610
RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
82-153 2.92e-08

RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). PSRP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410189 [Multi-domain]  Cd Length: 79  Bit Score: 51.08  E-value: 2.92e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd21610   5 VYVGNLAKTVTNELLKDFFSEKGKVLGAKVQRTPGTSKSNGFGFVSFSSEEDVEAAIQALNNSVLEGQKIRV 76
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
366-436 3.09e-08

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 50.76  E-value: 3.09e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKImtdeqGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12332   4 LFVGNLPNDITEEEFKELFQKYGEVSEVFL-----NKGKGFGFIRLDTRANAEAAKAELDGTPRKGRQLRV 69
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
263-333 3.14e-08

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 50.57  E-value: 3.14e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12608   3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVMKQ-------FAFVHMRGEAAADRAIRELNGRELHGRALVV 66
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
261-331 3.27e-08

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 51.07  E-value: 3.27e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK----PRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12318   1 TTLFVKNLNFKTTEEALKKHFEKCGPIRSVTIAKKKDPKgpllSMGYGFVEFKSPEAAQKALKQLQGTVLDGHAL 75
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
170-240 3.36e-08

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 50.62  E-value: 3.36e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12609   3 IFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEALNGKEVKGRRINV 66
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
366-437 3.41e-08

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 51.47  E-value: 3.41e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNL-QDEVDDERLKAEFSAFGTITSAKIMTDeQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12390   5 LFVDRLpKDFRDGSELRKLFSQVGKPTFCQLAMG-NGVPRGFAFVEFASAEDAEEAQQLLNGHDLQGSPIRVS 76
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
260-338 3.42e-08

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 51.47  E-value: 3.42e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 260 FTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV----G 334
Cdd:cd12236   1 FKTLFVARLSYDTTESKLRREFEKYGPIKRVRLVRDKkTGKSRGYAFIEFEHERDMKAAYKHADGKKIDGRRVLVdverG 80

                ....
gi 19114289 335 RAQK 338
Cdd:cd12236  81 RTVK 84
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
366-438 3.81e-08

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 50.69  E-value: 3.81e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12680   3 LLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERRADALKAMKQYNGVPLDGRPMKIQL 75
RRM1_SECp43 cd12610
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43); ...
81-148 3.86e-08

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region.


Pssm-ID: 410022 [Multi-domain]  Cd Length: 84  Bit Score: 50.78  E-value: 3.86e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIG-PVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKG 148
Cdd:cd12610   1 SLWMGDLEPYMDENFIKRAFATMGeTVLSVKIIRNRVTGGPAGYCFVEFADEATAERCLHKLNGKPIPG 69
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
263-333 3.97e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 50.30  E-value: 3.97e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12343   2 IFVGNLPDAATSEELRALFEKYGKVTECDIVKN-------YAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
263-334 4.03e-08

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 50.36  E-value: 4.03e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRgFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd21603   3 IFVKNLPLDTNNDEILDFFSKVGPIKSVFTSPKYKYNSL-WAFVTYKKGSDTEKAIKLLNGTLFKGRTIEVT 73
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
170-240 4.10e-08

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 51.07  E-value: 4.10e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12324   9 IFVTGVHEEAQEEDIHDKFAEFGEIKNLHLNLDrRTGFVKGYALVEYETKKEAQAAIEGLNGKELLGQTISV 80
RRM3_HuR cd12653
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup ...
363-442 4.19e-08

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410056 [Multi-domain]  Cd Length: 85  Bit Score: 50.83  E-value: 4.19e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12653   2 GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDfNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTN 81

                .
gi 19114289 442 K 442
Cdd:cd12653  82 K 82
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
79-153 4.20e-08

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 50.60  E-value: 4.20e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRD--AVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd21619   1 SNTIYVGNIDMTINEDALEKIFSRYGQVESVRRPPIhtDKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
263-337 4.20e-08

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 50.65  E-value: 4.20e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECA-QKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12226   2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDRGFAYIDLRTSEAAlQKCLSTLNGVKWKGSRLKIQLAK 77
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
365-439 4.22e-08

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 50.70  E-value: 4.22e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAG--KPLYVALA 439
Cdd:cd12376   2 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQlTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGasEPITVKFA 79
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
263-337 4.28e-08

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 50.79  E-value: 4.28e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd21607   5 IYCSNLPLSTAESDLYDLFETIGKVNNAELKYDETGDPTGSAVVEYENLDDADVCISKLNNYNYGGCDLKISYAK 79
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
81-149 4.37e-08

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 50.36  E-value: 4.37e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12393   3 TVYVSNLPFSLTNNDLHQIFSKYGKVVKVTILKDKETRKSKGVAFVLFLDRESAHNAVRAMNNKELFGR 71
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
261-331 4.44e-08

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 50.53  E-value: 4.44e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSlslVKDQNDKprGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12622   1 TTVYVGNLPPEVTQADLIPLFQNFGVIEE---VRVQRDK--GFGFVKYDTHEEAALAIQQLNGQPFLGRPI 66
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
267-333 4.51e-08

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 50.51  E-value: 4.51e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 267 NLDTEITEQEFSDlfgqFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12447  10 NVDDPWLKKEFEK----YGGVISARVITDRGsGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINV 73
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
263-333 4.54e-08

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 50.38  E-value: 4.54e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12336   4 LFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRI 74
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
263-339 4.55e-08

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 50.55  E-value: 4.55e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDElnDKEYKGKKLYVGRAQKK 339
Cdd:cd12672   8 VFVGGIDIRMDENEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYDDVDIQKIVES--QINFHGKKLKLGPAIRK 82
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
365-440 4.56e-08

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 50.89  E-value: 4.56e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12772   6 NLIVNYLPQNMTQEEFKSLFGSIGDIESCKLVRDKiTGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 82
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
170-238 4.57e-08

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 50.69  E-value: 4.57e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVdELGNAK-----GYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12318   3 LFVKNLNFKTTEEALKKHFEKCGPIRSVTIAK-KKDPKGpllsmGYGFVEFKSPEAAQKALKQLQGTVLDGHAL 75
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
158-245 4.60e-08

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 50.97  E-value: 4.60e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 158 RDPSLRkmgtgNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDK 236
Cdd:cd12671   2 SDRSLR-----SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDrETGKPKGYGFCEYQDQETALSAMRNLNGYELNGR 76

                ....*....
gi 19114289 237 KVYVGHHVS 245
Cdd:cd12671  77 ALRVDNAAS 85
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
170-242 4.65e-08

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 50.59  E-value: 4.65e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12398   3 VFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDrETGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDF 76
RRM2_PSRP2 cd21610
RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
366-439 5.05e-08

RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). PSRP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410189 [Multi-domain]  Cd Length: 79  Bit Score: 50.70  E-value: 5.05e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIM-TDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd21610   5 VYVGNLAKTVTNELLKDFFSEKGKVLGAKVQrTPGTSKSNGFGFVSFSSEEDVEAAIQALNNSVLEGQKIRVNKA 79
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
82-153 5.26e-08

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 50.30  E-value: 5.26e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12400   3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDKKTGKSKGCAFVEFDNQKALQKAL-KLHHTSLGGRKINV 73
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
264-333 5.26e-08

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 50.09  E-value: 5.26e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKdqndkPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12340   3 FVRPFPPDTSESAIREIFSPYGPVKEVKMLS-----DSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
169-238 5.30e-08

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 50.39  E-value: 5.30e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12618   4 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDmATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 74
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
263-335 5.40e-08

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 50.49  E-value: 5.40e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGR 335
Cdd:cd12370   3 VYVGSIYFELGEDTIRQAFAPFGPIKSIDMSWDPvTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKVGR 76
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
81-153 5.68e-08

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 50.48  E-value: 5.68e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLiKGRPCRI 153
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRDDGRSKGFGHVEFASAESAQKALEKSGQDL-GGREIRL 72
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
169-240 5.70e-08

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 50.40  E-value: 5.70e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12377   1 CIFVYNLAPDADESLLWQLFGPFGAVQNVKIIRDFTTNKcKGYGFVTMTNYDEAAVAIASLNGYRLGGRVLQV 73
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
366-425 6.08e-08

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 51.54  E-value: 6.08e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd21615  21 LFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDkETGKSRGYAFIVFKSESDAKNAFKEGN 81
RRM2_MSSP2 cd12474
RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
169-230 6.20e-08

RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409904 [Multi-domain]  Cd Length: 86  Bit Score: 50.42  E-value: 6.20e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12474   2 NLYISNLPLSMDEQELESMLKPFGQVISTRILRDANGTSRGVGFARMESTEKCEAIITHFNG 63
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
261-333 6.35e-08

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 50.06  E-value: 6.35e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 261 TN-VYIKNLDTEITEQEFSDLFGQFGEITSLSLvkdqnDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12351   7 TNcVWLDGLSENVTEQYLTRHFCRYGPVVKVVI-----DRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQV 75
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
171-242 6.35e-08

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 50.32  E-value: 6.35e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12284   2 YVGSLHFNITEDMLRGIFEPFGKIEFVQLQKDpETGRSKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKVGH 74
RRM3_MYEF2 cd12662
RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This ...
366-438 6.63e-08

RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410063 [Multi-domain]  Cd Length: 77  Bit Score: 49.97  E-value: 6.63e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12662   2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM-ENGKSKGCGTVRFDSPESAEKACRLMNGIKISGREIDVRL 73
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
169-240 7.41e-08

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 50.10  E-value: 7.41e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12650   2 NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVtGQSLGYGFVNYVDPSDAEKAINTLNGLRLQNKTIKV 74
RRM1_PES4_MIP6 cd21601
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
171-238 7.41e-08

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410180 [Multi-domain]  Cd Length: 80  Bit Score: 50.04  E-value: 7.41e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd21601   4 FIGDLDKDVTEEMLRDIFSKYKSLVSVKICLDsETKKSLGYGYLNFSDKEDAEKAIEEFNYTPIFGKEV 72
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
362-439 7.46e-08

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 50.28  E-value: 7.46e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGK--PLYVAL 438
Cdd:cd12651   1 KDTNLYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKlTGRPRGVAFVRYDKREEAQAAISALNGTIPEGGtqPLSVRL 80

                .
gi 19114289 439 A 439
Cdd:cd12651  81 A 81
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
169-232 7.60e-08

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 49.89  E-value: 7.60e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGML 232
Cdd:cd12651   4 NLYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKLtGRPRGVAFVRYDKREEAQAAISALNGTI 68
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
170-234 7.83e-08

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 49.88  E-value: 7.83e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLN 234
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLD 67
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
79-157 8.10e-08

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 49.78  E-value: 8.10e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSlgYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12454   3 KLSIFVGQLDPKTTDSELFRRFSKYGKIVDCKLIKRPEPVNA--FAFLRFESEEAAEAAVEEENHSEFLNKQIRVQKRE 79
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
365-440 8.28e-08

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 50.11  E-value: 8.28e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12770   3 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKiTGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 79
RRM2_SRSF1_4_like cd12339
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and ...
263-333 8.29e-08

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins; This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409776 [Multi-domain]  Cd Length: 70  Bit Score: 49.51  E-value: 8.29e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQndkpRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12339   3 VVVSNLPERASWQDLKDFMRKAGEVTYADVHRDR----EGEGVVEFTSEEDMKRAIEKLDGTEFNGRRIRV 69
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
366-439 8.35e-08

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 49.71  E-value: 8.35e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12352   1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMITE-HGGNDPYCFVEFYEHNHAAAALQAMNGRKILGKEVKVNWA 73
RRM_RBM11 cd12593
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily ...
81-153 8.71e-08

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 410006 [Multi-domain]  Cd Length: 75  Bit Score: 49.80  E-value: 8.71e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12593   3 TVFVGNLHSNVNEEILYELFLQAGPLTKVTIAKDK-EGKPKSFGFVCFKHAESVPYAIALLNGIRLYGRPIKL 74
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
170-240 8.83e-08

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 49.83  E-value: 8.83e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSC---KVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd21619   4 IYVGNIDMTINEDALEKIFSRYGQVESVrrpPIHTDKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM3_hnRNPM_like cd12387
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
366-436 9.47e-08

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409821 [Multi-domain]  Cd Length: 71  Bit Score: 49.51  E-value: 9.47e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEqGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12387   1 IFVRNLPFDYTWQKLKDKFKDCGHVTFASIKMEN-GKSKGCGTVRFDSPEDAENACRMMNGSKQSGREIDV 70
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
81-149 9.62e-08

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 50.02  E-value: 9.62e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12237   6 TLFVGRLSLQTTEEKLKEVFSRYGDIRRLRLVRDIVTGFSKRYAFIEYKEERDALHAYRDAKKLVIDQY 74
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
264-333 1.01e-07

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 49.58  E-value: 1.01e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKdqndKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12524   5 FVRNINSSVEDEELRALFEQFGEIRTLYTAC----KHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDI 70
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
263-335 1.08e-07

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 49.52  E-value: 1.08e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGR 335
Cdd:cd12334   1 VYVGNLDEKVTEELLWELFIQAGPVVNVHMPKDRvTQQHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRVNK 74
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
81-153 1.08e-07

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 49.58  E-value: 1.08e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVA------SIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12409   1 RVYISNLSYSTTEEELEELLKDYKPVSvlipsyTVRGFRSR-KHRPLGIAYAEFSSVEEAEKVVKDLNGKVFKGRKLFV 78
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
251-339 1.10e-07

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 51.58  E-value: 1.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  251 SKVEALKANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGK 329
Cdd:PLN03134  25 SMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDrETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR 104
                         90
                 ....*....|
gi 19114289  330 KLYVGRAQKK 339
Cdd:PLN03134 105 HIRVNPANDR 114
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
169-240 1.20e-07

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 49.61  E-value: 1.20e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKIlsckVAVDEL--------GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12355   1 RLWIGNLDPRLTEYHLLKLLSKYGKI----KKFDFLfhktgplkGQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVV 76
RRM2_MSSP cd12244
RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) ...
261-328 1.21e-07

RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409690 [Multi-domain]  Cd Length: 82  Bit Score: 49.68  E-value: 1.21e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12244   1 TNLYISNLPLDMDEQDLENMLKPFGQVISTRILRDSKGQSRGVGFARMESREKCEDVISKFNGKVLKT 68
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
380-425 1.25e-07

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 49.50  E-value: 1.25e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 19114289 380 LKAEFSAFGTITSAKIM--TDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12278  24 LTKIFSKFGSGKIVGIYmpVDETGKTKGFAFVEYATPEEAKKAVKALN 71
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
263-326 1.27e-07

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 49.42  E-value: 1.27e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECaqkaVDELNDKEY 326
Cdd:cd12577   1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIMKDSATgRSRGFGFLTFEDPSS----VNEVMKKEH 61
RRM2_hnRNPM_like cd12386
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
263-333 1.27e-07

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409820 [Multi-domain]  Cd Length: 74  Bit Score: 49.28  E-value: 1.27e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12386   1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIREDKDGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRV 71
RRM3_HuC cd12655
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup ...
363-443 1.28e-07

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410057 [Multi-domain]  Cd Length: 85  Bit Score: 49.67  E-value: 1.28e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12655   1 GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDfTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTS 80

                ..
gi 19114289 442 KE 443
Cdd:cd12655  81 KQ 82
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
82-153 1.32e-07

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 49.33  E-value: 1.32e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12382   4 LFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKV 75
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
264-326 1.35e-07

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 49.30  E-value: 1.35e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKP-RGFGFVNYANHECAQKAVDELNDKEY 326
Cdd:cd12637   3 FVGSLPKTATEQEVRDLFEAYGEVEEVYLMKDPVTQQgTGCAFVKFAYKEEALAAIRSLNGTVT 66
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
366-436 1.35e-07

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 49.34  E-value: 1.35e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12566   5 LFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDKKtKKSKGFAYVLFLDPEDAVQAYNELDGKVFQGRLIHI 76
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
170-242 1.35e-07

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 49.03  E-value: 1.35e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12608   3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVM-------KQFAFVHMRGEAAADRAIRELNGRELHGRALVVEE 68
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
263-333 1.38e-07

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 49.34  E-value: 1.38e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12566   5 LFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDkKTKKSKGFAYVLFLDPEDAVQAYNELDGKVFQGRLIHI 76
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
92-156 1.39e-07

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 49.62  E-value: 1.39e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  92 TEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12641  20 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 84
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
265-333 1.48e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 48.80  E-value: 1.48e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12311   3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTReSRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRV 72
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
366-439 1.49e-07

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 49.07  E-value: 1.49e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLK----AEFSAFGTITsaKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12246   2 LYINNLNEKIKKDELKrslyALFSQFGPVL--DIVASKSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYA 77
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
366-442 1.54e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 49.29  E-value: 1.54e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ--RK 442
Cdd:cd12312   3 LFVRNVADDTRPDDLRREFGRYGPIVDVYIPLDfYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFAQgdRK 82
RRM_RBM7 cd12592
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily ...
263-338 1.60e-07

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.


Pssm-ID: 410005 [Multi-domain]  Cd Length: 75  Bit Score: 49.06  E-value: 1.60e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNdkeykGKKLYvGRAQK 338
Cdd:cd12592   4 LFVGNLDTKVTEELLFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN-----GIKLY-GRPLK 73
RRM_RBM11 cd12593
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily ...
263-340 1.71e-07

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 410006 [Multi-domain]  Cd Length: 75  Bit Score: 49.03  E-value: 1.71e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNdkeykGKKLYvGRAQKKH 340
Cdd:cd12593   4 VFVGNLHSNVNEEILYELFLQAGPLTKVTIAKDKEGKPKSFGFVCFKHAESVPYAIALLN-----GIRLY-GRPIKLQ 75
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
366-443 1.79e-07

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 49.15  E-value: 1.79e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKE 443
Cdd:cd12324   9 IFVTGVHEEAQEEDIHDKFAEFGEIKNLHLNLDRRtGFVKGYALVEYETKKEAQAAIEGLNGKELLGQTISVDWAFVKG 87
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
366-436 1.82e-07

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 48.84  E-value: 1.82e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12336   4 LFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRI 74
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
82-150 1.83e-07

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 48.86  E-value: 1.83e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12377   2 IFVYNLAPDADESLLWQLFGPFGAVQNVKIIRDFTTNKCKGYGFVTMTNYDEAAVAIASLNGYRLGGRV 70
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
81-150 1.88e-07

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 48.78  E-value: 1.88e-07
                        10        20        30        40        50        60        70
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavtrrslgYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12251   3 VLYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD--------YAFVHFEERDDAVKAMEEMNGKELEGSE 64
RRM4_NCL cd12406
RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to ...
366-442 1.92e-07

RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409840 [Multi-domain]  Cd Length: 78  Bit Score: 48.76  E-value: 1.92e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKaefSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRK 442
Cdd:cd12406   3 LFVKGLSEDTTEETLK---EAFEGAISARIATDrDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKPK 77
RRM3_HuB cd12654
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup ...
363-442 1.92e-07

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241098 [Multi-domain]  Cd Length: 86  Bit Score: 48.94  E-value: 1.92e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12654   3 GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDfNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN 82

                .
gi 19114289 442 K 442
Cdd:cd12654  83 K 83
RRM1_PES4_MIP6 cd21601
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
261-322 1.93e-07

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410180 [Multi-domain]  Cd Length: 80  Bit Score: 48.88  E-value: 1.93e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPR-GFGFVNYANHECAQKAVDELN 322
Cdd:cd21601   1 TALFIGDLDKDVTEEMLRDIFSKYKSLVSVKICLDSETKKSlGYGYLNFSDKEDAEKAIEEFN 63
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
171-240 1.96e-07

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 48.56  E-value: 1.96e-07
                        10        20        30        40        50        60        70
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gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKgYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12352   2 YVGNLDRQVTEDLILQLFSQIGPCKSCKMITEHGGNDP-YCFVEFYEHNHAAAALQAMNGRKILGKEVKV 70
RRM2_TIAR cd12617
RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup ...
169-238 1.97e-07

RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410029 [Multi-domain]  Cd Length: 80  Bit Score: 48.84  E-value: 1.97e-07
                        10        20        30        40        50        60        70
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gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12617   3 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDmATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 73
RRM2_PSP1 cd12589
RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This ...
172-227 1.99e-07

RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410002 [Multi-domain]  Cd Length: 80  Bit Score: 48.84  E-value: 1.99e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEH 227
Cdd:cd12589   4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPPARKALER 59
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
366-436 2.06e-07

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 48.83  E-value: 2.06e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd21605   4 IFVGNLPFDCTWEDLKDHFSQVGEVIRADIVT-SRGRHRGMGTVEFTNKEDVDRAISKFDHTMFMGREIFV 73
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
260-331 2.17e-07

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.


Pssm-ID: 409695 [Multi-domain]  Cd Length: 78  Bit Score: 48.74  E-value: 2.17e-07
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gi 19114289 260 FTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12249   1 GCEVFVGKIPRDVFEDELVPLFEKCGKIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKTLNNYEIRPGKL 72
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
170-247 2.23e-07

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 49.25  E-value: 2.23e-07
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRR 247
Cdd:cd12237   7 LFVGRLSLQTTEEKLKEVFSRYGDIRRLRLVRDIVtGFSKRYAFIEYKEERDALHAYRDAKKLVIDQYEIFVDFECERT 85
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
170-233 2.32e-07

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 48.47  E-value: 2.32e-07
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVdelgnAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12346   4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPP-----GKGCGFVQFVNRASAEAAIQKLQGTPI 62
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
263-333 2.41e-07

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 48.45  E-value: 2.41e-07
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12306   2 IYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFTgQPKGFAYIEFVDKSSVENAL-LLNESEFRGRQIKV 72
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
81-153 2.52e-07

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 48.66  E-value: 2.52e-07
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12671   8 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRV 80
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
261-339 2.66e-07

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 48.20  E-value: 2.66e-07
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVkdqndKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12227   3 TTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMI-----PPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNK 76
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
82-145 2.74e-07

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 48.39  E-value: 2.74e-07
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN--YTL 145
Cdd:cd12361   2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQILRDKQTGQSKGCAFVTFSTREEALRAIEALHnkKTM 67
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
169-234 2.86e-07

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 48.47  E-value: 2.86e-07
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gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLN 234
Cdd:cd12652   2 NLYVSGLPKTMTQKELEQLFSQFGRIITSRILCDNVtGLSRGVGFIRFDKRVEAERAIKALNGTIPP 68
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
171-240 3.04e-07

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 48.77  E-value: 3.04e-07
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gi 19114289 171 FIKNLDPAIDNK-ALHDTFSAFGKILSCKVAVDElGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12390   6 FVDRLPKDFRDGsELRKLFSQVGKPTFCQLAMGN-GVPRGFAFVEFASAEDAEEAQQLLNGHDLQGSPIRV 75
RRM2_TDP43 cd12322
RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
261-336 3.19e-07

RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409761 [Multi-domain]  Cd Length: 71  Bit Score: 48.09  E-value: 3.19e-07
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gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQndkpRGFGFVNYANHECAQKAVDElnDKEYKGKKLYVGRA 336
Cdd:cd12322   1 RKVFVGRCTEDMTEDDLRQYFSQFGEVTDVFIPKPF----RAFAFVTFADDEVAQSLCGE--DHIIKGVSVHISNA 70
RRM1_RBM47 cd12485
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47); This ...
363-425 3.24e-07

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240929 [Multi-domain]  Cd Length: 78  Bit Score: 48.04  E-value: 3.24e-07
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gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12485   1 GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
82-142 3.28e-07

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 47.93  E-value: 3.28e-07
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12365   1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDREPNLPRGYAYVEFESPEDAEKAIKHMD 61
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
263-333 3.49e-07

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 48.10  E-value: 3.49e-07
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12494   4 LFVRNLATTVTEEILEKTFSQFGKLERVKKLKD-------YAFVHFEDRDAAVKAMDEMNGKEVEGEEIEI 67
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
81-155 3.60e-07

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 48.05  E-value: 3.60e-07
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVcrdaVTRRslGYAYVNFHNMEDGEKALDEL-NYTLIKGRPCRIMW 155
Cdd:cd12224   3 TLYVGGLGDKITEKDLRDHFYQFGEIRSITV----VARQ--QCAFVQFTTRQAAERAAERTfNKLIIKGRRLKVKW 72
RRM2_RBMS3 cd12475
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, ...
169-233 3.79e-07

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 240919 [Multi-domain]  Cd Length: 88  Bit Score: 48.17  E-value: 3.79e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12475   3 NLYISNLPISMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFNGKYL 67
RRM_FET cd12280
RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...
263-333 3.82e-07

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.


Pssm-ID: 409722 [Multi-domain]  Cd Length: 82  Bit Score: 48.18  E-value: 3.82e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITS--------LSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12280   1 IFVSGLPPDVTIDELADLFGQIGIIKRykdtwppkIKIYTDKEtGKPKGEATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
170-233 3.87e-07

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 47.78  E-value: 3.87e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12450   2 LFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDrDDGRSKGFGHVEFASAESAQKALEKSGQDLG 66
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
81-153 3.90e-07

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 47.78  E-value: 3.90e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12272   1 TVYIGNLAWDIDEDDLRELFAECCEITNVRLHTDKETGEFKGYGHVEFADEESLDAAL-KLAGTKLCGRPIRV 72
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
253-333 3.91e-07

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 48.39  E-value: 3.91e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 253 VEALKANFTNVYiknldteiteqEFSDLFGQFGEITSLSLVKDQNDkPRGFGFVNYANHECAQKAVDELNDKEYKGKKLY 332
Cdd:cd12390   7 VDRLPKDFRDGS-----------ELRKLFSQVGKPTFCQLAMGNGV-PRGFAFVEFASAEDAEEAQQLLNGHDLQGSPIR 74

                .
gi 19114289 333 V 333
Cdd:cd12390  75 V 75
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
263-336 3.94e-07

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 48.03  E-value: 3.94e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12231   3 LFIGGLPNYLNEDQVKELLQSFGKLKAFNLVKDsATGLSKGYAFCEYVDDNVTDQAIAGLNGMQLGDKKLLVQRA 77
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
366-441 4.06e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 47.62  E-value: 4.06e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITS---AKimtdeqgKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12373   2 VYVGNLGPRVTKRELEDAFEKYGPLRNvwvAR-------NPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
83-153 4.25e-07

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 47.98  E-value: 4.25e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  83 YVGELDPSVTEAMLFELFNSIGpVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDeLNYTLIKGRPCRI 153
Cdd:cd12402   6 YLGNLPYDVTEDDIEDFFRGLN-ISSVRLPRENGPGRLRGFGYVEFEDRESLIQALS-LNEESLKNRRIRV 74
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
82-153 4.34e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 47.62  E-value: 4.34e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIrvcrdAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12373   2 VYVGNLGPRVTKRELEDAFEKYGPLRNV-----WVARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRV 68
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
366-439 4.38e-07

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 47.99  E-value: 4.38e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFgtITSAKIMTDE-------QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12239   4 LYVKNLSKRVSEKDLKYIFGRF--VDSSSEEKNMfdirlmtEGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQF 81

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gi 19114289 439 A 439
Cdd:cd12239  82 A 82
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
170-240 4.51e-07

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 47.80  E-value: 4.51e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDrYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKV 73
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
82-149 4.56e-07

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 47.79  E-value: 4.56e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12370   3 VYVGSIYFELGEDTIRQAFAPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGR 70
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
263-333 4.65e-07

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 47.79  E-value: 4.65e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSD----LFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12451   2 IFVKGFDASLGEDTIRDelreHFGECGEVTNVRIPTDrETGELKGFAYIEFSTKEAKEKAL-ELNGSDIAGGNLVV 76
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
170-240 5.03e-07

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 47.65  E-value: 5.03e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12231   3 LFIGGLPNYLNEDQVKELLQSFGKLKAFNLVKDsATGLSKGYAFCEYVDDNVTDQAIAGLNGMQLGDKKLLV 74
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
263-333 5.15e-07

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 47.55  E-value: 5.15e-07
                        10        20        30        40        50        60        70
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12365   1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDRePNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 72
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
169-230 5.16e-07

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 47.62  E-value: 5.16e-07
                        10        20        30        40        50        60
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gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12376   2 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLtGVSRGVGFIRFDKRIEAEEAIKGLNG 64
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
263-333 5.35e-07

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409983 [Multi-domain]  Cd Length: 79  Bit Score: 47.39  E-value: 5.35e-07
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12567   5 LFVRNLPYTCTEEDLEKLFSKYGPLSEVHFPIDsLTKKPKGFAFVTYMIPEHAVKAYAELDGTVFQGRLLHL 76
RRM3_HuR cd12653
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup ...
263-341 5.36e-07

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410056 [Multi-domain]  Cd Length: 85  Bit Score: 47.74  E-value: 5.36e-07
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gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG-RAQKKH 340
Cdd:cd12653   5 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNtNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSfKTNKSH 84

                .
gi 19114289 341 E 341
Cdd:cd12653  85 K 85
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
366-426 5.39e-07

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 47.62  E-value: 5.39e-07
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQ 426
Cdd:cd12361   2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQILRDKQtGQSKGCAFVTFSTREEALRAIEALHN 63
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
366-439 5.44e-07

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 47.79  E-value: 5.44e-07
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMN-QRMLAG--KPLYVALA 439
Cdd:cd12635   4 LFVGMLGKQQSEDDVRRLFEPFGSIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHgSQTMPGasSSLVVKFA 80
RRM2_SECp43_like cd12345
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
170-242 5.59e-07

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409781 [Multi-domain]  Cd Length: 80  Bit Score: 47.65  E-value: 5.59e-07
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSA-FGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12345   4 LFVGDLAPDVTDYQLYETFSArYPSVRGAKVVMDPVtGRSKGYGFVRFGDESEQDRALTEMQGVYLGSRPIRVSP 78
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
366-440 5.63e-07

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 47.29  E-value: 5.63e-07
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gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKimtdeqgKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12495   4 LFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAK 71
RRM1_TIAR cd12616
RNA recognition motif 1 (RRM1) found in nucleolysin TIAR and similar proteins; This subgroup ...
81-164 5.71e-07

RNA recognition motif 1 (RRM1) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410028 [Multi-domain]  Cd Length: 81  Bit Score: 47.78  E-value: 5.71e-07
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gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSlgYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQrDP 160
Cdd:cd12616   1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT-TP 77

                ....
gi 19114289 161 SLRK 164
Cdd:cd12616  78 SSQK 81
RRM1_MSSP2 cd12471
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
164-225 5.89e-07

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409901 [Multi-domain]  Cd Length: 84  Bit Score: 47.81  E-value: 5.89e-07
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gi 19114289 164 KMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAI 225
Cdd:cd12471   2 QLSKTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNkCKGYGFVDFDSPSAAQKAV 64
RRM1_hnRNPA0 cd12326
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
362-421 5.92e-07

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409764 [Multi-domain]  Cd Length: 79  Bit Score: 47.61  E-value: 5.92e-07
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gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAV 421
Cdd:cd12326   1 QLCKLFIGGLNVQTTEEGLRAHFEAYGQLTDCVVVVNPQTKrSRCFGFVTYSSAEEADAAM 61
RRM3_CELF1_2 cd12638
RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and ...
168-240 6.37e-07

RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins; This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3.


Pssm-ID: 241082 [Multi-domain]  Cd Length: 92  Bit Score: 47.75  E-value: 6.37e-07
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gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12638   8 ANLFIYHLPQEFGDQDILQMFMPFGNVVSAKVFIDKQTNlSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKV 81
RRM1_MSSP cd12243
RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...
82-142 6.44e-07

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409689 [Multi-domain]  Cd Length: 71  Bit Score: 46.92  E-value: 6.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12243   3 VYIRGLPPNTTDEDLLLLCQSFGKIISTKAIIDKQTNKCKGYGFVDFDSPEAALKAIEGLN 63
RRM3_HuC cd12655
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup ...
263-341 6.46e-07

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410057 [Multi-domain]  Cd Length: 85  Bit Score: 47.74  E-value: 6.46e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG-RAQKKH 340
Cdd:cd12655   4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDfTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSfKTSKQH 83

                .
gi 19114289 341 E 341
Cdd:cd12655  84 K 84
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
263-336 6.47e-07

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 47.36  E-value: 6.47e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHEcaqkAVDELNDKEYK---GKKLYVGRA 336
Cdd:cd12329   2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDkKTNKRRGFCFITFDSEE----PVKKILETQFHvigGKKVEVKKA 75
RRM2_MSSP2 cd12474
RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
365-433 6.67e-07

RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409904 [Multi-domain]  Cd Length: 86  Bit Score: 47.72  E-value: 6.67e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKP 433
Cdd:cd12474   2 NLYISNLPLSMDEQELESMLKPFGQVISTRILRDANGTSRGVGFARMESTEKCEAIITHFNGKYIKTPP 70
RRM2_Bruno_like cd12636
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar ...
263-322 6.69e-07

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 410044 [Multi-domain]  Cd Length: 81  Bit Score: 47.56  E-value: 6.69e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12636   4 LFVGMLSKKCNESDVRIMFSPYGSIEECTVLRDQNGKSRGCAFVTFTSRQCAVNAIKAMH 63
RRM2_hnRNPA2B1 cd12581
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP ...
366-423 6.74e-07

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409995 [Multi-domain]  Cd Length: 80  Bit Score: 47.29  E-value: 6.74e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTE 423
Cdd:cd12581   3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQsGKKRGFGFVTFDDHDPVDKIVLQ 61
RRM_SARFH cd12534
RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and ...
263-333 6.80e-07

RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and similar proteins; This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240978 [Multi-domain]  Cd Length: 83  Bit Score: 47.41  E-value: 6.80e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEIT--------SLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12534   1 VFVSNLPPNTTEQDLAEHFGSIGIIKidkktgkpKIWLYKDKdTGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKV 80
RRM3_hnRNPM cd12661
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
366-438 6.92e-07

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410062 [Multi-domain]  Cd Length: 77  Bit Score: 47.18  E-value: 6.92e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12661   2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVRFESPEVAERACRMMNGIKLNGREIDVRI 73
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
273-324 6.95e-07

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 47.23  E-value: 6.95e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 19114289 273 TEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDK 324
Cdd:cd12361  12 SEEDVRPLFEQFGNIEEVQILRDKQTgQSKGCAFVTFSTREEALRAIEALHNK 64
RRM_SKAR cd12681
RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; ...
82-153 6.99e-07

RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410082 [Multi-domain]  Cd Length: 69  Bit Score: 46.88  E-value: 6.99e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRdavtrrsLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12681   3 LTVSNLHPSVTEDDIVELFSVIGALKRARLVR-------PGVAEVVYVRREDAITAIKKYNNRELDGQPMKC 67
RRM1_TatSF1_like cd12281
RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
261-337 7.10e-07

RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.


Pssm-ID: 409723 [Multi-domain]  Cd Length: 92  Bit Score: 47.54  E-value: 7.10e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITS--------LSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEY-KGKKL 331
Cdd:cd12281   2 TNVYVSGLPLDITVEEFVELFSKCGIIMEdpetgepkIKLYRDENGNLKGDALCCYLKEESVELALQLLDGTEIgRGYKI 81

                ....*.
gi 19114289 332 YVGRAQ 337
Cdd:cd12281  82 HVERAK 87
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
170-240 7.11e-07

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 47.17  E-value: 7.11e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12552   2 IYVSHLPHGFHEKELKKYFAQFGDLKNVRLARSkKTGNSKHYGFLEFVNPEDAMIAQKSMNNYLLMGKLLQV 73
RRM1_TIA1 cd12615
RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
81-156 7.25e-07

RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410027 [Multi-domain]  Cd Length: 74  Bit Score: 46.95  E-value: 7.25e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12615   1 TLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMD--TAGNDPYCFVEFHEHRHAAAALAAMNGRKIMGKEVKVNWA 74
RRM2_PSF cd12590
RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB) ...
172-233 7.44e-07

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.


Pssm-ID: 410003 [Multi-domain]  Cd Length: 80  Bit Score: 47.31  E-value: 7.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHV-NGMLL 233
Cdd:cd12590   4 VRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCsEGVFL 66
RRM_SRSF12 cd12560
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and ...
80-159 7.51e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins; This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409976 [Multi-domain]  Cd Length: 84  Bit Score: 47.30  E-value: 7.51e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQRD 159
Cdd:cd12560   1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYIPLDFYNRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQGD 80
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
262-328 8.38e-07

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 46.93  E-value: 8.38e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGE-ITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12652   2 NLYVSGLPKTMTQKELEQLFSQFGRiITSRILCDNVTGLSRGVGFIRFDKRVEAERAIKALNGTIPPG 69
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
82-150 8.70e-07

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 46.87  E-value: 8.70e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSL---GYAYVNFHNMEDGEKALdELNYTLIKGRP 150
Cdd:cd12298   3 IRVRNLDFELDEEALRGIFEKFGEIESINIPKKQKNRKGRhnnGFAFVTFEDADSAESAL-QLNGTLLDNRK 73
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
263-334 8.96e-07

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 46.85  E-value: 8.96e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNdkPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd12241   5 LYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTKE--TRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVVL 74
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
366-443 9.09e-07

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 47.09  E-value: 9.09e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEV-DDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKE 443
Cdd:cd12675   3 LIIRNLPWSIkKPVHLKKLFGRYGKVVEATIPRKKGGKLSGFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWAVSKN 81
RRM2_p54nrb_like cd12333
RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
366-426 9.44e-07

RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409770 [Multi-domain]  Cd Length: 80  Bit Score: 46.93  E-value: 9.44e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQ 426
Cdd:cd12333   2 LRVKNLSPYVSNELLEQAFSQFGDVERAVVIVDDRGRSTGEGIVEFSRKPGAQAALKRCSE 62
RRM1_hnRNPA3 cd12763
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) ...
366-422 9.65e-07

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 410156 [Multi-domain]  Cd Length: 81  Bit Score: 46.97  E-value: 9.65e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVT 422
Cdd:cd12763   5 LFIGGLSFETTDDSLREHFEQWGTLTDCVVMRDPQTKrSRGFGFVTYSCVEEVDAAMS 62
RRM2_MSSP2 cd12474
RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
261-327 9.76e-07

RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409904 [Multi-domain]  Cd Length: 86  Bit Score: 46.95  E-value: 9.76e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYK 327
Cdd:cd12474   1 TNLYISNLPLSMDEQELESMLKPFGQVISTRILRDANGTSRGVGFARMESTEKCEAIITHFNGKYIK 67
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
374-436 1.02e-06

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 46.64  E-value: 1.02e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 374 EVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12370  11 ELGEDTIRQAFAPFGPIKSIDMSWDPvTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74
RRM1_CID8_like cd12459
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein ...
81-157 1.03e-06

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409892 [Multi-domain]  Cd Length: 80  Bit Score: 46.64  E-value: 1.03e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRIMWSQ 157
Cdd:cd12459   4 TVYVSDIDQQVTEEQLAALFSNCGQVVDCRICGD--PNSVLRFAFIEFTDEEGARAAL-SLSGTMLGFYPVRVLPSK 77
RRM1_PSF cd12587
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB) ...
263-333 1.04e-06

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.


Pssm-ID: 410000 [Multi-domain]  Cd Length: 71  Bit Score: 46.39  E-value: 1.04e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLvkdqnDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12587   4 LFVGNLPADITEDEFKRLFAKYGEPGEVFI-----NKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRV 69
RRM2_MSSP1 cd12473
RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
261-327 1.09e-06

RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409903 [Multi-domain]  Cd Length: 85  Bit Score: 46.96  E-value: 1.09e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYK 327
Cdd:cd12473   1 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHFNGKFIK 67
RRM3_hnRNPM_like cd12387
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
170-240 1.10e-06

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409821 [Multi-domain]  Cd Length: 71  Bit Score: 46.43  E-value: 1.10e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDElGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12387   1 IFVRNLPFDYTWQKLKDKFKDCGHVTFASIKMEN-GKSKGCGTVRFDSPEDAENACRMMNGSKQSGREIDV 70
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
366-436 1.10e-06

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 46.78  E-value: 1.10e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12552   2 IYVSHLPHGFHEKELKKYFAQFGDLKNVRLARSKKtGNSKHYGFLEFVNPEDAMIAQKSMNNYLLMGKLLQV 73
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
81-155 1.11e-06

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 46.68  E-value: 1.11e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12622   2 TVYVGNLPPEVTQADLIPLFQNFGVIEEVRVQRDK------GFGFVKYDTHEEAALAIQQLNGQPFLGRPIKCSW 70
RRM1_p54nrb cd12588
RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
261-333 1.13e-06

RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410001 [Multi-domain]  Cd Length: 71  Bit Score: 46.48  E-value: 1.13e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12588   2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV 69
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
375-436 1.14e-06

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 46.84  E-value: 1.14e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 375 VDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12363  13 TTERDLREVFSRYGPIEKVQVVYDQQtGRSRGFGFVYFESVEDAKEAKERLNGQEIDGRRIRV 75
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
366-425 1.16e-06

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 46.88  E-value: 1.16e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12235   6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKtGDSLQYAFIEFETKESCEEAYFKMD 66
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
261-322 1.17e-06

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 46.55  E-value: 1.17e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSlslVKDQNDKprGFGFVNYANHECAQKAVDELN 322
Cdd:cd12346   2 TTVFVGGLDPNVTEEDLRVLFGPFGEIVY---VKIPPGK--GCGFVQFVNRASAEAAIQKLQ 58
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
168-236 1.17e-06

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 46.45  E-value: 1.17e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDK 236
Cdd:cd12680   1 TKLLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERRADALKAMKQYNGVPLDGR 69
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
170-227 1.18e-06

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 46.36  E-value: 1.18e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEH 227
Cdd:cd12325   1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKDPAtGRSRGFGFVTFKDPSSVDAVLAA 59
RRM2_RBMS3 cd12475
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, ...
261-327 1.19e-06

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 240919 [Multi-domain]  Cd Length: 88  Bit Score: 47.02  E-value: 1.19e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYK 327
Cdd:cd12475   2 TNLYISNLPISMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFNGKYLK 68
RRM3_HuD cd12656
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup ...
363-442 1.20e-06

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241100 [Multi-domain]  Cd Length: 86  Bit Score: 47.01  E-value: 1.20e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12656   3 GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDfNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN 82

                .
gi 19114289 442 K 442
Cdd:cd12656  83 K 83
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
366-425 1.22e-06

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 47.21  E-value: 1.22e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEF-SAFGT--------ITSAKIMTDE-------QGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12416   3 LCVRNLPKSVDDKKLKKLFlKAVKErakkkgvkIKEVKVMRDKkrlnsdgKGRSKGYGFVEFTEHEHALKALRALN 78
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
170-240 1.23e-06

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 46.55  E-value: 1.23e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEhvNGML-LNDKKVYV 240
Cdd:cd12330   2 IFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDhDTGRSRGFGFVTFDSESAVEKVLS--KGFHeLGGKKVEV 72
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
263-318 1.29e-06

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 46.36  E-value: 1.29e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAV 318
Cdd:cd12579   2 LFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADkDTGKKRGFGFVYFEDHDSADKAA 58
RRM2_hnRNPM cd12659
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
170-240 1.31e-06

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410060 [Multi-domain]  Cd Length: 76  Bit Score: 46.58  E-value: 1.31e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12659   3 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHV 73
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
263-333 1.36e-06

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 46.20  E-value: 1.36e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPrgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12338   2 IYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRRRGPP--FAFVEFEDPRDAEDAIRGRDGYDFDGYRLRV 70
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
170-240 1.39e-06

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 46.18  E-value: 1.39e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12316   2 LFVRNLPFTATEDELRELFEAFGKISEVHIPLDKQtKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73
RRM2_hnRPDL cd12585
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
263-319 1.40e-06

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409998 [Multi-domain]  Cd Length: 75  Bit Score: 46.15  E-value: 1.40e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVD 319
Cdd:cd12585   2 VFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDtKTNERRGFCFITYTDEEPVQKLLE 59
RRM2_MSSP1 cd12473
RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
365-433 1.45e-06

RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409903 [Multi-domain]  Cd Length: 85  Bit Score: 46.58  E-value: 1.45e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKP 433
Cdd:cd12473   2 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHFNGKFIKTPP 70
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
168-238 1.51e-06

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 45.96  E-value: 1.51e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSckvaVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12529   2 GTLVVFNLDPSISNDDLHQIFGAYGEIKE----IRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRI 68
RRM3_HuB cd12654
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup ...
166-249 1.65e-06

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241098 [Multi-domain]  Cd Length: 86  Bit Score: 46.63  E-value: 1.65e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 166 GTG-NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHH 243
Cdd:cd12654   1 GTGwCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDfNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK 80

                ....*.
gi 19114289 244 VSRRER 249
Cdd:cd12654  81 TNKTHK 86
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
366-436 1.66e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 45.68  E-value: 1.66e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMtdeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12343   2 IFVGNLPDAATSEELRALFEKYGKVTECDIV-------KNYAFVHMEKEEDAEDAIKALNGYEFMGSRINV 65
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
170-240 1.76e-06

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 46.10  E-value: 1.76e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKV--AVDELGNAK--GYGFVHFDSVESANAAIEhVNGMLLNDKKVYV 240
Cdd:cd12298   3 IRVRNLDFELDEEALRGIFEKFGEIESINIpkKQKNRKGRHnnGFAFVTFEDADSAESALQ-LNGTLLDNRKISV 76
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
259-331 1.87e-06

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 46.15  E-value: 1.87e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 259 NFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12618   1 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMaTGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 74
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
82-154 1.94e-06

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 45.85  E-value: 1.94e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIM 154
Cdd:cd12340   2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDS------NFAFVEFEELEDAIRAKDSVHGRVLNNEPLYVT 68
RRM_hnRNPC_like cd12341
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C) ...
366-434 1.96e-06

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins; This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes.


Pssm-ID: 409778 [Multi-domain]  Cd Length: 68  Bit Score: 45.70  E-value: 1.96e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQ-DEVDDERLKAEFSAFGTITSAKIMtdeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12341   3 IFVGNLPtDQMTKEDLEEIFSKYGKILGISLH-------KGYGFVQFDNEEDARAAVAGENGRTIKGQRL 65
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
366-436 1.96e-06

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 45.73  E-value: 1.96e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSakIMTdeQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12524   4 LFVRNINSSVEDEELRALFEQFGEIRT--LYT--ACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDI 70
RRM2_MSI cd12323
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, ...
263-330 2.06e-06

RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 240769 [Multi-domain]  Cd Length: 74  Bit Score: 45.89  E-value: 2.06e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVD----ELNDKEYKGKK 330
Cdd:cd12323   2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDkQTNRHRGFGFVTFESEDVVDKVCEihfhEINNKMVECKK 74
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
366-442 2.10e-06

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 45.93  E-value: 2.10e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEmnQRMLAGKPLYVALAQRK 442
Cdd:cd12672   8 VFVGGIDIRMDENEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYDDVDIQKIVES--QINFHGKKLKLGPAIRK 82
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
263-331 2.12e-06

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 45.71  E-value: 2.12e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPrgfgFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12276   4 LLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPSQK----FVEFYDVRDAEAALDGLNGRELLGGKL 68
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
81-154 2.19e-06

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 45.71  E-value: 2.19e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRslgyaYVNFHNMEDGEKALDELNYTLIKGRPCRIM 154
Cdd:cd12276   3 TLLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPSQK-----FVEFYDVRDAEAALDGLNGRELLGGKLKVA 71
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
263-337 2.26e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410071 [Multi-domain]  Cd Length: 77  Bit Score: 45.90  E-value: 2.26e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVdELNDKE-YKGKKLYVGRAQ 337
Cdd:cd12670   2 VFVGNLAFEAEEEGLWRYFGKCGAIESVRIVRDpKTNVGKGFAYVQFKDENAVEKAL-LLNEKPtMKGRKLRVSRAK 77
RRM6_RBM19 cd12571
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
261-321 2.31e-06

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409985 [Multi-domain]  Cd Length: 79  Bit Score: 45.88  E-value: 2.31e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD--QNDKPRGFGFVNYANHECAQKAVDEL 321
Cdd:cd12571   1 SKILVRNIPFQATVKEVRELFSTFGELKTVRLPKKmgGTGQHRGFGFVDFITKQDAKRAFDAL 63
RRM2_HuB cd12775
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup ...
168-230 2.40e-06

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410168 [Multi-domain]  Cd Length: 84  Bit Score: 45.87  E-value: 2.40e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12775   6 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVtGVSRGVGFIRFDKRIEAEEAIKGLNG 69
RRM1_MSSP1 cd12470
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
169-230 2.40e-06

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409900 [Multi-domain]  Cd Length: 86  Bit Score: 45.93  E-value: 2.40e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12470   9 NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNkCKGYGFVDFDSPAAAQKAVSALKA 71
RRM_SAFB1_SAFB2 cd12679
RNA recognition motif (RRM) found in scaffold attachment factor B1 (SAFB1), scaffold ...
363-436 2.53e-06

RNA recognition motif (RRM) found in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins; This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1.


Pssm-ID: 410080 [Multi-domain]  Cd Length: 76  Bit Score: 45.65  E-value: 2.53e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12679   1 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPgARCYGFVTMSTSEEATKCISHLHRTELHGRMISV 75
RRM2_HuC cd12776
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup ...
168-230 2.56e-06

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241220 [Multi-domain]  Cd Length: 81  Bit Score: 45.76  E-value: 2.56e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12776   2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVtGVSRGVGFIRFDKRIEAEEAIKGLNG 65
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
170-246 2.64e-06

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 45.64  E-value: 2.64e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSR 246
Cdd:cd12673   5 IFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDRAGVSKGYGFITFETQEDAQKILQEAEKLNYKDKKLNIGPAIRK 81
RRM_SLIRP cd12242
RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
366-420 2.64e-06

RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins; This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities.


Pssm-ID: 409688 [Multi-domain]  Cd Length: 73  Bit Score: 45.42  E-value: 2.64e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKA 420
Cdd:cd12242   2 LFVSNLPWTTGSSELKEYFSQFGKVKRCNLPFDkETGFHKGFGFVSFENEDGLRNA 57
RRM2_MYEF2 cd12660
RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This ...
170-240 2.65e-06

RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410061 [Multi-domain]  Cd Length: 76  Bit Score: 45.39  E-value: 2.65e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12660   3 IFVANLDFKVGWKKLKEVFSMAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRPMHV 73
RRM2_HuD cd12774
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup ...
168-230 2.66e-06

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410167 [Multi-domain]  Cd Length: 84  Bit Score: 45.87  E-value: 2.66e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12774   6 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVtGVSRGVGFIRFDKRIEAEEAIKGLNG 69
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
272-324 2.95e-06

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 45.39  E-value: 2.95e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 19114289 272 ITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDK 324
Cdd:cd12366  14 VTEDDLREAFSPFGEIQDIWVVKDkQTKESKGIAYVKFAKSSQAARAMEEMHGK 67
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
92-156 2.97e-06

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 45.75  E-value: 2.97e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  92 TEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12642  17 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYS 81
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
366-439 3.00e-06

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 45.12  E-value: 3.00e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12614   1 LYVGNLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGVNYGFVEYYDRRSAEIAIQTLNGRQIFGQEIKVNWA 74
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
366-425 3.13e-06

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 45.40  E-value: 3.13e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKI-MTDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12290   2 VYVELLPKNATHEWIEAVFSKYGEVVYVSIpRYKSTGDPKGFAFIEFETSESAQKAVKHFN 62
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
184-241 3.14e-06

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 45.48  E-value: 3.14e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 184 LHDTFSAFGKILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd12370  17 IRQAFAPFGPIKSIDMSWDPVTMKhKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKVG 75
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
264-331 3.20e-06

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 45.22  E-value: 3.20e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 264 YIKNLDTEITEQEFSD----LFGQFGEItsLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12246   3 YINNLNEKIKKDELKRslyaLFSQFGPV--LDIVASKSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPM 72
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
366-436 3.23e-06

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 45.69  E-value: 3.23e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12236   4 LFVARLSYDTTESKLRREFEKYGPIKRVRLVRDKKtGKSRGYAFIEFEHERDMKAAYKHADGKKIDGRRVLV 75
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
262-338 3.28e-06

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 45.56  E-value: 3.28e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd12619   3 NIFVGDLSPEVTDAALFNAFSDFPSCSDARVMWDQKTgRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPIRCNWATK 80
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
170-226 3.41e-06

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 46.27  E-value: 3.41e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIE 226
Cdd:cd12676   4 LFVRNLPFDATEDELYSHFSQFGPLKYARVVKDPAtGRSKGTAFVKFKNKEDADNCLS 61
RRM1_I_PABPs cd12378
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily ...
366-441 3.43e-06

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409812 [Multi-domain]  Cd Length: 80  Bit Score: 45.32  E-value: 3.43e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12378   2 LYVGDLHPDVTEAMLYEKFSPAGPVLSIRVCRDAvTRRSLGYAYVNFQQPADAERALDTLNFDVIKGKPIRIMWSQR 78
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
263-336 3.44e-06

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 45.12  E-value: 3.44e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYAnheCAQKAVDELNDKEYK--GKKLYVGRA 336
Cdd:cd12578   2 LFIGGLSYETTDDSLRNHFEQWGEITDVVVMKDpATKRSRGFGFVTYS---SASEVDAAMNARPHKvdGRVVEPKRA 75
RRM2_RAVER1 cd12665
RNA recognition motif 2 (RRM2) found found in vertebrate ribonucleoprotein PTB-binding 1 ...
265-333 3.46e-06

RNA recognition motif 2 (RRM2) found found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1); This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin.


Pssm-ID: 410066 [Multi-domain]  Cd Length: 77  Bit Score: 45.30  E-value: 3.46e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLV-KDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12665   4 IANLPPSYTQQQFEELVRPFGNLERCFLVySETTGHSKGYGFVEYMKKDSAARAKSDLLGKQLGTRTLYV 73
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
263-331 3.46e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 45.13  E-value: 3.46e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVK-DQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12397   1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMATfEDSGKCKGFAFVDFKEIESATNAVKGPINHSLNGRDL 70
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
366-425 3.48e-06

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 45.24  E-value: 3.48e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12365   1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDrEPNLPRGYAYVEFESPEDAEKAIKHMD 61
RRM2_SECp43 cd12612
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); ...
81-153 3.83e-06

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region.


Pssm-ID: 410024 [Multi-domain]  Cd Length: 82  Bit Score: 45.06  E-value: 3.83e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGP-VASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDEL-NYTLIKGRPCRI 153
Cdd:cd12612   3 SLFVGDLTPEVDDGMLYEFFLKRYPsCKGAKVVLDQ-LGNSRGYGFVRFSDENEQKRALTECqGASGLGGKPIRL 76
RRM3_HuB cd12654
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup ...
263-341 3.89e-06

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241098 [Multi-domain]  Cd Length: 86  Bit Score: 45.47  E-value: 3.89e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG-RAQKKH 340
Cdd:cd12654   6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNtNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSfKTNKTH 85

                .
gi 19114289 341 E 341
Cdd:cd12654  86 K 86
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
263-333 4.08e-06

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 44.98  E-value: 4.08e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12495   4 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMDEMNGKDLEGENIEI 67
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
366-440 4.08e-06

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 45.02  E-value: 4.08e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKimtdeqgKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12494   4 LFVRNLATTVTEEILEKTFSQFGKLERVK-------KLKDYAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVLAK 71
RRM2_HuR cd12773
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup ...
169-230 4.17e-06

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410166 [Multi-domain]  Cd Length: 84  Bit Score: 45.29  E-value: 4.17e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12773   2 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQAtGLSRGVAFIRFDKRSEAEEAITNFNG 64
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
367-434 4.17e-06

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 44.75  E-value: 4.17e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 367 FIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12622   4 YVGNLPPEVTQADLIPLFQNFGVIEEVRVQRD-----KGFGFVKYDTHEEAALAIQQLNGQPFLGRPI 66
RRM1_MYEF2 cd12658
RNA recognition motif 1 (RRM1) found in vertebrate myelin expression factor 2 (MEF-2); This ...
263-333 4.20e-06

RNA recognition motif 1 (RRM1) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410059 [Multi-domain]  Cd Length: 76  Bit Score: 44.97  E-value: 4.20e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLF-GQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12658   2 VFISNIPYDMKWQAIKDLMrEKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLSGRPLNI 73
RRM4_RBM45 cd12369
RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
279-333 4.33e-06

RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409804 [Multi-domain]  Cd Length: 68  Bit Score: 44.59  E-value: 4.33e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 279 DLFGQFGEITSLSLVKDQNdkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12369  18 DVFCRFGNLIDVYLVPGKN-----VGYAKYADRESAEEAITTLHGKEVNGVKLKV 67
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
170-243 4.38e-06

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 44.92  E-value: 4.38e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDElgNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHH 243
Cdd:cd12241   5 LYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTK--ETRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY 76
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
182-246 4.44e-06

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 44.98  E-value: 4.44e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 182 KALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSR 246
Cdd:cd12642  19 RDLREVFSRYGPLAGVNVVYDQrTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRVDYSITK 84
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
261-322 4.50e-06

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 44.67  E-value: 4.50e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12384   1 TKIFVGGLPYHTTDDSLREYFEQFGEIEEAVVITDrQTGKSRGYGFVTMADREAAERACKDPN 63
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
365-439 4.51e-06

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 45.01  E-value: 4.51e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAG--KPLYVALA 439
Cdd:cd12652   2 NLYVSGLPKTMTQKELEQLFSQFGRIITSRILCDNvTGLSRGVGFIRFDKRVEAERAIKALNGTIPPGatEPITVKFA 79
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
80-142 4.62e-06

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 44.93  E-value: 4.62e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12376   1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLN 63
RRM1_MSSP1 cd12470
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
261-322 4.63e-06

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409900 [Multi-domain]  Cd Length: 86  Bit Score: 45.16  E-value: 4.63e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12470   8 TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTtNKCKGYGFVDFDSPAAAQKAVSALK 70
RRM2_DAZAP1 cd12327
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
263-337 4.65e-06

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409765 [Multi-domain]  Cd Length: 80  Bit Score: 44.80  E-value: 4.65e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDElNDKEYKGKKLYVGRAQ 337
Cdd:cd12327   5 VFVGGIPHNCGETELRDYFKRYGVVTEVVMMYDAeKQRSRGFGFITFEDEQSVDQAVNM-HFHDIMGKKVEVKRAE 79
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
77-139 4.68e-06

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 45.10  E-value: 4.68e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  77 PTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALD 139
Cdd:cd12229   1 PDNHQLFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGGRLPNFGFVVFDDPEAVQKILA 63
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
263-336 4.79e-06

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 44.70  E-value: 4.79e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKdqNDK-PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12407   3 LHVSNIPFRFRDPDLRQMFGQFGTILDVEIIF--NERgSKGFGFVTFANSADADRAREKLNGTVVEGRKIEVNNA 75
RRM1_hnRNPAB cd12757
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
168-237 4.90e-06

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 410151 [Multi-domain]  Cd Length: 80  Bit Score: 44.96  E-value: 4.90e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEH----VNGMLLNDKK 237
Cdd:cd12757   5 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDpNTGRSRGFGFILFKDAASVDKVLEQkehrLDGRVIDPKK 79
RRM_U2AF35_like cd12287
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
268-333 4.95e-06

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409729 [Multi-domain]  Cd Length: 101  Bit Score: 45.33  E-value: 4.95e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 268 LDTEITEQEFSDLF-------GQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12287  25 LSEEEIQEHFDEFYedvflelSRFGEIEDLVVCSNLNDHLLGNVYVKFESEEDAEAALQALNGRYYAGRPLYP 97
RRM3_NCL cd12405
RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to ...
79-153 5.06e-06

RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409839 [Multi-domain]  Cd Length: 72  Bit Score: 44.48  E-value: 5.06e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSigpVASIRVCRDavTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12405   1 SKTLVVNNLSYSATEESLQSVFEK---ATSIRIPQN--NGRPKGYAFVEFESVEDAKEALESCNNTEIEGRSIRL 70
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
61-149 5.14e-06

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 49.17  E-value: 5.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    61 STPTNASSVAT----PSGTAPTSAS--LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDG 134
Cdd:TIGR01661 245 SPPATDGQTAGlaagAQISASDGAGycIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEA 324
                          90
                  ....*....|....*
gi 19114289   135 EKALDELNYTLIKGR 149
Cdd:TIGR01661 325 AMAILSLNGYTLGNR 339
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
170-226 5.16e-06

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 44.53  E-value: 5.16e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIE 226
Cdd:cd12391   2 VFVSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKGKSKGYCYVEFKDEESAQKALK 58
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
169-242 5.19e-06

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 45.10  E-value: 5.19e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12771   6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKItGQSLGYGFVNYIEPKDAEKAINTLNGLRLQTKTIKVSY 80
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
263-333 5.41e-06

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 44.33  E-value: 5.41e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEItslsLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd21617   2 VYVGNLPLDISEEEILQLFKAFNPV----LVKKIRSGFKCFAFVDLGSDENVKLAIQQLNGTLFGGRRLVV 68
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
375-441 5.43e-06

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 44.62  E-value: 5.43e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 375 VDDERLKAEFSAFGTITSAKImtdEQGKSKGFgfVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12305  14 ITEDVLKKAFSPFGNIINISM---EIEKNCAF--VTFEKMESADQAIAELNGTTVEGVQLKVSIARR 75
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
263-333 5.82e-06

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 44.23  E-value: 5.82e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLvkdqndkPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12337   2 VYIGRLPYRARERDVERFFRGYGRIRDINL-------KNGFGFVEFEDPRDADDAVYELNGKELCGERVIV 65
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
262-333 5.94e-06

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 44.55  E-value: 5.94e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12417   1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSaRTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
79-154 6.06e-06

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409983 [Multi-domain]  Cd Length: 79  Bit Score: 44.69  E-value: 6.06e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIM 154
Cdd:cd12567   2 SGRLFVRNLPYTCTEEDLEKLFSKYGPLSEVHFPIDSLTKKPKGFAFVTYMIPEHAVKAYAELDGTVFQGRLLHLL 77
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
158-242 6.17e-06

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 44.31  E-value: 6.17e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 158 RDPSLRKMgtgnvfiknldpaidnkalhdtFSAFGKILSCKVAVDELGnAKGYGFVHFDSVESANAAIEHVNGMLLNDKK 237
Cdd:cd12407  13 RDPDLRQM----------------------FGQFGTILDVEIIFNERG-SKGFGFVTFANSADADRAREKLNGTVVEGRK 69

                ....*
gi 19114289 238 VYVGH 242
Cdd:cd12407  70 IEVNN 74
RRM3_hnRNPM cd12661
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
170-240 6.20e-06

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410062 [Multi-domain]  Cd Length: 77  Bit Score: 44.48  E-value: 6.20e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVdELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12661   2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVRFESPEVAERACRMMNGIKLNGREIDV 71
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
366-440 6.35e-06

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 44.71  E-value: 6.35e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKA----EFSAFGTITSAKIMTDEQGKSkgFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12453   5 LFVASLSSARSDEELCAavtnHFSKWGELLNVKVLKDWSNRP--YAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKAK 81
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
82-150 6.35e-06

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 44.53  E-value: 6.35e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPV--ASIRVCRDAVTRrslGYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVkdVKIIKDRAGVSK---GYGFVTFETQEDAEKIQKWGANLVFKGKK 72
RRM3_HuD cd12656
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup ...
263-341 6.57e-06

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241100 [Multi-domain]  Cd Length: 86  Bit Score: 44.70  E-value: 6.57e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG-RAQKKH 340
Cdd:cd12656   6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNtNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSfKTNKTH 85

                .
gi 19114289 341 E 341
Cdd:cd12656  86 K 86
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
169-242 6.59e-06

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 44.70  E-value: 6.59e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12649   2 NLIVNYLPQDLTDREFRALFRAIGPVNTCKIVRDKKtGYSYGFGFVDFTSEEDAQRAIKTLNGLQLQNKRLKVAY 76
RRM3_HuC cd12655
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup ...
170-249 6.62e-06

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410057 [Multi-domain]  Cd Length: 85  Bit Score: 44.66  E-value: 6.62e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRRE 248
Cdd:cd12655   4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNkCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTSKQH 83

                .
gi 19114289 249 R 249
Cdd:cd12655  84 K 84
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
168-242 6.93e-06

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 44.32  E-value: 6.93e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12382   2 GKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNkSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQ 77
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
81-148 7.11e-06

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 44.53  E-value: 7.11e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRD---AVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKG 148
Cdd:cd12318   2 TLFVKNLNFKTTEEALKKHFEKCGPIRSVTIAKKkdpKGPLLSMGYGFVEFKSPEAAQKALKQLQGTVLDG 72
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
263-333 7.13e-06

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 44.35  E-value: 7.13e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLvkDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12599   2 VYVGNLPMDIREREVEDLFSKYGPVVSIDL--KIPPRPPAYAFVEFEDARDAEDAIRGRDGYDFDGHRLRV 70
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
79-156 7.15e-06

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 44.35  E-value: 7.15e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIrvcrDAVTRRslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12227   2 STTLWVGHLSKKVTQEELKNLFEEYGEIQSI----DMIPPR--GCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWA 73
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
365-452 7.22e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 45.05  E-value: 7.22e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKS-KGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKE 443
Cdd:cd12559   7 SLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRpRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFAQGDR 86

                ....*....
gi 19114289 444 VRRSQLEAQ 452
Cdd:cd12559  87 KTPNQMKAK 95
RRM1_hnRNPD cd12756
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) ...
170-237 7.24e-06

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically.


Pssm-ID: 410150 [Multi-domain]  Cd Length: 74  Bit Score: 44.22  E-value: 7.24e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEH----VNGMLLNDKK 237
Cdd:cd12756   1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPItGRSRGFGFVLFKESESVDKVMDQkehkLNGKVIDPKR 73
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
79-149 7.39e-06

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 44.33  E-value: 7.39e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12566   2 TGRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDKKTKKSKGFAYVLFLDPEDAVQAYNELDGKVFQGR 72
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
81-153 7.55e-06

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 44.61  E-value: 7.55e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRD--AVTRrslgYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12260   6 TVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDetQPTR----YAFVEFAEQTSVINAL-KLNGKMFGGRPLKV 75
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
366-439 7.58e-06

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 44.18  E-value: 7.58e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12231   3 LFIGGLPNYLNEDQVKELLQSFGKLKAFNLVKDsATGLSKGYAFCEYVDDNVTDQAIAGLNGMQLGDKKLLVQRA 77
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
273-333 7.64e-06

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 44.61  E-value: 7.64e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 273 TEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12641  20 TERDLREVFSKYGPIADVSIVYDQQSRrSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 81
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
272-338 7.65e-06

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 44.23  E-value: 7.65e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 272 ITEQEFSDLFGQFGEITSLSLvkdqnDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd12305  14 ITEDVLKKAFSPFGNIINISM-----EIEKNCAFVTFEKMESADQAIAELNGTTVEGVQLKVSIARR 75
RRM_UHM_SPF45_PUF60 cd12374
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ...
373-432 7.93e-06

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain.


Pssm-ID: 409809 [Multi-domain]  Cd Length: 85  Bit Score: 44.52  E-value: 7.93e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 373 DEVDDErLKAEFSAFGTITSAKIMTDEQGKSKGFG--FVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:cd12374  17 EDLKDE-IKEECSKYGKVLNVIIHEVASSEADDAVrvFVEFEDADEAIKAFRALNGRFFGGR 77
RRM3_HuD cd12656
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup ...
166-249 8.15e-06

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241100 [Multi-domain]  Cd Length: 86  Bit Score: 44.31  E-value: 8.15e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 166 GTG-NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHH 243
Cdd:cd12656   1 GTGwCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDfNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK 80

                ....*.
gi 19114289 244 VSRRER 249
Cdd:cd12656  81 TNKTHK 86
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
80-149 8.16e-06

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 44.50  E-value: 8.16e-06
                        10        20        30        40        50        60        70
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gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12651   3 TNLYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKLTGRPRGVAFVRYDKREEAQAAISALNGTIPEGG 72
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
366-444 8.26e-06

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 44.33  E-value: 8.26e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKS-KGFGFVCYTTPEEAnkavtemnQRMLAGKPLYVALAQRKEV 444
Cdd:cd12229   6 LFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGGRlPNFGFVVFDDPEAV--------QKILANKPIMFRGEHRLNV 77
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
170-240 8.80e-06

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 43.83  E-value: 8.80e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12336   4 LFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRI 74
RRM3_hnRNPM_like cd12387
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
263-333 8.93e-06

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409821 [Multi-domain]  Cd Length: 71  Bit Score: 43.73  E-value: 8.93e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSlVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12387   1 IFVRNLPFDYTWQKLKDKFKDCGHVTFAS-IKMENGKSKGCGTVRFDSPEDAENACRMMNGSKQSGREIDV 70
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
170-240 9.05e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 43.77  E-value: 9.05e-06
                        10        20        30        40        50        60        70
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gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAvdelGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12373   2 VYVGNLGPRVTKRELEDAFEKYGPLRNVWVA----RNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRV 68
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
264-333 9.05e-06

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 43.90  E-value: 9.05e-06
                        10        20        30        40        50        60        70
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gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12358   2 YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-----GGYAFVDCPDQSWADKAIEKLNGKILQGKVIEV 66
RRM2_RBMS3 cd12475
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, ...
365-433 9.35e-06

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 240919 [Multi-domain]  Cd Length: 88  Bit Score: 44.32  E-value: 9.35e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKP 433
Cdd:cd12475   3 NLYISNLPISMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHFNGKYLKTPP 71
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
170-230 9.58e-06

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 43.86  E-value: 9.58e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKvavdelgNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12494   4 LFVRNLATTVTEEILEKTFSQFGKLERVK-------KLKDYAFVHFEDRDAAVKAMDEMNG 57
RRM3_U2AF65 cd12232
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
373-434 9.58e-06

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409679 [Multi-domain]  Cd Length: 89  Bit Score: 44.12  E-value: 9.58e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 373 DEVDDerLKAEFSAFGTITSAKI--MTDEQGKSKGFG--FVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12232  23 EILED--VKEECSKYGKVLSVVIprPEAEGVDVPGVGkvFVEFEDVEDAQKAQKALAGRKFDGRTV 86
RRM2_RBM45 cd12367
RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
377-421 9.73e-06

RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409802 [Multi-domain]  Cd Length: 74  Bit Score: 43.90  E-value: 9.73e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 19114289 377 DERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12367  14 EEDLREKFKEFGDIEYCSIVKDKNtGESKGFGYVKFLKPSQAALAI 59
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
169-242 9.76e-06

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 44.34  E-value: 9.76e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12772   6 NLIVNYLPQNMTQEEFKSLFGSIGDIESCKLVRDKItGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSY 80
RRM1_ACF cd12486
RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
263-331 9.99e-06

RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409912 [Multi-domain]  Cd Length: 78  Bit Score: 43.81  E-value: 9.99e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12486   4 IFIGKLPRDLFEDELVPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEARNAIKQLNNYEIRNGRL 72
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
170-226 1.02e-05

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 43.93  E-value: 1.02e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIE 226
Cdd:cd12272   2 VYIGNLAWDIDEDDLRELFAECCEITNVRLHTDkETGEFKGYGHVEFADEESLDAALK 59
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
263-333 1.05e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 43.76  E-value: 1.05e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12283   2 VFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDRNSrRSKGVAYVEFYDVESVPLAL-ALTGQRLLGQPIMV 72
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
267-320 1.05e-05

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 43.93  E-value: 1.05e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 267 NLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDE 320
Cdd:cd12321   6 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDPKTgRSKGFGFVRFASYETQVKVLSQ 60
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
366-421 1.09e-05

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 44.18  E-value: 1.09e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFG--TITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12313   5 LILRGLDVLTTEEDILSALQAHAdlPIKDVRLIRDKLtGTSRGFAFVEFSSLEDATQVM 63
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
261-333 1.17e-05

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 43.91  E-value: 1.17e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12297   1 CTLWVTNFPPSYDERSIRDLFGDYGVILSVRLPSLRYNTSRRFCYIDFTSPESARAAVELLNGLLEEGYTLVV 73
RRM1_RBMS3 cd12472
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, ...
261-321 1.19e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 409902 [Multi-domain]  Cd Length: 80  Bit Score: 44.03  E-value: 1.19e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDEL 321
Cdd:cd12472   5 TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNtNQCKGYGFVDFDSPAAAQKAVASL 66
RRM2_RIM4_like cd12454
RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; ...
366-444 1.20e-05

RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409888 [Multi-domain]  Cd Length: 80  Bit Score: 43.61  E-value: 1.20e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSkGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYValaQRKEV 444
Cdd:cd12454   6 IFVGQLDPKTTDSELFRRFSKYGKIVDCKLIKRPEPVN-AFAFLRFESEEAAEAAVEEENHSEFLNKQIRV---QKREL 80
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
365-434 1.21e-05

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 43.42  E-value: 1.21e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12354   2 TVYVGNITKGLTEALLQQTFSPFGQILEVRVFPD-----KGYAFIRFDSHEAATHAIVSVNGTIINGQAV 66
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
169-242 1.23e-05

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 43.94  E-value: 1.23e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12770   3 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKItGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 77
RRM2_PSF cd12590
RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB) ...
366-421 1.24e-05

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.


Pssm-ID: 410003 [Multi-domain]  Cd Length: 80  Bit Score: 43.84  E-value: 1.24e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12590   2 LSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAF 57
RRM1_hnRNPAB cd12757
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
362-428 1.24e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 410151 [Multi-domain]  Cd Length: 80  Bit Score: 43.81  E-value: 1.24e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRM 428
Cdd:cd12757   3 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDpNTGRSRGFGFILFKDAASVDKVLEQKEHRL 70
RRM1_MSSP2 cd12471
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
365-424 1.28e-05

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409901 [Multi-domain]  Cd Length: 84  Bit Score: 43.96  E-value: 1.28e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEM 424
Cdd:cd12471   7 NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTtNKCKGYGFVDFDSPSAAQKAVTAL 67
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
366-434 1.30e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 43.46  E-value: 1.30e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdeqgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12346   4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPP-----GKGCGFVQFVNRASAEAAIQKLQGTPIGGSRI 67
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
261-333 1.31e-05

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410019 [Multi-domain]  Cd Length: 67  Bit Score: 43.41  E-value: 1.31e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12607   1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAMEAIRGLDNTEFQGKRMHV 66
RRM3_Bruno_like cd12640
RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar ...
261-333 1.31e-05

RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 241084 [Multi-domain]  Cd Length: 79  Bit Score: 43.83  E-value: 1.31e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12640   5 CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDkQTNLSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRLKV 78
RRM1_RBMS3 cd12472
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, ...
164-225 1.32e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 409902 [Multi-domain]  Cd Length: 80  Bit Score: 43.65  E-value: 1.32e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 164 KMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAI 225
Cdd:cd12472   1 QLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNqCKGYGFVDFDSPAAAQKAV 63
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
82-153 1.41e-05

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 43.46  E-value: 1.41e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIG--PVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12372   1 LYVGNLQWWTTDEDLEGACASFGvvDVKEIKFFEHKANGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRPCVV 74
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
366-434 1.42e-05

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 43.38  E-value: 1.42e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12320   3 LIVKNVPFEATRKEIRELFSPFGQLKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHL 71
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
263-334 1.42e-05

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 43.54  E-value: 1.42e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYVG 334
Cdd:cd12272   2 VYIGNLAWDIDEDDLRELFAECCEITNVRLHTDKETgEFKGYGHVEFADEESLDAAL-KLAGTKLCGRPIRVD 73
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
265-341 1.46e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 43.62  E-value: 1.46e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 265 IKNLDTEI-TEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKKHE 341
Cdd:cd12675   5 IRNLPWSIkKPVHLKKLFGRYGKVVEATIPRKKGGKLSGFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWAVSKNT 82
RRM_FET cd12280
RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...
366-438 1.47e-05

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.


Pssm-ID: 409722 [Multi-domain]  Cd Length: 82  Bit Score: 43.55  E-value: 1.47e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAK--------IMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12280   1 IFVSGLPPDVTIDELADLFGQIGIIKRYKdtwppkikIYTDKEtGKPKGEATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80

                ..
gi 19114289 437 AL 438
Cdd:cd12280  81 SL 82
RRM2_VICKZ cd12359
RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds ...
261-333 1.48e-05

RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 409794 [Multi-domain]  Cd Length: 76  Bit Score: 43.51  E-value: 1.48e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFgfVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12359   1 RKIQIRNIPPHARWEDLDSLLSTYGTVENCEQVNTKSETATVN--VTYESPEQAQQAVNKLNGYQYEGSALKV 71
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
76-153 1.48e-05

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 43.81  E-value: 1.48e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  76 APTSAslYVGELDPSVTEAMLFELFNSIgPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12401   4 PPFTA--YVGNLPFNTVQGDLDAIFKDL-KVRSVRLVRDRETDKFKGFCYVEFEDLESLKEAL-EYDGALFEDRPLRV 77
RRM1_RBM47 cd12485
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47); This ...
263-331 1.49e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240929 [Multi-domain]  Cd Length: 78  Bit Score: 43.41  E-value: 1.49e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12485   4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELNNYEIRPGRL 72
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
263-333 1.51e-05

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 43.32  E-value: 1.51e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12552   2 IYVSHLPHGFHEKELKKYFAQFGDLKNVRLARSkKTGNSKHYGFLEFVNPEDAMIAQKSMNNYLLMGKLLQV 73
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
172-248 1.55e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 43.62  E-value: 1.55e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 172 IKNLDPAIDNKA-LHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRRE 248
Cdd:cd12675   5 IRNLPWSIKKPVhLKKLFGRYGKVVEATIPRKKGGKLSGFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWAVSKNT 82
RRM2_MSI cd12323
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, ...
366-432 1.55e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 240769 [Multi-domain]  Cd Length: 74  Bit Score: 43.19  E-value: 1.55e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVT----EMNQRMLAGK 432
Cdd:cd12323   2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQtNRHRGFGFVTFESEDVVDKVCEihfhEINNKMVECK 73
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
79-153 1.56e-05

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 43.73  E-value: 1.56e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12411   9 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83
RRM1_hnRNPM_like cd12385
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
367-436 1.59e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409819 [Multi-domain]  Cd Length: 76  Bit Score: 43.17  E-value: 1.59e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 367 FIKNLQDEVDDERLKAEF-SAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12385   3 FISNIPYDYKWQDLKDLFrEKVGEVTYVELFKDENGKSRGCGIVEFKDLESVQKALETMNRYELKGRKLVV 73
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
263-324 1.61e-05

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 43.47  E-value: 1.61e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEI--TSLSLVKDQNDkPRGFGFVNYANHECAQKAVDELNDK 324
Cdd:cd12290   2 VYVELLPKNATHEWIEAVFSKYGEVvyVSIPRYKSTGD-PKGFAFIEFETSESAQKAVKHFNSP 64
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
364-439 1.61e-05

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 43.25  E-value: 1.61e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 364 VNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMtdeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12608   1 MKIFVGNVDEDTSQEELSALFEPYGAVLSCAVM-------KQFAFVHMRGEAAADRAIRELNGRELHGRALVVEES 69
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
384-434 1.65e-05

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 43.43  E-value: 1.65e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 19114289 384 FSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12393  22 FSKYGKVVKVTILKDkETRKSKGVAFVLFLDRESAHNAVRAMNNKELFGRTL 73
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
82-152 1.66e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 43.20  E-value: 1.66e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCR 152
Cdd:cd12397   1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMATFEDSGKCKGFAFVDFKEIESATNAVKGPINHSLNGRDLR 71
RRM2_hnRNPA2B1 cd12581
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP ...
269-318 1.72e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409995 [Multi-domain]  Cd Length: 80  Bit Score: 43.43  E-value: 1.72e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 19114289 269 DTEitEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAV 318
Cdd:cd12581  11 DTE--EHHLRDYFEEYGKIDTIEIITDrQSGKKRGFGFVTFDDHDPVDKIV 59
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
261-317 1.73e-05

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 43.95  E-value: 1.73e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKA 317
Cdd:cd12676   2 RTLFVRNLPFDATEDELYSHFSQFGPLKYARVVKDPaTGRSKGTAFVKFKNKEDADNC 59
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
263-333 1.74e-05

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 42.98  E-value: 1.74e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12586   4 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI 69
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
267-331 1.84e-05

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 42.88  E-value: 1.84e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 267 NLDTEITEQEFSDLFGQFGEItslslvKDQNDKP--RGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12529   8 NLDPSISNDDLHQIFGAYGEI------KEIRETPnkRHHKFIEFYDVRSAEAALKALNKSEIAGKRI 68
RRM_RBM11 cd12593
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily ...
170-233 1.85e-05

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 410006 [Multi-domain]  Cd Length: 75  Bit Score: 43.25  E-value: 1.85e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12593   4 VFVGNLHSNVNEEILYELFLQAGPLTKVTIAKDKEGKPKSFGFVCFKHAESVPYAIALLNGIRL 67
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
171-240 1.91e-05

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 43.38  E-value: 1.91e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12236   5 FVARLSYDTTESKLRREFEKYGPIKRVRLVRDKKtGKSRGYAFIEFEHERDMKAAYKHADGKKIDGRRVLV 75
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
263-322 2.00e-05

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 43.17  E-value: 2.00e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12635   4 LFVGMLGKQQSEDDVRRLFEPFGSIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63
RRM3_MYEF2 cd12662
RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This ...
170-240 2.00e-05

RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410063 [Multi-domain]  Cd Length: 77  Bit Score: 43.04  E-value: 2.00e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVdELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12662   2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM-ENGKSKGCGTVRFDSPESAEKACRLMNGIKISGREIDV 71
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
367-437 2.00e-05

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 42.77  E-value: 2.00e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 367 FIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVtEMNQRMLAGKPLYVA 437
Cdd:cd12272   3 YIGNLAWDIDEDDLRELFAECCEITNVRLHTDkETGEFKGYGHVEFADEESLDAAL-KLAGTKLCGRPIRVD 73
RRM1_hnRPDL cd12758
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
366-432 2.02e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 410152 [Multi-domain]  Cd Length: 76  Bit Score: 43.04  E-value: 2.02e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKaVTEMNQRMLAGK 432
Cdd:cd12758   2 MFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPvTGRSRGFGFVLFKDAASVDK-VLELKEHKLDGK 68
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
90-142 2.09e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 43.08  E-value: 2.09e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 19114289  90 SVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12366  13 SVTEDDLREAFSPFGEIQDIWVVKDKQTKESKGIAYVKFAKSSQAARAMEEMH 65
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
170-240 2.28e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 42.60  E-value: 2.28e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEhVNGMLLNDKKVYV 240
Cdd:cd12283   2 VFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDRnSRRSKGVAYVEFYDVESVPLALA-LTGQRLLGQPIMV 72
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
366-436 2.35e-05

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 43.35  E-value: 2.35e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12411  12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKtGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83
RRM2_PSP1 cd12589
RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This ...
366-421 2.38e-05

RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410002 [Multi-domain]  Cd Length: 80  Bit Score: 43.06  E-value: 2.38e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12589   2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPPARKAL 57
RRM2_RBM45 cd12367
RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
273-327 2.45e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409802 [Multi-domain]  Cd Length: 74  Bit Score: 42.75  E-value: 2.45e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 273 TEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELnDKEYK 327
Cdd:cd12367  13 TEEDLREKFKEFGDIEYCSIVKDKNTGeSKGFGYVKFLKPSQAALAIENC-DRSFK 67
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
366-436 2.54e-05

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 42.59  E-value: 2.54e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVtEMNQRMLAGKPLYV 436
Cdd:cd12400   3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDkKTGKSKGCAFVEFDNQKALQKAL-KLHHTSLGGRKINV 73
RRM4_MRN1 cd12522
RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This ...
262-335 2.62e-05

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409942 [Multi-domain]  Cd Length: 81  Bit Score: 42.90  E-value: 2.62e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 262 NVYIKNLD--TEITEQEFSDLFGQFGEITSLSLVKDQNdkprgFGFVNYANHECAQKAVDELNDKE-YKGKKLYVGR 335
Cdd:cd12522   5 NVYIGNIDdvRVLTEERLRHDFSQYGEIEQVNFLREKN-----CAFVNFTNIANAIKAIDKIKSKPyYKDLKINFGK 76
RRM3_HuR cd12653
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup ...
170-249 2.66e-05

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410056 [Multi-domain]  Cd Length: 85  Bit Score: 43.12  E-value: 2.66e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRRE 248
Cdd:cd12653   5 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDfNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSFKTNKSH 84

                .
gi 19114289 249 R 249
Cdd:cd12653  85 K 85
RRM_SCAF8 cd12462
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and ...
261-331 2.67e-05

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409895 [Multi-domain]  Cd Length: 79  Bit Score: 42.75  E-value: 2.67e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVkdqndKPRGFGFVNYANHECAQKAVDELNDKEYK-GKKL 331
Cdd:cd12462   3 TTLWVGQVDKKATQQDLTNLFEEFGQIESINMI-----PPRGCAYVCMVHRQDAYRALQKLSTGSFKiGSKI 69
RRM1_MSSP2 cd12471
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
261-321 2.67e-05

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409901 [Multi-domain]  Cd Length: 84  Bit Score: 42.81  E-value: 2.67e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVDEL 321
Cdd:cd12471   6 TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTtNKCKGYGFVDFDSPSAAQKAVTAL 67
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
172-229 2.70e-05

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 43.36  E-value: 2.70e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 172 IKNLDPAIDNKALHDTF---------SAFGKILSCKVAVDE-------LGNAKGYGFVHFDSVESANAAIEHVN 229
Cdd:cd12416   5 VRNLPKSVDDKKLKKLFlkavkerakKKGVKIKEVKVMRDKkrlnsdgKGRSKGYGFVEFTEHEHALKALRALN 78
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
366-436 2.73e-05

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 42.59  E-value: 2.73e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12334   1 VYVGNLDEKVTEELLWELFIQAGPVVNVHMPKDrVTQQHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
170-238 2.76e-05

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 42.56  E-value: 2.76e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12307   2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSkKTGKSKGYAFVEFEDPEVAKIVAETMNNYLLFERLL 71
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
377-439 2.89e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 42.69  E-value: 2.89e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 377 DERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAG--KPLYVALA 439
Cdd:cd12366  16 EDDLREAFSPFGEIQDIWVVKDKQTKeSKGIAYVKFAKSSQAARAMEEMHGKCLGDdtKPIKVLIA 81
RRM2_TIAR cd12617
RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup ...
262-338 3.02e-05

RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410029 [Multi-domain]  Cd Length: 80  Bit Score: 42.67  E-value: 3.02e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQK 338
Cdd:cd12617   3 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDmATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATR 80
RRM1_SRSF6 cd12596
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 ...
263-337 3.02e-05

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides.


Pssm-ID: 410009 [Multi-domain]  Cd Length: 72  Bit Score: 42.25  E-value: 3.02e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLvkdqndkPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12596   4 VYIGRLSYHVREKDIQRFFSGYGKLLEVDL-------KNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHAR 71
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
82-329 3.03e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 47.20  E-value: 3.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    82 LYVGELDPSVTEAMLFELFN----SIG--------PVASIRVCRDAvtrrslGYAYVNFHNMEDGEK--ALDEL---NYT 144
Cdd:TIGR01642 178 LYVGGIPPEFVEEAVVDFFNdlmiATGyhkaedgkHVSSVNINKEK------NFAFLEFRTVEEATFamALDSIiysNVF 251
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   145 LIKGRP--------CRIMWSQRDPSLRKMGTGN-------------VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD- 202
Cdd:TIGR01642 252 LKIRRPhdyipvpqITPEVSQKNPDDNAKNVEKlvnsttvldskdrIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDi 331
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   203 ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVghhvsRRERQSKVEALKANFTNVYIKNL-------------- 268
Cdd:TIGR01642 332 ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHV-----QRACVGANQATIDTSNGMAPVTLlakalsqsilqigg 406
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   269 --------------DTEITEQEFSDL-------FGQFGEITSLSLVKDQNDKPRGFG----FVNYANHECAQKAVDELND 323
Cdd:TIGR01642 407 kptkvvqltnlvtgDDLMDDEEYEEIyedvkteFSKYGPLINIVIPRPNGDRNSTPGvgkvFLEYADVRSAEKAMEGMNG 486

                  ....*.
gi 19114289   324 KEYKGK 329
Cdd:TIGR01642 487 RKFNDR 492
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
79-448 3.04e-05

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 47.12  E-value: 3.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVcrdavtrrsLGYAYVNFHNMEDGEKALDELNYT-----LIKGRPCRI 153
Cdd:TIGR01649   2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMM---------LPGKRQALVEFEDEESAKACVNFAtsvpiYIRGQPAFF 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   154 MWS-----QRD-PSLRKMGTGN----VFIKNLDPAIDNKALHDTFSAFGKILscKVAVDElGNAKGYGFVHFDSVESANA 223
Cdd:TIGR01649  73 NYStsqeiKRDgNSDFDSAGPNkvlrVIVENPMYPITLDVLYQIFNPYGKVL--RIVTFT-KNNVFQALVEFESVNSAQH 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   224 AiehvnGMLLNDKKVYVGHHVSRRErQSKVEALkanftNVYIKNLDTeiteQEFS--DLFGQFGEITSLSLVKDQN---- 297
Cdd:TIGR01649 150 A-----KAALNGADIYNGCCTLKIE-YAKPTRL-----NVKYNDDDS----RDYTnpDLPGRRDPGLDQTHRQRQPallg 214
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   298 DKPRGFGFVNYANHECAQKAvdelndkeykgkkLYVG-RAQKKHEREEELRKRYEQMKLEK--------MNKYQGVnLFI 368
Cdd:TIGR01649 215 QHPSSYGHDGYSSHGGPLAP-------------LAGGdRMGPPHGPPSRYRPAYEAAPLAPaissygpaGGGPGSV-LMV 280
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   369 KNL-QDEVDDERLKAEFSAFGTITSAKIMTDEqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEVRRS 447
Cdd:TIGR01649 281 SGLhQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPP 356

                  .
gi 19114289   448 Q 448
Cdd:TIGR01649 357 R 357
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
171-236 3.09e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 42.60  E-value: 3.09e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFgkILSCKVAVDEL-------GNAKGYGFVHFDSVESANAAIEHVNGMLLNDK 236
Cdd:cd12239   5 YVKNLSKRVSEKDLKYIFGRF--VDSSSEEKNMFdirlmteGRMKGQAFITFPSEELAEKALNLTNGYVLHGK 75
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
82-151 3.09e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 42.26  E-value: 3.09e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTlIKGRPC 151
Cdd:cd12328   2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIVTDKETGKKRGFAFVTFDDHDSVDKIVLQKYHT-INGHRC 70
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
91-151 3.12e-05

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 42.39  E-value: 3.12e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  91 VTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNytLIKGRPC 151
Cdd:cd12321  11 TTEQDLKEYFSTFGEVLMVQVKKDPKTGRSKGFGFVRFASYETQVKVLSQRH--MIDGRWC 69
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
170-236 3.15e-05

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 42.45  E-value: 3.15e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDK 236
Cdd:cd12674   3 LFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDpETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGH 70
RRM1_RBM4 cd12606
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
170-234 3.16e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410018 [Multi-domain]  Cd Length: 67  Bit Score: 42.10  E-value: 3.16e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLLN 234
Cdd:cd12606   3 LFIGNLPREATEEEIRSLFEQYGKVTECDII-------KNYGFVHMEDKSAADEAIRNLHHYKLH 60
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
170-242 3.18e-05

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 42.31  E-value: 3.18e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKvavdeLGNakGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12337   2 VYIGRLPYRARERDVERFFRGYGRIRDIN-----LKN--GFGFVEFEDPRDADDAVYELNGKELCGERVIVEH 67
RRM_RDM1 cd12364
RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar ...
82-150 3.30e-05

RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins; This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA.


Pssm-ID: 409799 [Multi-domain]  Cd Length: 81  Bit Score: 42.74  E-value: 3.30e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  82 LYVGELDPSVTEA----MLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN-YTLIKGRP 150
Cdd:cd12364   3 LFVWNISPKLTEEeiyeSLCKAFSAFGLLYSVRVFPNAAVATPGFYAFVKFYSARDASRAQKALNgKWLFQGSP 76
RRM_SLIRP cd12242
RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
170-224 3.32e-05

RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins; This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities.


Pssm-ID: 409688 [Multi-domain]  Cd Length: 73  Bit Score: 42.34  E-value: 3.32e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAA 224
Cdd:cd12242   2 LFVSNLPWTTGSSELKEYFSQFGKVKRCNLPFDkETGFHKGFGFVSFENEDGLRNA 57
PHA03378 PHA03378
EBNA-3B; Provisional
439-549 3.50e-05

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 46.98  E-value: 3.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  439 AQRKEVRRSQLEAQIQARNQFRLQQQVAAAAGIPAVQYGATGPLIYGPGGYPIPAAVNGRGMPMVPGHNGPMPMypgmpt 518
Cdd:PHA03378 714 AQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQAPPAPQ------ 787
                         90       100       110
                 ....*....|....*....|....*....|.
gi 19114289  519 QFPAGGPAPGYPGMNarGPVPAQGRPMMMPG 549
Cdd:PHA03378 788 QRPRGAPTPQPPPQA--GPTSMQLMPRAAPG 816
RRM2_hnRNPAB cd12584
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
263-320 3.50e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 409997 [Multi-domain]  Cd Length: 80  Bit Score: 42.63  E-value: 3.50e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDE 320
Cdd:cd12584   7 IFVGGLNPETTEEKIREYFGEFGEIEAIELPMDpKTNKRRGFVFITFKEEDPVKKILEK 65
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
82-149 3.51e-05

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 42.32  E-value: 3.51e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVcrdaVTRRS---LGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12392   5 LFVKGLPFSCTKEELEELFKQHGTVKDVRL----VTYRNgkpKGLAYVEYENEADASQAVLKTDGTEIKDH 71
RRM1_RBM19_MRD1 cd12315
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple ...
172-240 3.54e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409754 [Multi-domain]  Cd Length: 81  Bit Score: 42.53  E-value: 3.54e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGK-----ILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12315   5 VKNLPLSLDEDQFRRLFSQKCKdigltITDCKLLTKSGGVSRRFGFVGFKDEEDAQKAKEFFNGTYFRTSKVTV 78
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
170-248 3.57e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 42.51  E-value: 3.57e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEhVNGMLLNDKKVYVGHHVSRRE 248
Cdd:cd12579   2 LFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKDtGKKRGFGFVYFEDHDSADKAAV-VKFHSINGHRVEVKKAVPKEE 80
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
256-349 3.57e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 43.12  E-value: 3.57e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 256 LKANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd12559   1 LRPPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFyTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQ 80
                        90
                ....*....|....*
gi 19114289 335 RAQKKHEREEELRKR 349
Cdd:cd12559  81 FAQGDRKTPNQMKAK 95
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
363-436 3.59e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.


Pssm-ID: 409695 [Multi-domain]  Cd Length: 78  Bit Score: 42.19  E-value: 3.59e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLA-GKPLYV 436
Cdd:cd12249   1 GCEVFVGKIPRDVFEDELVPLFEKCGKIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKTLNNYEIRpGKLLGV 75
RRM1_CID8_like cd12459
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein ...
263-318 3.60e-05

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409892 [Multi-domain]  Cd Length: 80  Bit Score: 42.40  E-value: 3.60e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRgFGFVNYANHECAQKAV 318
Cdd:cd12459   5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRICGDPNSVLR-FAFIEFTDEEGARAAL 59
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
68-148 3.62e-05

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 46.55  E-value: 3.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289    68 SVATPSGTAPTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIK 147
Cdd:TIGR01659 182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPE 261

                  .
gi 19114289   148 G 148
Cdd:TIGR01659 262 G 262
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
172-240 3.64e-05

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 42.64  E-value: 3.64e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGK--ILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEHVNGML----LNDKKVYV 240
Cdd:cd12313   7 LRGLDVLTTEEDILSALQAHADlpIKDVRLIRDKLTGTsRGFAFVEFSSLEDATQVMDALQNLLppfkIDGRVVSV 82
RRM3_TIA1 cd12621
RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
170-233 3.70e-05

RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410032 [Multi-domain]  Cd Length: 72  Bit Score: 42.36  E-value: 3.70e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12621   3 VYCGGVTSGLTEQLMRQTFSPFGQIMEIRVFPD-----KGYSFVRFNSHESAAHAIVSVNGTTI 61
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
170-230 3.70e-05

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 42.12  E-value: 3.70e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12399   1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDrETKRPRGFGFVELQEEESAEKAIAKLDG 62
RRM_SRSF12 cd12560
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and ...
365-440 3.72e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins; This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409976 [Multi-domain]  Cd Length: 84  Bit Score: 42.68  E-value: 3.72e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12560   2 SLFVRNVADATRPEDLRREFGRYGPIVDVYIPLDfYNRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQ 78
RRM1_hnRPDL cd12758
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
170-237 3.78e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 410152 [Multi-domain]  Cd Length: 76  Bit Score: 42.27  E-value: 3.78e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIE----HVNGMLLNDKK 237
Cdd:cd12758   2 MFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVtGRSRGFGFVLFKDAASVDKVLElkehKLDGKLIDPKR 74
RRM3_HuB cd12654
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup ...
78-142 3.80e-05

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241098 [Multi-domain]  Cd Length: 86  Bit Score: 42.78  E-value: 3.80e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12654   2 TGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66
RRM3_HuD cd12656
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup ...
78-142 3.82e-05

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241100 [Multi-domain]  Cd Length: 86  Bit Score: 42.77  E-value: 3.82e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12656   2 TGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLN 66
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
263-439 3.82e-05

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.81  E-value: 3.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-------DKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYVGR 335
Cdd:TIGR01642 178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKhvssvniNKEKNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIRR 256
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   336 AQKKH---EREEELRKRYEQMKLEKMNKYQGVN--------LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKS 403
Cdd:TIGR01642 257 PHDYIpvpQITPEVSQKNPDDNAKNVEKLVNSTtvldskdrIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDiATGLS 336
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 19114289   404 KGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:TIGR01642 337 KGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA 372
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
171-231 3.86e-05

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 42.22  E-value: 3.86e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGM 231
Cdd:cd12361   3 FVGMIPKTASEEDVRPLFEQFGNIEEVQILRDKqTGQSKGCAFVTFSTREEALRAIEALHNK 64
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
81-155 3.94e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 41.92  E-value: 3.94e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRV-----CrdavtrrslgyAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12346   3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIppgkgC-----------GFVQFVNRASAEAAIQKLQGTPIGGSRIRLSW 71
RRM1_DAZAP1 cd12574
RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
263-319 3.96e-05

RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409988 [Multi-domain]  Cd Length: 82  Bit Score: 42.33  E-value: 3.96e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVD 319
Cdd:cd12574   2 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKtTNQSRGFGFVKFKDPNCVGTVLA 59
RRM2_Crp79_Mug28 cd21621
RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
265-334 3.98e-05

RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410200 [Multi-domain]  Cd Length: 74  Bit Score: 41.93  E-value: 3.98e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEI--TSLSLVKDQndKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVG 334
Cdd:cd21621   3 VLNLPTDMTPKDLYNLFSEHGKVegTAINQVPDN--RGRRYGEVAMNSYEDCQKALEYFNGYVYKGYILEVF 72
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
178-221 4.03e-05

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 42.01  E-value: 4.03e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 19114289 178 AIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESA 221
Cdd:cd12321  10 KTTEQDLKEYFSTFGEVLMVQVKKDPKtGRSKGFGFVRFASYETQ 54
RRM1_HuR cd12769
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup ...
169-242 4.08e-05

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410162 [Multi-domain]  Cd Length: 82  Bit Score: 42.33  E-value: 4.08e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12769   4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVaGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY 78
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
71-161 4.16e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 43.87  E-value: 4.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   71 TPSGTAPT----------SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDE 140
Cdd:PLN03134  16 SSNGNVPVtsmlgslrlmSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
                         90       100
                 ....*....|....*....|.
gi 19114289  141 LNYTLIKGRPCRIMWSQRDPS 161
Cdd:PLN03134  96 MDGKELNGRHIRVNPANDRPS 116
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
170-240 4.20e-05

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 42.21  E-value: 4.20e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12334   1 VYVGNLDEKVTEELLWELFIQAGPVVNVHMPKDRVTQQhQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
170-238 4.22e-05

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 42.05  E-value: 4.22e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12622   3 VYVGNLPPEVTQADLIPLFQNFGVIEEVRVQRD-----KGFGFVKYDTHEEAALAIQQLNGQPFLGRPI 66
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
170-230 4.27e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 41.87  E-value: 4.27e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAI----EHVNG 230
Cdd:cd12328   2 LFVGGLKEDVEEEDLREYFSQFGKVESVEIVTDkETGKKRGFAFVTFDDHDSVDKIVlqkyHTING 67
RRM_RALY cd12604
RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly; This subgroup ...
170-233 4.39e-05

RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly; This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch.


Pssm-ID: 410016 [Multi-domain]  Cd Length: 76  Bit Score: 41.94  E-value: 4.39e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKALHDT-FSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12604   4 VFIGNLNTAVVKKSDVETiFSKYGRVVGCSVH-------KGYAFVQYTNERHARAAVIGENGRVL 61
RRM5_MRD1 cd12570
RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 ...
366-439 4.43e-05

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241014 [Multi-domain]  Cd Length: 76  Bit Score: 42.11  E-value: 4.43e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12570   3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQYA 76
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
365-439 4.53e-05

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 42.01  E-value: 4.53e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAvteMNQR-MLAGKPLYVALA 439
Cdd:cd12321   1 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDPKtGRSKGFGFVRFASYETQVKV---LSQRhMIDGRWCDVKLP 74
RRM1_MYEF2 cd12658
RNA recognition motif 1 (RRM1) found in vertebrate myelin expression factor 2 (MEF-2); This ...
388-436 4.55e-05

RNA recognition motif 1 (RRM1) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410059 [Multi-domain]  Cd Length: 76  Bit Score: 41.89  E-value: 4.55e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 19114289 388 GTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12658  25 GEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLSGRPLNI 73
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
170-238 4.70e-05

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 41.88  E-value: 4.70e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILscKVAV---DELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12393   4 VYVSNLPFSLTNNDLHQIFSKYGKVV--KVTIlkdKETRKSKGVAFVLFLDRESAHNAVRAMNNKELFGRTL 73
RRM1_hnRNPD_like cd12575
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
366-432 4.80e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409989 [Multi-domain]  Cd Length: 72  Bit Score: 41.78  E-value: 4.80e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKaVTEMNQRMLAGK 432
Cdd:cd12575   1 MFIGGLSWDTSKKDLKDYFSKFGEVVDCTIKLDPvTGRSRGFGFVLFKDAESVDK-VLDQKEHKLDGK 67
RRM_RBM7 cd12592
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily ...
366-434 5.12e-05

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.


Pssm-ID: 410005 [Multi-domain]  Cd Length: 75  Bit Score: 41.74  E-value: 5.12e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12592   4 LFVGNLDTKVTEELLFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPL 72
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
170-238 5.27e-05

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 41.66  E-value: 5.27e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12397   1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMATFEdSGKCKGFAFVDFKEIESATNAVKGPINHSLNGRDL 70
RRM2_CELF1_2 cd12634
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-1, CELF-2 and ...
366-426 5.37e-05

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins; This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3.


Pssm-ID: 410042 [Multi-domain]  Cd Length: 81  Bit Score: 41.97  E-value: 5.37e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQ 426
Cdd:cd12634   4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFSTRAMAQNAIKAMHQ 64
RRM3_HuC cd12655
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup ...
82-142 5.37e-05

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410057 [Multi-domain]  Cd Length: 85  Bit Score: 41.97  E-value: 5.37e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12655   4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLN 64
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
263-333 5.44e-05

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 41.91  E-value: 5.44e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRgFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12260   7 VYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDETQPTR-YAFVEFAEQTSVINAL-KLNGKMFGGRPLKV 75
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
263-333 5.51e-05

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 41.37  E-value: 5.51e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12609   3 IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALNGKEVKGRRINV 66
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
170-238 5.60e-05

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 41.71  E-value: 5.60e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAI--EHVngmlLNDKKV 238
Cdd:cd12577   1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIMKDSAtGRSRGFGFLTFEDPSSVNEVMkkEHV----LDGKII 68
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
167-238 5.90e-05

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 41.47  E-value: 5.90e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 167 TGNVFIKNLDPAIDNKALHDTFSAFGKILSckvaVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12276   1 QGTLLVFNLDAPVSNDELKSLFSKFGEIKE----IRPTPDKPSQKFVEFYDVRDAEAALDGLNGRELLGGKL 68
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
263-323 5.98e-05

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 41.41  E-value: 5.98e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDELND 323
Cdd:cd12307   2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTgKSKGYAFVEFEDPEVAKIVAETMNN 63
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
170-240 6.11e-05

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 41.51  E-value: 6.11e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVaVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd21605   4 IFVGNLPFDCTWEDLKDHFSQVGEVIRADI-VTSRGRHRGMGTVEFTNKEDVDRAISKFDHTMFMGREIFV 73
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
80-148 6.29e-05

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 41.54  E-value: 6.29e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKG 148
Cdd:cd12652   1 ANLYVSGLPKTMTQKELEQLFSQFGRIITSRILCDNVTGLSRGVGFIRFDKRVEAERAIKALNGTIPPG 69
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
366-425 6.43e-05

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 41.41  E-value: 6.43e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEA-NKAVTEMN 425
Cdd:cd12226   2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDRGFAYIDLRTSEAAlQKCLSTLN 62
RRM1_MSSP1 cd12470
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
365-425 6.49e-05

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409900 [Multi-domain]  Cd Length: 86  Bit Score: 42.08  E-value: 6.49e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12470   9 NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTtNKCKGYGFVDFDSPAAAQKAVSALK 70
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
263-337 6.51e-05

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 41.68  E-value: 6.51e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPrgFGFVNYANHECAQKAVDeLNDKEYKGKKLYVGRAQ 337
Cdd:cd12225   3 IHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTR--FAWVEFATDASALSALN-LDGTTLGGHPLRVSPSK 74
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
170-240 6.52e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 41.33  E-value: 6.52e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEhVNGMLLNDKKVYV 240
Cdd:cd12395   2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDrETGIGKGFGYVLFKDKDSVDLALK-LNGSKLRGRKLRV 72
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
167-242 6.58e-05

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 41.62  E-value: 6.58e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 167 TGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12309   2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGY 77
RRM_YRA1_MLO3 cd12267
RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA ...
261-333 6.58e-05

RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins; This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p.


Pssm-ID: 409711 [Multi-domain]  Cd Length: 78  Bit Score: 41.64  E-value: 6.58e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLF-GQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGK---KLYV 333
Cdd:cd12267   1 SKVIVSNLPKDVTEAQIREYFvSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRLDDGNrkmKVEV 77
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
82-152 6.66e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.


Pssm-ID: 409695 [Multi-domain]  Cd Length: 78  Bit Score: 41.42  E-value: 6.66e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRrSLGYAYVNFHNMEDGEKALDELNytLIKGRPCR 152
Cdd:cd12249   4 VFVGKIPRDVFEDELVPLFEKCGKIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVKTLN--NYEIRPGK 71
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
264-324 6.72e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 41.66  E-value: 6.72e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQK----AVDELNDK 324
Cdd:cd12576   3 FIGGLSWQTTPEGLREYFSKFGEITECMVMRDPTTKrSRGFGFVTFSDPASVDKvlaqGPHELDGK 68
RRM2_HuD cd12774
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup ...
262-328 6.79e-05

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410167 [Multi-domain]  Cd Length: 84  Bit Score: 42.02  E-value: 6.79e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12774   7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQvTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 74
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
81-149 6.81e-05

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 41.51  E-value: 6.81e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVasIRVcrDAVTR--RSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd21605   3 SIFVGNLPFDCTWEDLKDHFSQVGEV--IRA--DIVTSrgRHRGMGTVEFTNKEDVDRAISKFDHTMFMGR 69
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
263-331 6.81e-05

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 41.42  E-value: 6.81e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKP-RGFGFVNYANHECAQKAVdELNDKEYKGKKL 331
Cdd:cd12291   2 VYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDSKEfKGSVFVEFKTEEEAKKFL-EKEKLKYKGKEL 70
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
165-240 6.90e-05

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 41.59  E-value: 6.90e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 165 MGTGNVFIKNLDPAIDNKALHDTFSAFGKILscKVAVDELgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12351   5 MPTNCVWLDGLSENVTEQYLTRHFCRYGPVV--KVVIDRQ---KGMALVLYDEVECAQAAVKETKGRKIGGRKIQV 75
RRM_G3BP1 cd12463
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 1 (G3BP1) ...
366-445 6.91e-05

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins; This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript.


Pssm-ID: 409896 [Multi-domain]  Cd Length: 80  Bit Score: 41.78  E-value: 6.91e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKImtDEQGKSKGFGFVCYTTPEEAnkavtemnQRMLAGKPLYValaqRKEVR 445
Cdd:cd12463   6 LFVGNLPHDVDKSELKEFFQGYGNVVELRI--NSGGKLPNFGFVVFDDPEPV--------QKILSNRPIKF----RGEVR 71
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
170-242 7.09e-05

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 41.91  E-value: 7.09e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKgYGFVHFDSVESANAAIEhVNGMLLNDKKVYVGH 242
Cdd:cd12260   7 VYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDETQPTR-YAFVEFAEQTSVINALK-LNGKMFGGRPLKVNH 77
RRM2_p54nrb cd12591
RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
366-421 7.18e-05

RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410004 [Multi-domain]  Cd Length: 80  Bit Score: 41.44  E-value: 7.18e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAV 421
Cdd:cd12591   2 LTVKNLPQFVSNELLEEAFSVFGQVERAVVIVDDRGRPTGKGIVEFSGKPAARKAL 57
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
167-241 7.26e-05

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 41.51  E-value: 7.26e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 167 TGNVFIKNLDPAIDNKALHDTFSAFGKILSCKV----AVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd12223   1 TTNLYVGNLPPSVTEEVLLREFGRFGPLASVKImwprTEEERRRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKLG 79
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
366-436 7.29e-05

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 41.50  E-value: 7.29e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdeqgkSKGFGFVCYTTPEEANKAVTEM-NQRMLAGKPLYV 436
Cdd:cd12224   4 LYVGGLGDKITEKDLRDHFYQFGEIRSITVVA-----RQQCAFVQFTTRQAAERAAERTfNKLIIKGRRLKV 70
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
264-333 7.53e-05

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 41.44  E-value: 7.53e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGeITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDeLNDKEYKGKKLYV 333
Cdd:cd12402   6 YLGNLPYDVTEDDIEDFFRGLN-ISSVRLPRENGPgRLRGFGYVEFEDRESLIQALS-LNEESLKNRRIRV 74
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
366-422 7.94e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 41.28  E-value: 7.94e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVT 422
Cdd:cd12576   2 MFIGGLSWQTTPEGLREYFSKFGEITECMVMRDPTTKrSRGFGFVTFSDPASVDKVLA 59
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
81-149 7.98e-05

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 41.09  E-value: 7.98e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12417   1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSARTPGSRCYGYVTMASVEEADLCIKSLNKTELHGR 69
RRM_hnRNPC cd12603
RNA recognition motif (RRM) found in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 ...
366-447 8.23e-05

RNA recognition motif (RRM) found in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2); This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site.


Pssm-ID: 410015 [Multi-domain]  Cd Length: 84  Bit Score: 41.55  E-value: 8.23e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQD-EVDDERLKAEFSAFGTITSAKImtdeqgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKEV 444
Cdd:cd12603   9 VFIGNLNTlVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKV 81

                ...
gi 19114289 445 RRS 447
Cdd:cd12603  82 NRS 84
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
171-238 8.26e-05

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 41.37  E-value: 8.26e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 171 FIKNLDPAID----NKALHDTFSAFGKILSCKVavdeLGNAKGYG--FVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12246   3 YINNLNEKIKkdelKRSLYALFSQFGPVLDIVA----SKSLKMRGqaFVVFKDVESATNALRALQGFPFYGKPM 72
RRM2_PSP1 cd12589
RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This ...
265-323 8.27e-05

RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410002 [Multi-domain]  Cd Length: 80  Bit Score: 41.52  E-value: 8.27e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELND 323
Cdd:cd12589   4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPPARKALERCSD 62
RRM1_hnRNPM cd12657
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
263-333 8.28e-05

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410058 [Multi-domain]  Cd Length: 76  Bit Score: 41.41  E-value: 8.28e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQ-FGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12657   2 VFISNIPFDVKWQTLKDLVKEkVGEVTYVELLMDAEGKSRGCAVVEFKTEESMKKAVEVLNKHSFNGRPLKV 73
RRM4_RBM45 cd12369
RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
183-240 8.38e-05

RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409804 [Multi-domain]  Cd Length: 68  Bit Score: 41.12  E-value: 8.38e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 183 ALHDTFSAFGKILSckvaVDELGNaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12369  15 ILEDVFCRFGNLID----VYLVPG-KNVGYAKYADRESAEEAITTLHGKEVNGVKLKV 67
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
82-153 8.43e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 41.20  E-value: 8.43e-05
                        10        20        30        40        50        60        70
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gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12329   2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKIL-ETQFHVIGGKKVEV 72
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
170-240 8.50e-05

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 41.00  E-value: 8.50e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12365   1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDREPNlPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 72
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
268-324 8.51e-05

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 41.52  E-value: 8.51e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 268 LDTEITEQEFSDLFGQFG-EITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDK 324
Cdd:cd12344   7 LEPWMDEAYISSCFAKTGeEVVSVKIIRNkQTGKSAGYCFVEFATQEAAEQALEHLNGK 65
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
182-246 8.55e-05

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 41.53  E-value: 8.55e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 182 KALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSR 246
Cdd:cd12641  22 RDLREVFSKYGPIADVSIVYDQQSRrSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 87
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
264-333 8.63e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 41.44  E-value: 8.63e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFgeITSLSLVKDQND-------KPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12239   5 YVKNLSKRVSEKDLKYIFGRF--VDSSSEEKNMFDirlmtegRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVV 79
RRM2_HuB cd12775
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup ...
262-328 8.77e-05

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410168 [Multi-domain]  Cd Length: 84  Bit Score: 41.63  E-value: 8.77e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12775   7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQvTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPPG 74
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
170-230 9.13e-05

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 41.13  E-value: 9.13e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKIlsckvavDELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12495   4 LFVRNLANTVTEEILEKAFSQFGKL-------ERVKKLKDYAFIHFDERDGAVKAMDEMNG 57
RRM1_hnRNPD_like cd12575
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
170-236 9.36e-05

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409989 [Multi-domain]  Cd Length: 72  Bit Score: 41.01  E-value: 9.36e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAI---EH-VNGMLLNDK 236
Cdd:cd12575   1 MFIGGLSWDTSKKDLKDYFSKFGEVVDCTIKLDPVtGRSRGFGFVLFKDAESVDKVLdqkEHkLDGKVIDPK 72
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
81-153 9.55e-05

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 40.95  E-value: 9.55e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIrvcRDAVTRRSlgYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12529   3 TLVVFNLDPSISNDDLHQIFGAYGEIKEI---RETPNKRH--HKFIEFYDVRSAEAALKALNKSEIAGKRIKL 70
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
82-153 9.55e-05

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 41.12  E-value: 9.55e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12371   3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRV 74
RRM2_HuC cd12776
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup ...
365-439 9.96e-05

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241220 [Multi-domain]  Cd Length: 81  Bit Score: 41.14  E-value: 9.96e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMN-QRML-AGKPLYVALA 439
Cdd:cd12776   3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQvTGVSRGVGFIRFDKRIEAEEAIKGLNgQKPLgAAEPITVKFA 80
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
272-333 1.00e-04

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 40.89  E-value: 1.00e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 272 ITEQEFSDLFGQFGEITSLslvkdqnDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12233  12 TREEDIEKLFEPFGPLVRC-------DIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTV 66
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
262-339 1.02e-04

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 41.23  E-value: 1.02e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKeykgkklYVGRAQKK 339
Cdd:cd12309   4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSGQ-------YIGRNQIK 74
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
169-240 1.05e-04

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 41.21  E-value: 1.05e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12297   2 TLWVTNFPPSYDERSIRDLFGDYGVILSVRLPSLRYNTSRRFCYIDFTSPESARAAVELLNGLLEEGYTLVV 73
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
164-215 1.05e-04

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 41.31  E-value: 1.05e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 19114289 164 KMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHF 215
Cdd:cd12672   2 KIMPNTVFVGGIDIRMDENEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 53
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
81-155 1.07e-04

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 41.23  E-value: 1.07e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRdavTRRSLG--YAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12309   4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKR---PPRGQGnaYAFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGY 77
RRM3_CELF3_4_5_6 cd12639
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
262-333 1.10e-04

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 241083 [Multi-domain]  Cd Length: 79  Bit Score: 40.99  E-value: 1.10e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12639   6 NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRaTNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV 78
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
170-240 1.11e-04

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 40.86  E-value: 1.11e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 170 VFIKNLDPAIDNKALHDT----FSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEhVNGMLLNDKKVYV 240
Cdd:cd12451   2 IFVKGFDASLGEDTIRDElrehFGECGEVTNVRIPTDrETGELKGFAYIEFSTKEAKEKALE-LNGSDIAGGNLVV 76
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
79-153 1.12e-04

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 40.84  E-value: 1.12e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12262   3 SRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEK------NCAFVNYLNIANAIKAVQELPIKNPKFKKVRI 71
RRM2_HuD cd12774
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup ...
365-439 1.16e-04

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410167 [Multi-domain]  Cd Length: 84  Bit Score: 41.25  E-value: 1.16e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAG--KPLYVALA 439
Cdd:cd12774   7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQvTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGatEPITVKFA 84
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
261-331 1.22e-04

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 40.67  E-value: 1.22e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVdelndKEYKGKKL 331
Cdd:cd12680   1 TKLLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERRADALKAM-----KQYNGVPL 66
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
167-241 1.24e-04

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 40.86  E-value: 1.24e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 167 TGNVFIKNLDPAIDNKALHDTFSAFGKILscKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd12350   2 TRTLFIGNLEKTTTYGDLRNIFERFGEII--DIDIKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRLKLG 74
RRM1_RBM46 cd12484
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 46 (RBM46); This ...
263-331 1.25e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409911 [Multi-domain]  Cd Length: 78  Bit Score: 41.03  E-value: 1.25e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12484   4 VFVGKIPRDMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIKMLNNYEIRPGKF 72
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
182-237 1.26e-04

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 41.03  E-value: 1.26e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 182 KALHDTFSAFG--KILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLnDKK 237
Cdd:cd12278  22 KVLTKIFSKFGsgKIVGIYMPVDETGKTKGFAFVEYATPEEAKKAVKALNGYKL-DKK 78
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
261-323 1.32e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 41.10  E-value: 1.32e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYI-KNLDTEITEQEFSDLFGQFGE--ITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELND 323
Cdd:cd12313   2 TNVLIlRGLDVLTTEEDILSALQAHADlpIKDVRLIRDkLTGTSRGFAFVEFSSLEDATQVMDALQN 68
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
366-434 1.34e-04

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 40.63  E-value: 1.34e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIM-TDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12307   2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSrSKKTGKSKGYAFVEFEDPEVAKIVAETMNNYLLFERLL 71
RRM3_ACF cd12498
RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
82-153 1.34e-04

RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409921 [Multi-domain]  Cd Length: 83  Bit Score: 41.06  E-value: 1.34e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVcrdavtRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12498  11 LYVRNLMLSTTEETIEKEFSNIKPGAVERV------KKIRDYAFVHFYNREDAVNAMNALNGKVIDGSPIEV 76
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
170-230 1.39e-04

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 40.86  E-value: 1.39e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12635   4 LFVGMLGKQQSEDDVRRLFEPFGSIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64
RRM_G3BP2 cd12464
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 2 (G3BP2) ...
366-445 1.39e-04

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins; This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain.


Pssm-ID: 409897 [Multi-domain]  Cd Length: 83  Bit Score: 40.72  E-value: 1.39e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEAnkavtemnQRMLAGKPLYValaqRKEV 444
Cdd:cd12464   8 LFVGNLPHDIDENELKEFFMSFGNVVELRINTKGVgGKLPNFGFVVFDDSDPV--------QRILNAKPIMF----RGEV 75

                .
gi 19114289 445 R 445
Cdd:cd12464  76 R 76
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
82-150 1.40e-04

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 40.43  E-value: 1.40e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  82 LYVGELDPSVTEAMLFELF-NSIGPVASIRVCRDavtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12358   1 LYIGNLSSDVNESDLRQLFeEHKIPVSSVLVKKG-------GYAFVDCPDQSWADKAIEKLNGKILQGKV 63
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
170-242 1.41e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.


Pssm-ID: 410008 [Multi-domain]  Cd Length: 70  Bit Score: 40.31  E-value: 1.41e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKIlsckvavDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12595   2 VFIGRLNPAAREKDVERFFKGYGRI-------RDIDLKRGFGFVEFEDPRDADDAVYELDGKELCNERVTIEH 67
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
366-443 1.42e-04

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 40.50  E-value: 1.42e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdeqgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQRKE 443
Cdd:cd12227   5 LWVGHLSKKVTQEELKNLFEEYGEIQSIDMIP-----PRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77
RRM4_MRD1 cd12319
RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 ...
263-338 1.45e-04

RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409758 [Multi-domain]  Cd Length: 84  Bit Score: 40.93  E-value: 1.45e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSlSLVKDQNDKPR-------GFGFVNYANHECAQKAVDELNDKEYKGKKLYVGR 335
Cdd:cd12319   3 LFVKNLNFSTTNQHLTDVFKHLDGFVF-ARVKTKPDPKRpgktlsmGFGFVGFKTKEQAQAALKAMDGFVLDGHKLEVKF 81

                ...
gi 19114289 336 AQK 338
Cdd:cd12319  82 SHR 84
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
81-164 1.48e-04

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 40.64  E-value: 1.48e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRImwsqrDP 160
Cdd:cd12673   4 RIFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDR-AGVSKGYGFITFETQEDAQKILQEAEKLNYKDKKLNI-----GP 77

                ....
gi 19114289 161 SLRK 164
Cdd:cd12673  78 AIRK 81
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
82-149 1.49e-04

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 40.68  E-value: 1.49e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRrslGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12241   5 LYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTKETR---GTAFVVYEDIFDAKNACDHLSGFNVCNR 69
RRM3_RBM47 cd12497
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This ...
263-337 1.50e-04

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409920 [Multi-domain]  Cd Length: 74  Bit Score: 40.72  E-value: 1.50e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFgEITSLSLVKdqndKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12497   4 LYVRNLMIETTEDTIKKIFGQF-NPGCVERVK----KIRDYAFVHFASRDDAVVAMNNLNGTELEGSCIEVTLAK 73
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
365-426 1.51e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 40.50  E-value: 1.51e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeqgksKGFGFVCYTTPEEANKAVTEMNQ 426
Cdd:cd12523   5 NVYLGNLPESITEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTLPL 61
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
82-146 1.52e-04

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 40.62  E-value: 1.52e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCR--DAVTRRslgYAYVNFHNMEDGEKALDELNYTLI 146
Cdd:cd12565   3 IIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRtkDGKSRR---FGFIGFKSEEEAQKAVKYFNKTFI 66
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
170-240 1.55e-04

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 40.31  E-value: 1.55e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnakgYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12251   4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD-------YAFVHFEERDDAVKAMEEMNGKELEGSEIEV 67
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
263-319 1.59e-04

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 40.47  E-value: 1.59e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSL-VKDQNDKPRGFGFVNYANHECAQKAVD 319
Cdd:cd12229   6 LFVGNLPHDITEDELKEFFSRFGNVLELRInSKGGGGRLPNFGFVVFDDPEAVQKILA 63
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
365-429 1.62e-04

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 40.46  E-value: 1.62e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRML 429
Cdd:cd12309   4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSGQYI 68
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
169-221 1.65e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 40.50  E-value: 1.65e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 19114289 169 NVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESA 221
Cdd:cd12523   5 NVYLGNLPESITEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANA 52
RRM4_RBM19_RRM3_MRD1 cd12317
RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
265-336 1.80e-04

RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 (RRM3) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409756 [Multi-domain]  Cd Length: 72  Bit Score: 40.32  E-value: 1.80e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12317   5 VKNLPFGATEEELRELFEKFGTLGRLLLPPS-----RTIALVEFLEPQDARRAFKKLAYKRFKHVPLYLEWA 71
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
82-145 1.80e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 40.20  E-value: 1.80e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTL 145
Cdd:cd12325   1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKDPATGRSRGFGFVTFKDPSSVDAVLAARPHTL 64
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
170-241 1.81e-04

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 40.35  E-value: 1.81e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKI----LSCKVAVDELgnakgYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd21603   3 IFVKNLPLDTNNDEILDFFSKVGPIksvfTSPKYKYNSL-----WAFVTYKKGSDTEKAIKLLNGTLFKGRTIEVT 73
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
365-436 1.81e-04

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 40.67  E-value: 1.81e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12556  10 NLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMSGRVIGRNPIKI 81
RRM2_NEFsp cd12274
RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This ...
263-331 1.84e-04

RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp; This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities.


Pssm-ID: 409717 [Multi-domain]  Cd Length: 71  Bit Score: 40.23  E-value: 1.84e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELN-DKEYKGKKL 331
Cdd:cd12274   1 IYVSGFKKSLTEEDLQERFSQLSDLEAVFLPKDlQSGKHKKYCFLKFRSSQSAQAALDIITgEWKLKGRRA 71
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
263-337 1.85e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.


Pssm-ID: 410008 [Multi-domain]  Cd Length: 70  Bit Score: 40.31  E-value: 1.85e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLvkdqndkPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12595   2 VFIGRLNPAAREKDVERFFKGYGRIRDIDL-------KRGFGFVEFEDPRDADDAVYELDGKELCNERVTIEHAR 69
RRM2_PSRP2 cd21610
RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
263-336 1.94e-04

RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). PSRP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410189 [Multi-domain]  Cd Length: 79  Bit Score: 40.30  E-value: 1.94e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVK-DQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd21610   5 VYVGNLAKTVTNELLKDFFSEKGKVLGAKVQRtPGTSKSNGFGFVSFSSEEDVEAAIQALNNSVLEGQKIRVNKA 79
RRM2_Crp79_Mug28 cd21621
RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
172-241 1.97e-04

RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410200 [Multi-domain]  Cd Length: 74  Bit Score: 40.00  E-value: 1.97e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCkvAVDELGNAKG--YGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd21621   3 VLNLPTDMTPKDLYNLFSEHGKVEGT--AINQVPDNRGrrYGEVAMNSYEDCQKALEYFNGYVYKGYILEVF 72
RRM_PPARGC1A_like cd12357
RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma ...
170-227 1.98e-04

RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators; This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing.


Pssm-ID: 409793 [Multi-domain]  Cd Length: 91  Bit Score: 40.49  E-value: 1.98e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAkgYGFVHFDSVESANAAIEH 227
Cdd:cd12357   5 VYVGKLEQDTTRSELRRRFEVFGEIEECTVHFRERGDK--YGFVTYRYSEDAFLALEN 60
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
91-149 2.01e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409925 [Multi-domain]  Cd Length: 72  Bit Score: 40.09  E-value: 2.01e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  91 VTEAMLFELFNSIGPVAsIRVCRDAVTRRSlGYAYVNFHNMEDGEKALdELNYTLIKGR 149
Cdd:cd12502  12 VKEKQIREFFSPLKPVA-IRIVKNAHGNKT-GYVFVDFKSEEDVEKAL-KRNKDYMGGR 67
RRM1_RBM46 cd12484
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 46 (RBM46); This ...
363-425 2.02e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409911 [Multi-domain]  Cd Length: 78  Bit Score: 40.26  E-value: 2.02e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12484   1 GCEVFVGKIPRDMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIKMLN 63
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
81-150 2.05e-04

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 40.21  E-value: 2.05e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRvcrDAVTRRSlgYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12527   3 SLVILNLLPAVSSFTLREIFQVYGDVKDVR---ETPLKPS--QRFVEFFDVRDAARALHEMNGKEIFGKR 67
RRM2_HuB cd12775
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup ...
365-439 2.06e-04

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410168 [Multi-domain]  Cd Length: 84  Bit Score: 40.47  E-value: 2.06e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAG--KPLYVALA 439
Cdd:cd12775   7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQvTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPPGatEPITVKFA 84
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
170-240 2.12e-04

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 40.09  E-value: 2.12e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVavdeLGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd21617   2 VYVGNLPLDISEEEILQLFKAFNPVLVKKI----RSGFKCFAFVDLGSDENVKLAIQQLNGTLFGGRRLVV 68
RRM_RALYL cd12605
RNA recognition motif (RRM) found in vertebrate RNA-binding Raly-like protein (RALYL); This ...
170-233 2.13e-04

RNA recognition motif (RRM) found in vertebrate RNA-binding Raly-like protein (RALYL); This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain.


Pssm-ID: 410017 [Multi-domain]  Cd Length: 69  Bit Score: 40.02  E-value: 2.13e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 170 VFIKNLDPAIDNKA-LHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12605   4 VFIGNLNTAIVKKAdIEAIFAKYGKIVGCSVH-------KGYAFVQYMSERHARAAVAGENARII 61
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
366-437 2.15e-04

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 39.99  E-value: 2.15e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIM-TDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12389   2 LCVTNLPLSFTEEQFEELVRPYGNVERCFLVySEVTGESKGYGFVEYTSKESAIRAKNQLHGRQIGGRALQVD 74
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
366-440 2.16e-04

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 40.44  E-value: 2.16e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAG---KPLYVALAQ 440
Cdd:cd12637   2 LFVGSLPKTATEQEVRDLFEAYGEVEEVYLMKDPVTQqGTGCAFVKFAYKEEALAAIRSLNGTVTFDgcsRPVEVRFAE 80
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
170-240 2.19e-04

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 40.39  E-value: 2.19e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12392   5 LFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISV 75
RRM1_MSI2 cd12760
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and ...
257-339 2.20e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins; This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 410153 [Multi-domain]  Cd Length: 93  Bit Score: 40.50  E-value: 2.20e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 257 KANFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAV----DELNDKEYKGKKL 331
Cdd:cd12760   1 QHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKrSRGFGFVTFADPASVDKVLaqphHELDSKTIDPKVA 80

                ....*...
gi 19114289 332 YVGRAQKK 339
Cdd:cd12760  81 FPRRAQPK 88
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
365-438 2.24e-04

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 40.05  E-value: 2.24e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12297   2 TLWVTNFPPSYDERSIRDLFGDYGVILSVRLPSLRYNTSRRFCYIDFTSPESARAAVELLNGLLEEGYTLVVKI 75
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
82-149 2.25e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 40.05  E-value: 2.25e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNyTLIKGR 149
Cdd:cd12384   3 IFVGGLPYHTTDDSLREYFEQFGEIEEAVVITDRQTGKSRGYGFVTMADREAAERACKDPN-PIIDGR 69
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
82-149 2.26e-04

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 39.79  E-value: 2.26e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavtrrslgYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12608   3 IFVGNVDEDTSQEELSALFEPYGAVLSCAVMKQ--------FAFVHMRGEAAADRAIRELNGRELHGR 62
RRM_II_PABPN1 cd12550
RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; ...
81-154 2.28e-04

RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain.


Pssm-ID: 409966 [Multi-domain]  Cd Length: 76  Bit Score: 40.17  E-value: 2.28e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDeLNYTLIKGRPCRIM 154
Cdd:cd12550   1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFADKESVRTALA-LDESLFRGRQIKVM 73
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
366-437 2.36e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 39.94  E-value: 2.36e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12311   1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTReSRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRVQ 73
RRM1_SRSF6 cd12596
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 ...
170-242 2.42e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides.


Pssm-ID: 410009 [Multi-domain]  Cd Length: 72  Bit Score: 39.94  E-value: 2.42e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILsckvavdELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12596   4 VYIGRLSYHVREKDIQRFFSGYGKLL-------EVDLKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEH 69
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
170-237 2.47e-04

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410071 [Multi-domain]  Cd Length: 77  Bit Score: 40.12  E-value: 2.47e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIehvngmLLNDKK 237
Cdd:cd12670   2 VFVGNLAFEAEEEGLWRYFGKCGAIESVRIVRDPKTNvGKGFAYVQFKDENAVEKAL------LLNEKP 64
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
366-438 2.66e-04

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 39.99  E-value: 2.66e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ---GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12372   1 LYVGNLQWWTTDEDLEGACASFGVVDVKEIKFFEHkanGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRPCVVTP 76
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
366-436 2.72e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 39.52  E-value: 2.72e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTeMNQRMLAGKPLYV 436
Cdd:cd12283   2 VFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDRNsRRSKGVAYVEFYDVESVPLALA-LTGQRLLGQPIMV 72
RRM1_hnRNPR cd12482
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
261-333 2.73e-04

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains.


Pssm-ID: 409909 [Multi-domain]  Cd Length: 79  Bit Score: 39.96  E-value: 2.73e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYK-GKKLYV 333
Cdd:cd12482   2 TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPlSGQNRGYAFITFCNKEAAQEAVKLCDNYEIRpGKHLGV 76
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
81-157 2.75e-04

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 39.75  E-value: 2.75e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSlgyAYVNFHNMEDGEKALDeLNYTLIKGRPCRIMWSQ 157
Cdd:cd12225   2 TIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTRF---AWVEFATDASALSALN-LDGTTLGGHPLRVSPSK 74
RRM2_MSSP cd12244
RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) ...
82-150 2.84e-04

RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409690 [Multi-domain]  Cd Length: 82  Bit Score: 40.05  E-value: 2.84e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTrRSLGyayVNFHNMEDGEKA---LDELNYTLIKGRP 150
Cdd:cd12244   3 LYISNLPLDMDEQDLENMLKPFGQVISTRILRDSKG-QSRG---VGFARMESREKCedvISKFNGKVLKTPS 70
RRM2_p54nrb cd12591
RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
172-226 3.09e-04

RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410004 [Multi-domain]  Cd Length: 80  Bit Score: 39.90  E-value: 3.09e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIE 226
Cdd:cd12591   4 VKNLPQFVSNELLEEAFSVFGQVERAVVIVDDRGRPTGKGIVEFSGKPAARKALD 58
RRM3_CELF1_2 cd12638
RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and ...
262-343 3.33e-04

RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins; This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3.


Pssm-ID: 241082 [Multi-domain]  Cd Length: 92  Bit Score: 40.05  E-value: 3.33e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKKH 340
Cdd:cd12638   9 NLFIYHLPQEFGDQDILQMFMPFGNVVSAKVFIDkQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSKN 88

                ...
gi 19114289 341 ERE 343
Cdd:cd12638  89 DSK 91
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
366-420 3.39e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 39.47  E-value: 3.39e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNL-QDEVDDERLKAEFSAFGTITSAKImtdeqGKSKGFGFVCYTTPEEANKA 420
Cdd:cd12257   4 LEVRNIpPELNNITKLREHFSKFGTIVNIQV-----NYNPESALVQFSTSEEANKA 54
RRM_EWS cd12533
RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup ...
263-333 3.48e-04

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.


Pssm-ID: 409950 [Multi-domain]  Cd Length: 84  Bit Score: 39.82  E-value: 3.48e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEI-----TSLSLVKDQNDK----PRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12533   3 IYVQGLNENVTLEELADFFKHCGVVkinkrTGQPMINIYTDKetgkPKGDATVSYEDPPAAKAAVEWFDGKDFQGNKLKV 82
RRM_hnRNPC cd12603
RNA recognition motif (RRM) found in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 ...
159-233 3.54e-04

RNA recognition motif (RRM) found in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2); This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site.


Pssm-ID: 410015 [Multi-domain]  Cd Length: 84  Bit Score: 39.63  E-value: 3.54e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 159 DPslRKMGTgNVFIKNLDPAIDNKA-LHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12603   1 DP--RSMNS-RVFIGNLNTLVVKKSdVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMI 66
RRM4_MRD1 cd12319
RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 ...
170-240 3.60e-04

RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409758 [Multi-domain]  Cd Length: 84  Bit Score: 39.77  E-value: 3.60e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAV--DELGNAK----GYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12319   3 LFVKNLNFSTTNQHLTDVFKHLDGFVFARVKTkpDPKRPGKtlsmGFGFVGFKTKEQAQAALKAMDGFVLDGHKLEV 79
RRM_RBM7 cd12592
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily ...
170-233 3.61e-04

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.


Pssm-ID: 410005 [Multi-domain]  Cd Length: 75  Bit Score: 39.43  E-value: 3.61e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLL 233
Cdd:cd12592   4 LFVGNLDTKVTEELLFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKL 67
RRM3_TIAR cd12620
RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup ...
170-230 3.62e-04

RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 241064 [Multi-domain]  Cd Length: 73  Bit Score: 39.62  E-value: 3.62e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12620   3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNG 58
RRM1_MSI2 cd12760
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and ...
366-447 3.70e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins; This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 410153 [Multi-domain]  Cd Length: 93  Bit Score: 40.11  E-value: 3.70e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVT----EMNQRMLAGKPLYVALAQ 440
Cdd:cd12760   7 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKrSRGFGFVTFADPASVDKVLAqphhELDSKTIDPKVAFPRRAQ 86

                ....*..
gi 19114289 441 RKEVRRS 447
Cdd:cd12760  87 PKMVTRT 93
RRM_SCAF4 cd12461
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and ...
261-327 3.73e-04

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins; The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409894 [Multi-domain]  Cd Length: 81  Bit Score: 39.65  E-value: 3.73e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVkdqndKPRGFGFVNYANHECAQKAVDELNDKEYK 327
Cdd:cd12461   5 TTLWVGQLDKRTTQQDVASLLEEFGQIESINMI-----PPRGCAYIVMVHRQDAYRALQKLSRGNYK 66
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
263-330 3.75e-04

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 39.60  E-value: 3.75e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ---NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKK 330
Cdd:cd12372   1 LYVGNLQWWTTDEDLEGACASFGVVDVKEIKFFEhkaNGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRP 71
RRM1_hnRNPA2B1 cd12762
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP ...
82-149 3.76e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 410155 [Multi-domain]  Cd Length: 81  Bit Score: 39.65  E-value: 3.76e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTlIKGR 149
Cdd:cd12762   5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHS-IDGR 71
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
87-149 3.81e-04

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 39.32  E-value: 3.81e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  87 LDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGR 149
Cdd:cd12451  11 LGEDTIRDELREHFGECGEVTNVRIPTDRETGELKGFAYIEFSTKEAKEKAL-ELNGSDIAGG 72
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
265-322 3.83e-04

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 39.89  E-value: 3.83e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 265 IKNLDTEITEQEFSDLF---------GQFGEITSLSLVKDQND-------KPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12416   5 VRNLPKSVDDKKLKKLFlkavkerakKKGVKIKEVKVMRDKKRlnsdgkgRSKGYGFVEFTEHEHALKALRALN 78
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
82-153 3.85e-04

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 39.20  E-value: 3.85e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12332   4 LFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGK------GFGFIRLDTRANAEAAKAELDGTPRKGRQLRV 69
RRM_RALYL cd12605
RNA recognition motif (RRM) found in vertebrate RNA-binding Raly-like protein (RALYL); This ...
366-434 3.95e-04

RNA recognition motif (RRM) found in vertebrate RNA-binding Raly-like protein (RALYL); This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain.


Pssm-ID: 410017 [Multi-domain]  Cd Length: 69  Bit Score: 39.25  E-value: 3.95e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDE-VDDERLKAEFSAFGTITSAKImtdeqgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12605   4 VFIGNLNTAiVKKADIEAIFAKYGKIVGCSV-------HKGYAFVQYMSERHARAAVAGENARIIAGQPL 66
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
82-142 3.97e-04

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 39.62  E-value: 3.97e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd21607   5 IYCSNLPLSTAESDLYDLFETIGKVNNAELKYDE-TGDPTGSAVVEYENLDDADVCISKLN 64
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
172-228 4.09e-04

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 39.14  E-value: 4.09e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHV 228
Cdd:cd12320   5 VKNVPFEATRKEIRELFSPFGQLKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61
RRM3_RBM46 cd12496
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 46 (RBM46); This ...
366-440 4.13e-04

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409919 [Multi-domain]  Cd Length: 74  Bit Score: 39.22  E-value: 4.13e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAF--GTITSAKIMTDeqgkskgFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12496   4 LYVRNLMISTTEETIKAEFNKFkpGVVERVKKLRD-------YAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAK 73
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
170-261 4.18e-04

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 39.70  E-value: 4.18e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAID----NKALHDTFSAFGKILSCKVAVDELGnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVyvghhvs 245
Cdd:cd12453   5 LFVASLSSARSdeelCAAVTNHFSKWGELLNVKVLKDWSN--RPYAFVQYTNTEDAKNALVNGHNTLLDGRHL------- 75
                        90
                ....*....|....*.
gi 19114289 246 rrerqsKVEALKANFT 261
Cdd:cd12453  76 ------RVEKAKVNRT 85
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
82-157 4.18e-04

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 39.20  E-value: 4.18e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavtrrslgYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12495   4 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAK 71
RRM1_hnRNPD cd12756
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) ...
366-432 4.45e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically.


Pssm-ID: 410150 [Multi-domain]  Cd Length: 74  Bit Score: 39.21  E-value: 4.45e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKaVTEMNQRMLAGK 432
Cdd:cd12756   1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPiTGRSRGFGFVLFKESESVDK-VMDQKEHKLNGK 67
RRM1_hnRNPM cd12657
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
367-436 4.52e-04

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410058 [Multi-domain]  Cd Length: 76  Bit Score: 39.10  E-value: 4.52e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 367 FIKNLQDEVDDERLKAEF-SAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12657   3 FISNIPFDVKWQTLKDLVkEKVGEVTYVELLMDAEGKSRGCAVVEFKTEESMKKAVEVLNKHSFNGRPLKV 73
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
184-240 4.57e-04

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 39.23  E-value: 4.57e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 184 LHDTFSAFGKILscKVAVDelgNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12305  19 LKKAFSPFGNII--NISME---IEKNCAFVTFEKMESADQAIAELNGTTVEGVQLKV 70
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
82-157 4.62e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 39.10  E-value: 4.62e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSlGYAYVNFHNMEDG-EKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12226   2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDR-GFAYIDLRTSEAAlQKCLSTLNGVKWKGSRLKIQLAK 77
RRM2_HuC cd12776
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup ...
262-328 4.64e-04

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 241220 [Multi-domain]  Cd Length: 81  Bit Score: 39.21  E-value: 4.64e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGE-ITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKG 328
Cdd:cd12776   3 NLYVSGLPKTMSQKEMEQLFSQYGRiITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLG 70
RRM1_FCA cd12633
RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar ...
263-324 4.68e-04

RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 241077 [Multi-domain]  Cd Length: 80  Bit Score: 39.18  E-value: 4.68e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDK 324
Cdd:cd12633   2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKrTGHQQGCCFVKYSTRDEADRAIRALHNQ 64
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
263-333 4.77e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 241042 [Multi-domain]  Cd Length: 72  Bit Score: 39.01  E-value: 4.77e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPrgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12598   2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVP--FAFVRFEDPRDAEDAVFGRNGYDFGQCRLRV 70
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
261-333 4.90e-04

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 39.41  E-value: 4.90e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFG-----EITSLSLVKDQNDKPRG-FGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd21620   2 RSLYVGNLPQTCQSEDLIILFEPYGnvcgaHIASRKKVKVSWVKPSKlFAFVEFETKEAATTAIVLLNGITYMGCQLKV 80
RRM2_Bruno_like cd12636
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar ...
170-229 5.11e-04

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 410044 [Multi-domain]  Cd Length: 81  Bit Score: 39.09  E-value: 5.11e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVN 229
Cdd:cd12636   4 LFVGMLSKKCNESDVRIMFSPYGSIEECTVLRDQNGKSRGCAFVTFTSRQCAVNAIKAMH 63
RRM1_hnRNPD_like cd12575
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
263-327 5.17e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409989 [Multi-domain]  Cd Length: 72  Bit Score: 39.08  E-value: 5.17e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDElndKEYK 327
Cdd:cd12575   1 MFIGGLSWDTSKKDLKDYFSKFGEVVDCTIKLDPVTgRSRGFGFVLFKDAESVDKVLDQ---KEHK 63
RRM2_DAZAP1 cd12327
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
362-440 5.27e-04

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409765 [Multi-domain]  Cd Length: 80  Bit Score: 39.02  E-value: 5.27e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 362 QGVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTpEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12327   1 KSKKVFVGGIPHNCGETELRDYFKRYGVVTEVVMMYDaEKQRSRGFGFITFED-EQSVDQAVNMHFHDIMGKKVEVKRAE 79
RRM3_ACF cd12498
RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
366-440 5.29e-04

RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409921 [Multi-domain]  Cd Length: 83  Bit Score: 39.13  E-value: 5.29e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAF--GTITSAKIMTDeqgkskgFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQ 440
Cdd:cd12498  11 LYVRNLMLSTTEETIEKEFSNIkpGAVERVKKIRD-------YAFVHFYNREDAVNAMNALNGKVIDGSPIEVTLAK 80
RRM1_hnRNPA2B1 cd12762
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP ...
366-422 5.30e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 410155 [Multi-domain]  Cd Length: 81  Bit Score: 39.26  E-value: 5.30e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVT 422
Cdd:cd12762   5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKrSRGFGFVTFSSMAEVDAAMA 62
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
90-150 5.41e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 38.70  E-value: 5.41e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  90 SVTEAMLFELFNSIGPVA-SIRVCRDAVTRRSlGYAYVNFHNMEDGEKALdELNYTLIKGRP 150
Cdd:cd12254  10 SATEEDIRDFFSGLDIPPdGIHIVYDDDGRPT-GEAYVEFASEEDAQRAL-RRHKGKMGGRY 69
RRM_SKAR cd12681
RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; ...
261-333 5.42e-04

RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410082 [Multi-domain]  Cd Length: 69  Bit Score: 38.79  E-value: 5.42e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12681   1 TRLTVSNLHPSVTEDDIVELFSVIGALKRARLVRP------GVAEVVYVRREDAITAIKKYNNRELDGQPMKC 67
RRM1_ACF cd12486
RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
363-425 5.56e-04

RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409912 [Multi-domain]  Cd Length: 78  Bit Score: 39.19  E-value: 5.56e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:cd12486   1 GCEIFIGKLPRDLFEDELVPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEARNAIKQLN 63
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
82-148 5.60e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 38.75  E-value: 5.60e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavtrrslgYAYVNFHNMEDGEKALDELNYTLIKG 148
Cdd:cd12343   2 IFVGNLPDAATSEELRALFEKYGKVTECDIVKN--------YAFVHMEKEEDAEDAIKALNGYEFMG 60
RRM2_hnRNPAB cd12584
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
82-153 5.67e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 409997 [Multi-domain]  Cd Length: 80  Bit Score: 39.16  E-value: 5.67e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNmEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12584   7 IFVGGLNPETTEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKE-EDPVKKILEKKFHNVSGSKCEI 77
RRM2_hnRPDL cd12585
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
366-432 5.70e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409998 [Multi-domain]  Cd Length: 75  Bit Score: 38.83  E-value: 5.70e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:cd12585   2 VFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKtNERRGFCFITYTDEEPVQKLLESRYHQIGSGK 69
RRM_NCBP2 cd12240
RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
263-322 5.72e-04

RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins; This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC.


Pssm-ID: 409686 [Multi-domain]  Cd Length: 78  Bit Score: 39.09  E-value: 5.72e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12240   1 LYVGNLSFYTTEEQIYELFSKCGDIKRIIMGLDKFKKtPCGFCFVEYYSREDAENAVKYLN 61
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
82-149 5.89e-04

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 38.71  E-value: 5.89e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12307   2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFEDPEVAKIVAETMNNYLLFER 69
RRM_SLT11 cd12265
RNA recognition motif (RRM) found in pre-mRNA-splicing factor SLT11 and similar proteins; This ...
171-234 6.02e-04

RNA recognition motif (RRM) found in pre-mRNA-splicing factor SLT11 and similar proteins; This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities.


Pssm-ID: 409709 [Multi-domain]  Cd Length: 86  Bit Score: 39.31  E-value: 6.02e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESANAAIEHVNGMLLN 234
Cdd:cd12265   6 FLFGIDDDLPEWKISDYFEQFGKLKSLVVSHR-----AKCGFVRFETRELAEAFAAAISENGLN 64
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
171-240 6.17e-04

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 38.82  E-value: 6.17e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12332   5 FVGNLPNDITEEEFKELFQKYGEVSEVFLNKG-----KGFGFIRLDTRANAEAAKAELDGTPRKGRQLRV 69
RRM_YRA1_MLO3 cd12267
RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA ...
84-149 6.34e-04

RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins; This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p.


Pssm-ID: 409711 [Multi-domain]  Cd Length: 78  Bit Score: 38.94  E-value: 6.34e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  84 VGELDPSVTEAMLFELFNS-IGPVASIRVCRDAvTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12267   5 VSNLPKDVTEAQIREYFVSqIGPIKRVLLSYNE-GGKSTGIANITFKRAGDATKAYDKFNGRLDDGN 70
RRM3_HuR cd12653
RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup ...
82-142 6.39e-04

RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410056 [Multi-domain]  Cd Length: 85  Bit Score: 39.27  E-value: 6.39e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12653   5 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLN 65
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
366-434 6.53e-04

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 39.07  E-value: 6.53e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12555  10 LFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMSGKVIGRNPI 78
RRM1_RBM4 cd12606
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
263-322 6.71e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410018 [Multi-domain]  Cd Length: 67  Bit Score: 38.64  E-value: 6.71e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkprgFGFVNYANHECAQKAVDELN 322
Cdd:cd12606   3 LFIGNLPREATEEEIRSLFEQYGKVTECDIIKN-------YGFVHMEDKSAADEAIRNLH 55
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
170-229 6.81e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 38.51  E-value: 6.81e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVN 229
Cdd:cd12384   3 IFVGGLPYHTTDDSLREYFEQFGEIEEAVVITDrQTGKSRGYGFVTMADREAAERACKDPN 63
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
265-334 7.01e-04

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 38.70  E-value: 7.01e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVkdqndKPRGFGFVNYANHECAQKAVDELND-KEYKGKKLYVG 334
Cdd:cd12247   7 LQNLPEETTKEMLEMLFNQFPGFKEVRLV-----PRRGIAFVEFETEEQATVALQALQGfKITPGHAMKIS 72
RRM_ARP_like cd12452
RNA recognition motif (RRM) found in yeast asparagine-rich protein (ARP) and similar proteins; ...
263-318 7.03e-04

RNA recognition motif (RRM) found in yeast asparagine-rich protein (ARP) and similar proteins; This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response.


Pssm-ID: 409886 [Multi-domain]  Cd Length: 83  Bit Score: 39.04  E-value: 7.03e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFG--EITSLSLVKDQNDKPRGFGFVNYANHECAQKAV 318
Cdd:cd12452   3 LYMNGLPHDTTQSELESWFTQHGvrPVAFWTLKTPEQIKPSGSGFAVFQSHEEAAESL 60
RRM_U2AF35 cd12538
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
93-150 7.14e-04

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.


Pssm-ID: 409954 [Multi-domain]  Cd Length: 104  Bit Score: 39.27  E-value: 7.14e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  93 EAMLFELFNSIGPVASIRVCrDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12538  41 EDVFVELEEKYGEIEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVNDLNNRWFNGQP 97
RRM3_MYEF2 cd12662
RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This ...
263-333 7.23e-04

RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410063 [Multi-domain]  Cd Length: 77  Bit Score: 38.80  E-value: 7.23e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITsLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12662   2 IFVRNLPFDLTWQKLKEKFSQCGHVM-FAEIKMENGKSKGCGTVRFDSPESAEKACRLMNGIKISGREIDV 71
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
96-153 7.43e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 38.67  E-value: 7.43e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  96 LFELFNSIGPVASIRVCRdavTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12246  20 LYALFSQFGPVLDIVASK---SLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRI 74
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
82-137 7.61e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 38.57  E-value: 7.61e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKA 137
Cdd:cd12578   2 LFIGGLSYETTDDSLRNHFEQWGEITDVVVMKDPATKRSRGFGFVTYSSASEVDAA 57
RRM2_hnRNPA3 cd12582
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) ...
366-423 7.87e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409996 [Multi-domain]  Cd Length: 80  Bit Score: 38.78  E-value: 7.87e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTE 423
Cdd:cd12582   3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQsGKKRGFAFVTFDDHDTVDKIVVQ 61
RRM2_HuR cd12773
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup ...
262-322 7.92e-04

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410166 [Multi-domain]  Cd Length: 84  Bit Score: 38.74  E-value: 7.92e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGE-ITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12773   2 NLYISGLPRTMTQKDVEDMFSRFGRiINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITNFN 63
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
170-240 7.99e-04

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 38.45  E-value: 7.99e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDEL---GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12372   1 LYVGNLQWWTTDEDLEGACASFGVVDVKEIKFFEHkanGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRPCVV 74
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
268-334 8.25e-04

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 38.71  E-value: 8.25e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 268 LDTEITEQEFSDLFGQFGEITSLSLVKDqndKPrgFGFVNYANHECAQKAVDELNDKEY----KGKKLYVG 334
Cdd:cd12431  11 LGNGVSREQLLEVFEKYGTVEDIVMLPG---KP--YSFVSFKSVEEAAKAYNALNGKELelpqQNVPLYLS 76
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
96-156 8.26e-04

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 38.62  E-value: 8.26e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  96 LFELFNSIGPVASIRVCRDAVTRRSlGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12675  18 LKKLFGRYGKVVEATIPRKKGGKLS-GFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWA 77
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
365-434 8.29e-04

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.


Pssm-ID: 409727 [Multi-domain]  Cd Length: 85  Bit Score: 38.68  E-value: 8.29e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEVdderlKAEFSAFGTITSAKIMTDEqgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12285  18 DNWDDEIKEDV-----IEECSKYGPVLHIYVDKNS---PQGNVYVKFKTIEAAQKCVQAMNGRWFDGRQI 79
RRM1_FCA cd12633
RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar ...
366-431 8.35e-04

RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 241077 [Multi-domain]  Cd Length: 80  Bit Score: 38.79  E-value: 8.35e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEM-NQRMLAG 431
Cdd:cd12633   2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRtGHQQGCCFVKYSTRDEADRAIRALhNQRTLPG 69
RRM1_RBMS3 cd12472
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, ...
365-424 8.73e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3); This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines.


Pssm-ID: 409902 [Multi-domain]  Cd Length: 80  Bit Score: 38.64  E-value: 8.73e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEM 424
Cdd:cd12472   6 NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNtNQCKGYGFVDFDSPAAAQKAVASL 66
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
82-150 9.11e-04

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 38.51  E-value: 9.11e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRV--CRDAVTRRslgYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12297   3 LWVTNFPPSYDERSIRDLFGDYGVILSVRLpsLRYNTSRR---FCYIDFTSPESARAAVELLNGLLEEGYT 70
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
366-439 9.42e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 38.12  E-value: 9.42e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTpEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12329   2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKtNKRRGFCFITFDS-EEPVKKILETQFHVIGGKKVEVKKA 75
RRM2_hnRNPA1 cd12580
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) ...
366-423 9.54e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.


Pssm-ID: 409994 [Multi-domain]  Cd Length: 77  Bit Score: 38.41  E-value: 9.54e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTE 423
Cdd:cd12580   3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRgSGKKRGFAFVTFDDHDSVDKIVIQ 61
RRM2_SRSF1_4_like cd12339
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and ...
397-432 9.69e-04

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins; This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409776 [Multi-domain]  Cd Length: 70  Bit Score: 37.96  E-value: 9.69e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 19114289 397 TDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGK 432
Cdd:cd12339  30 ADVHRDREGEGVVEFTSEEDMKRAIEKLDGTEFNGR 65
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
172-240 9.86e-04

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410019 [Multi-domain]  Cd Length: 67  Bit Score: 38.02  E-value: 9.86e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDelgnakgYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12607   5 VGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAMEAIRGLDNTEFQGKRMHV 66
RRM1_SRSF1 cd12597
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
259-333 9.87e-04

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 410010 [Multi-domain]  Cd Length: 79  Bit Score: 38.29  E-value: 9.87e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 259 NFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPrgFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12597   3 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 75
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
82-153 1.01e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 38.28  E-value: 1.01e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12579   2 LFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKDTGKKRGFGFVYFEDHDSADKAA-VVKFHSINGHRVEV 72
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
265-336 1.01e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions.


Pssm-ID: 409684 [Multi-domain]  Cd Length: 73  Bit Score: 38.00  E-value: 1.01e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGeITSLSLVKDQNdKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12238   4 VRHLPPELSEDDKEDLLKHFG-ATSVRVMKRRG-KLKHTAFATFDNEQAASKALSRLHQLKILGKRLVVEYA 73
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
79-156 1.02e-03

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 38.03  E-value: 1.02e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVASIRvcrDAVTRRslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12524   1 SRTLFVRNINSSVEDEELRALFEQFGEIRTLY---TACKHR--GFIMVSYYDIRAAQSAKRALQGTELGGRKLDIHFS 73
RRM2_HuD cd12774
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup ...
80-142 1.02e-03

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410167 [Multi-domain]  Cd Length: 84  Bit Score: 38.55  E-value: 1.02e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12774   6 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 68
RRM3_TIA1 cd12621
RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
81-157 1.03e-03

RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410032 [Multi-domain]  Cd Length: 72  Bit Score: 38.12  E-value: 1.03e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12621   2 TVYCGGVTSGLTEQLMRQTFSPFGQIMEIRVFPDK------GYSFVRFNSHESAAHAIVSVNGTTIEGHVVKCYWGK 72
RRM3_TIA1 cd12621
RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
263-335 1.03e-03

RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410032 [Multi-domain]  Cd Length: 72  Bit Score: 38.12  E-value: 1.03e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGK--KLYVGR 335
Cdd:cd12621   3 VYCGGVTSGLTEQLMRQTFSPFGQIMEIRVFPD-----KGYSFVRFNSHESAAHAIVSVNGTTIEGHvvKCYWGK 72
RRM1_hnRNPA2B1 cd12762
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP ...
260-309 1.03e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 410155 [Multi-domain]  Cd Length: 81  Bit Score: 38.49  E-value: 1.03e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 19114289 260 FTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYA 309
Cdd:cd12762   2 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPaSKRSRGFGFVTFS 52
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
82-153 1.03e-03

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 38.07  E-value: 1.03e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12330   2 IFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDHDTGRSRGFGFVTFDSESAVEKVL-SKGFHELGGKKVEV 72
RRM2_HuB cd12775
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup ...
80-142 1.03e-03

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410168 [Multi-domain]  Cd Length: 84  Bit Score: 38.55  E-value: 1.03e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12775   6 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN 68
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
82-157 1.05e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 38.09  E-value: 1.05e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDavtrrslgYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12494   4 LFVRNLATTVTEEILEKTFSQFGKLERVKKLKD--------YAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVLAK 71
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast ...
170-241 1.07e-03

RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 410025 [Multi-domain]  Cd Length: 80  Bit Score: 38.26  E-value: 1.07e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 170 VFIKNLDPAIDNKALHDTF-SAFGKILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241
Cdd:cd12613   4 IFVGDLSPTTNESDLVSLFqSRFPSCKSAKIMTDPVtGVSRGYGFVRFSDENDQQRALIEMQGKYCQGRPLRIS 77
RRM_PPARGC1A_like cd12357
RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma ...
366-422 1.07e-03

RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators; This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing.


Pssm-ID: 409793 [Multi-domain]  Cd Length: 91  Bit Score: 38.56  E-value: 1.07e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSkgFGFVCYTTPEEANKAVT 422
Cdd:cd12357   5 VYVGKLEQDTTRSELRRRFEVFGEIEECTVHFRERGDK--YGFVTYRYSEDAFLALE 59
RRM1_hnRNPAB cd12757
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
263-327 1.08e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 410151 [Multi-domain]  Cd Length: 80  Bit Score: 38.42  E-value: 1.08e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVDElndKEYK 327
Cdd:cd12757   7 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTgRSRGFGFILFKDAASVDKVLEQ---KEHR 69
RRM2_hnRNPA1 cd12580
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) ...
263-318 1.08e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.


Pssm-ID: 409994 [Multi-domain]  Cd Length: 77  Bit Score: 38.02  E-value: 1.08e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAV 318
Cdd:cd12580   3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRgSGKKRGFAFVTFDDHDSVDKIV 59
RRM1_MSSP2 cd12471
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; ...
78-161 1.10e-03

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2; This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409901 [Multi-domain]  Cd Length: 84  Bit Score: 38.57  E-value: 1.10e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRpcriMWSQ 157
Cdd:cd12471   4 SKTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ----MAKQ 79

                ....
gi 19114289 158 RDPS 161
Cdd:cd12471  80 QEQD 83
RRM1_hnRNPR cd12482
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
82-149 1.12e-03

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains.


Pssm-ID: 409909 [Multi-domain]  Cd Length: 79  Bit Score: 38.03  E-value: 1.12e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDEL-NYTLIKGR 149
Cdd:cd12482   4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCNKEAAQEAVKLCdNYEIRPGK 72
RRM_SRSF12 cd12560
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and ...
261-337 1.13e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins; This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409976 [Multi-domain]  Cd Length: 84  Bit Score: 38.44  E-value: 1.13e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12560   1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYIPLDfYNRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQ 78
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
427-567 1.14e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 42.01  E-value: 1.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  427 RMLAGKPLYVALAQRKEVRRSQLEAQIQARNQFRLQQQVAAAAGIPAVQYGATGPLIYGPGGYPIPAAVNGRGMPMVPGH 506
Cdd:PRK14951 360 RLLAFKPAAAAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPA 439
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  507 NGPMPMYPGMPTQFPAGGPAPGYPGMNARGPVPAQGRPMmmpgsvPSAGPAEAEAVPAVPG 567
Cdd:PRK14951 440 AAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPA------PAAAPAAARLTPTEEG 494
RRM1_Mug28 cd21620
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated ...
170-232 1.15e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410199 [Multi-domain]  Cd Length: 84  Bit Score: 38.26  E-value: 1.15e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVA-VDELGNA-----KGYGFVHFDSVESANAAIEHVNGML 232
Cdd:cd21620   4 LYVGNLPQTCQSEDLIILFEPYGNVCGAHIAsRKKVKVSwvkpsKLFAFVEFETKEAATTAIVLLNGIT 72
RRM1_U1A cd12477
RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); ...
170-236 1.17e-03

RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409906 [Multi-domain]  Cd Length: 89  Bit Score: 38.42  E-value: 1.17e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDN----KALHDTFSAFGKILSckVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDK 236
Cdd:cd12477   6 IYINNLNEKIKKdelkKSLHAIFSRFGQILD--ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 74
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
366-436 1.17e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions.


Pssm-ID: 409684 [Multi-domain]  Cd Length: 73  Bit Score: 38.00  E-value: 1.17e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGtITSAKIMTDeQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12238   2 LLVRHLPPELSEDDKEDLLKHFG-ATSVRVMKR-RGKLKHTAFATFDNEQAASKALSRLHQLKILGKRLVV 70
RRM_SARFH cd12534
RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and ...
366-439 1.21e-03

RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and similar proteins; This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240978 [Multi-domain]  Cd Length: 83  Bit Score: 38.17  E-value: 1.21e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAK--------IMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12534   1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKktgkpkiwLYKDkDTGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKV 80

                ...
gi 19114289 437 ALA 439
Cdd:cd12534  81 SLA 83
RRM1_hnRNPA_like cd12578
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
170-224 1.26e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409992 [Multi-domain]  Cd Length: 78  Bit Score: 38.19  E-value: 1.26e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAA 224
Cdd:cd12578   2 LFIGGLSYETTDDSLRNHFEQWGEITDVVVMKDPATKrSRGFGFVTYSSASEVDAA 57
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
261-337 1.28e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 38.12  E-value: 1.28e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12312   1 TSLFVRNVADDTRPDDLRREFGRYGPIVDVYIPLDfYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQFAQ 78
RRM1_MSI1 cd12759
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 1 (Musashi-1) and ...
82-145 1.31e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins; This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 241203 [Multi-domain]  Cd Length: 77  Bit Score: 38.06  E-value: 1.31e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTL 145
Cdd:cd12759   3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 66
RRM2_p54nrb_like cd12333
RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
265-324 1.35e-03

RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409770 [Multi-domain]  Cd Length: 80  Bit Score: 38.07  E-value: 1.35e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDK 324
Cdd:cd12333   4 VKNLSPYVSNELLEQAFSQFGDVERAVVIVDDRGRSTGEGIVEFSRKPGAQAALKRCSEG 63
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
82-142 1.42e-03

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 38.13  E-value: 1.42e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12637   2 LFVGSLPKTATEQEVRDLFEAYGEVEEVYLMKDPVTQQGTGCAFVKFAYKEEALAAIRSLN 62
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
91-142 1.43e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 37.97  E-value: 1.43e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 19114289  91 VTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12415  12 TTEEDLKEFFSKFGEVKYARIVLDKDTGHSKGTAFVQFKTKESADKCIEAAN 63
RRM_II_PABPN1L cd12551
RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2) ...
81-154 1.44e-03

RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2); This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain.


Pssm-ID: 409967 [Multi-domain]  Cd Length: 77  Bit Score: 37.89  E-value: 1.44e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRIM 154
Cdd:cd12551   1 SVYVGNVDYGSTADELEAHFNGCGPINRVTILCDKFSGHPKGYAYIEFATRSSVQAAV-ALDESSFRGRVIKVL 73
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
365-434 1.45e-03

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 37.76  E-value: 1.45e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMtdeqgKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12262   5 NVYVGNLDDSLTEEEIRGILEKYGEIESIKIL-----KEKNCAFVNYLNIANAIKAVQELPIKNPKFKKV 69
RRM2_p54nrb cd12591
RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
265-326 1.48e-03

RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410004 [Multi-domain]  Cd Length: 80  Bit Score: 37.97  E-value: 1.48e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEY 326
Cdd:cd12591   4 VKNLPQFVSNELLEEAFSVFGQVERAVVIVDDRGRPTGKGIVEFSGKPAARKALDRCSDGAF 65
RRM1_NGR1_NAM8_like cd12611
RNA recognition motif 1 (RRM1) found in yeast negative growth regulatory protein NGR1, yeast ...
82-158 1.51e-03

RNA recognition motif 1 (RRM1) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM1 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 410023 [Multi-domain]  Cd Length: 84  Bit Score: 37.84  E-value: 1.51e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIG--PVaSIRVCRDAVT--RRSLGYAYVNFHNMEDGEKALdELNYTLIKG---RPCRIM 154
Cdd:cd12611   2 LWMGDLEPWMDENFIKQIWASLGlkPV-NVKVIRSKSGglNGNAGYCFVEFPSPHAAQNAL-SLNGTPIPGsesRTFKLN 79

                ....
gi 19114289 155 WSQR 158
Cdd:cd12611  80 WASG 83
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
366-433 1.58e-03

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 37.67  E-value: 1.58e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFG-TITSAKIMTDEQ-GKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKP 433
Cdd:cd12344   2 LWMGDLEPWMDEAYISSCFAKTGeEVVSVKIIRNKQtGKSAGYCFVEFATQEAAEQALEHLNGKPIPNTQ 71
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
160-242 1.64e-03

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 37.97  E-value: 1.64e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 160 PSLRKMGTGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVY 239
Cdd:cd12556   1 PEDDQRATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMSGRVIGRNPIK 80

                ...
gi 19114289 240 VGH 242
Cdd:cd12556  81 IGY 83
RRM1_hnRNPA1 cd12761
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) ...
263-319 1.66e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.


Pssm-ID: 410154 [Multi-domain]  Cd Length: 81  Bit Score: 37.73  E-value: 1.66e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAVD 319
Cdd:cd12761   5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKrSRGFGFVTYATVEEVDAAMN 62
RRM_PRC cd12624
RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma ...
170-226 1.69e-03

RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins; This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410035 [Multi-domain]  Cd Length: 91  Bit Score: 37.87  E-value: 1.69e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNakGYGFVHFDSVESANAAIE 226
Cdd:cd12624   5 VYIGKIRGRMTRSELKDRFSVFGEIEECTIHFREEGD--NYGFVTYRYTEDAFAAIE 59
RRM_RALY cd12604
RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly; This subgroup ...
261-336 1.69e-03

RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly; This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch.


Pssm-ID: 410016 [Multi-domain]  Cd Length: 76  Bit Score: 37.70  E-value: 1.69e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQ-EFSDLFGQFGEITSLSLVKdqndkprGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12604   2 SRVFIGNLNTAVVKKsDVETIFSKYGRVVGCSVHK-------GYAFVQYTNERHARAAVIGENGRVLAGQTLDINMA 71
RRM1_hnRNPA0 cd12326
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
263-318 1.72e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409764 [Multi-domain]  Cd Length: 79  Bit Score: 37.59  E-value: 1.72e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDK-PRGFGFVNYANHECAQKAV 318
Cdd:cd12326   5 LFIGGLNVQTTEEGLRAHFEAYGQLTDCVVVVNPQTKrSRCFGFVTYSSAEEADAAM 61
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
167-241 1.79e-03

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 37.78  E-value: 1.79e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 167 TGNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFdsVESANAaiehVNGMLLNDKKVYVG 241
Cdd:cd12566   2 TGRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDkKTKKSKGFAYVLF--LDPEDA----VQAYNELDGKVFQG 71
RRM_RBM44 cd12248
RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; ...
82-153 1.80e-03

RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells.


Pssm-ID: 409694 [Multi-domain]  Cd Length: 77  Bit Score: 37.59  E-value: 1.80e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  82 LYVGELDPSVTEA---MLFELFNsigpVASIRVCRDAVTRRslgYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12248   4 VHVGNLAPSVSEEdllMHFEKYH----VSKISIQKLSMNYR---YASLTFDDASDAQAAVKEMNGKDISGRKVKV 71
RRM1_hnRNPD cd12756
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) ...
263-327 1.81e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically.


Pssm-ID: 410150 [Multi-domain]  Cd Length: 74  Bit Score: 37.67  E-value: 1.81e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDElndKEYK 327
Cdd:cd12756   1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPiTGRSRGFGFVLFKESESVDKVMDQ---KEHK 63
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
171-230 1.85e-03

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 37.75  E-value: 1.85e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12637   3 FVGSLPKTATEQEVRDLFEAYGEVEEVYLMKDPVTQQgTGCAFVKFAYKEEALAAIRSLNG 63
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
175-230 1.88e-03

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 37.67  E-value: 1.88e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 175 LDPAIDNKALHDTFSAFG-KILSCKVAVDEL-GNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12344   7 LEPWMDEAYISSCFAKTGeEVVSVKIIRNKQtGKSAGYCFVEFATQEAAEQALEHLNG 64
RRM1_PSF cd12587
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB) ...
366-436 1.91e-03

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.


Pssm-ID: 410000 [Multi-domain]  Cd Length: 71  Bit Score: 37.15  E-value: 1.91e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKImtdeqGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12587   4 LFVGNLPADITEDEFKRLFAKYGEPGEVFI-----NKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRV 69
RRM1_TIA1 cd12615
RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
263-336 1.95e-03

RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410027 [Multi-domain]  Cd Length: 74  Bit Score: 37.32  E-value: 1.95e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ--NDKprgFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12615   2 LYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTagNDP---YCFVEFHEHRHAAAALAAMNGRKIMGKEVKVNWA 74
RRM_SLT11 cd12265
RNA recognition motif (RRM) found in pre-mRNA-splicing factor SLT11 and similar proteins; This ...
259-323 1.95e-03

RNA recognition motif (RRM) found in pre-mRNA-splicing factor SLT11 and similar proteins; This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities.


Pssm-ID: 409709 [Multi-domain]  Cd Length: 86  Bit Score: 37.77  E-value: 1.95e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 259 NFTNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQndkprGFGFVNYANHECAQKAVDELND 323
Cdd:cd12265   1 SIKSFFLFGIDDDLPEWKISDYFEQFGKLKSLVVSHRA-----KCGFVRFETRELAEAFAAAISE 60
RRM1_hnRNPA0 cd12326
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
170-226 1.99e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409764 [Multi-domain]  Cd Length: 79  Bit Score: 37.59  E-value: 1.99e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIE 226
Cdd:cd12326   5 LFIGGLNVQTTEEGLRAHFEAYGQLTDCVVVVNpQTKRSRCFGFVTYSSAEEADAAMA 62
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
267-333 2.10e-03

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 37.69  E-value: 2.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 267 NLDTeiTEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12237  13 SLQT--TEEKLKEVFSRYGDIRRLRLVRDiVTGFSKRYAFIEYKEERDALHAYRDAKKLVIDQYEIFV 78
RRM_RALY cd12604
RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly; This subgroup ...
366-439 2.16e-03

RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly; This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch.


Pssm-ID: 410016 [Multi-domain]  Cd Length: 76  Bit Score: 37.32  E-value: 2.16e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 366 LFIKNLQDE-VDDERLKAEFSAFGTITSAKImtdeqgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALA 439
Cdd:cd12604   4 VFIGNLNTAvVKKSDVETIFSKYGRVVGCSV-------HKGYAFVQYTNERHARAAVIGENGRVLAGQTLDINMA 71
RRM2_HuR cd12773
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup ...
365-439 2.17e-03

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410166 [Multi-domain]  Cd Length: 84  Bit Score: 37.58  E-value: 2.17e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDE-QGKSKGFGFVCYTTPEEANKAVTEMNQRMLAG--KPLYVALA 439
Cdd:cd12773   2 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQaTGLSRGVAFIRFDKRSEAEEAITNFNGHKPPGssEPITVKFA 79
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
93-149 2.18e-03

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 37.38  E-value: 2.18e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  93 EAMLFELFNSIGPVASIRVCRDavTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12407  14 DPDLRQMFGQFGTILDVEIIFN--ERGSKGFGFVTFANSADADRAREKLNGTVVEGR 68
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
82-149 2.27e-03

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 37.15  E-value: 2.27e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12552   2 IYVSHLPHGFHEKELKKYFAQFGDLKNVRLARSKKTGNSKHYGFLEFVNPEDAMIAQKSMNNYLLMGK 69
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
170-229 2.27e-03

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 37.31  E-value: 2.27e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSckVAVDEL---GNAKGYGFVHFDSVESANAAIEHVN 229
Cdd:cd12290   2 VYVELLPKNATHEWIEAVFSKYGEVVY--VSIPRYkstGDPKGFAFIEFETSESAQKAVKHFN 62
PRK13729 PRK13729
conjugal transfer pilus assembly protein TraB; Provisional
420-553 2.28e-03

conjugal transfer pilus assembly protein TraB; Provisional


Pssm-ID: 184281 [Multi-domain]  Cd Length: 475  Bit Score: 40.96  E-value: 2.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  420 AVTEMNQRMLAGKPLYVALAQRKEV---RRSQLEAQIQarnqfRLQQQVAAAAGipavQYGATGPLIYGPGGYPIPAAVN 496
Cdd:PRK13729  70 ATTEMQVTAAQMQKQYEEIRRELDVlnkQRGDDQRRIE-----KLGQDNAALAE----QVKALGANPVTATGEPVPQMPA 140
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  497 GRGMPMVPGHNGPMPMypGMPTQFPAGGPAPG--YPGMNARGPVPAQGRPMMMPGSVPS 553
Cdd:PRK13729 141 SPPGPEGEPQPGNTPV--SFPPQGSVAVPPPTafYPGNGVTPPPQVTYQSVPVPNRIQR 197
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
365-420 2.39e-03

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 37.21  E-value: 2.39e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKA 420
Cdd:cd12348   1 HLWVGNLPENVREEKIIEHFKRFGRVESVKILPKRGSEGGVAAFVDFVDIKSAQKA 56
RRM1_p54nrb cd12588
RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
366-436 2.48e-03

RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410001 [Multi-domain]  Cd Length: 71  Bit Score: 36.85  E-value: 2.48e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12588   4 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV 69
RRM1_RBM45 cd12366
RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
184-235 2.49e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409801 [Multi-domain]  Cd Length: 81  Bit Score: 37.30  E-value: 2.49e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 19114289 184 LHDTFSAFGKILSCKVAVDELGN-AKGYGFVHFDSVESANAAIEHVNGMLLND 235
Cdd:cd12366  19 LREAFSPFGEIQDIWVVKDKQTKeSKGIAYVKFAKSSQAARAMEEMHGKCLGD 71
PHA03247 PHA03247
large tegument protein UL36; Provisional
490-590 2.49e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.46  E-value: 2.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   490 PIPAAVNGRGMPMVPGHNG----PMPMYPGMPTQfPAGGPAPGYPGMNARGPVPAqGRPMMMPGSVPSAGPAEAEAVPAV 565
Cdd:PHA03247 2711 APHALVSATPLPPGPAAARqaspALPAAPAPPAV-PAGPATPGGPARPARPPTTA-GPPAPAPPAAPAAGPPRRLTRPAV 2788
                          90       100
                  ....*....|....*....|....*
gi 19114289   566 PGMPERFTAADLAAVPEESRKQVLG 590
Cdd:PHA03247 2789 ASLSESRESLPSPWDPADPPAAVLA 2813
RRM_SLTM cd12678
RNA recognition motif (RRM) found in Scaffold attachment factor (SAF)-like transcription ...
365-436 2.63e-03

RNA recognition motif (RRM) found in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins; This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines.


Pssm-ID: 410079 [Multi-domain]  Cd Length: 74  Bit Score: 36.99  E-value: 2.63e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGK-SKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12678   1 NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPgAKCYGIVTMSSSTEVARCISHLHRTELHGQQISV 73
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
82-138 2.66e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 37.04  E-value: 2.66e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKAL 138
Cdd:cd12576   2 MFIGGLSWQTTPEGLREYFSKFGEITECMVMRDPTTKRSRGFGFVTFSDPASVDKVL 58
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
263-333 2.66e-03

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 36.82  E-value: 2.66e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12400   3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDKkTGKSKGCAFVEFDNQKALQKAL-KLHHTSLGGRKINV 73
RRM4_RBM19_RRM3_MRD1 cd12317
RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
366-436 2.76e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 (RRM3) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409756 [Multi-domain]  Cd Length: 72  Bit Score: 36.85  E-value: 2.76e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITsAKIMTdeqgKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12317   3 ILVKNLPFGATEEELRELFEKFGTLG-RLLLP----PSRTIALVEFLEPQDARRAFKKLAYKRFKHVPLYL 68
RRM1_MSSP1 cd12470
RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; ...
78-160 2.78e-03

RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1; This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis.


Pssm-ID: 409900 [Multi-domain]  Cd Length: 86  Bit Score: 37.46  E-value: 2.78e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  78 TSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRimWSQ 157
Cdd:cd12470   6 SKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAK--QQE 83

                ...
gi 19114289 158 RDP 160
Cdd:cd12470  84 QDP 86
RRM1_RAVER cd12388
RNA recognition motif 1 (RRM1) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
263-333 2.84e-03

RNA recognition motif 1 (RRM1) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM1 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409822 [Multi-domain]  Cd Length: 70  Bit Score: 36.80  E-value: 2.84e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGeitslsLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12388   2 ILVRNLPNDITAQEVHDLLADYG------LKYCHVDKAKGTAFVTLLNGEQAGTAILKFHQSSYRDRQLSV 66
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
264-330 2.84e-03

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 37.00  E-value: 2.84e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSlVKDQNDKPRgFGFVNYANHECAQKAVDELnDKEYKGKK 330
Cdd:cd12350   6 FIGNLEKTTTYGDLRNIFERFGEIIDID-IKKQNGNPQ-YAFLQYCDIASVVKAIKKM-DGEYLGNN 69
RRM_U2AFBPL cd12540
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 ...
374-436 2.95e-03

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.


Pssm-ID: 409956 [Multi-domain]  Cd Length: 105  Bit Score: 37.63  E-value: 2.95e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 374 EVDDERLKA-----------EFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12540  28 EYSEEDLYSdflefyedvlpEFKKFGKVVQFKVCCNSEPHLRGNVYVQYQSEEEALKAFTSFNGRWYAGKQLQC 101
RRM2_MSI1 cd12572
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homolog 1 (Musashi-1) and ...
263-330 2.98e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins; This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409986 [Multi-domain]  Cd Length: 74  Bit Score: 36.94  E-value: 2.98e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQN-DKPRGFGFVNYANHECAQKAVD----ELNDKEYKGKK 330
Cdd:cd12572   2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTtNRHRGFGFVTFESEDIVEKVCEihfhEINNKMVECKK 74
RRM2_hnRPDL cd12585
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP ...
82-153 3.06e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 409998 [Multi-domain]  Cd Length: 75  Bit Score: 36.90  E-value: 3.06e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12585   2 VFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVQKLL-ESRYHQIGSGKCEI 72
RRM2_RAVER1 cd12665
RNA recognition motif 2 (RRM2) found found in vertebrate ribonucleoprotein PTB-binding 1 ...
172-240 3.15e-03

RNA recognition motif 2 (RRM2) found found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1); This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin.


Pssm-ID: 410066 [Multi-domain]  Cd Length: 77  Bit Score: 36.83  E-value: 3.15e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSCKVAVDE-LGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12665   4 IANLPPSYTQQQFEELVRPFGNLERCFLVYSEtTGHSKGYGFVEYMKKDSAARAKSDLLGKQLGTRTLYV 73
RRM2_HuR cd12773
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup ...
80-142 3.31e-03

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410166 [Multi-domain]  Cd Length: 84  Bit Score: 37.20  E-value: 3.31e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  80 ASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12773   1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITNFN 63
RRM2_RAVER2 cd12666
RNA recognition motif 2 (RRM2) found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2); ...
265-333 3.44e-03

RNA recognition motif 2 (RRM2) found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2); This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs.


Pssm-ID: 410067 [Multi-domain]  Cd Length: 77  Bit Score: 36.79  E-value: 3.44e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12666   4 ITNLPISFTLQEFEELVRAYGNIERCFLVYSEvTGHSKGYGFVEYMKKDSAAKARLELLGKQLGESSLFA 73
Cytadhesin_P30 pfam07271
Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 ...
413-569 3.48e-03

Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localized on the tip organelle. It is thought that it is important in cytadherence and virulence. The N-terminus contains two predicted transmembrane helices followed by a long region of a short 6 residue proline rich repeat.


Pssm-ID: 429374 [Multi-domain]  Cd Length: 275  Bit Score: 39.95  E-value: 3.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   413 TPEEANKAVTEMNQRMLAGKPLYValaQRKEVRRSQLEAQIQARNQFRLQQQVAAAAGIPavQYGATGPLIYGPGGYPIP 492
Cdd:pfam07271 128 TEQQNTAEPTQPAGVNVANQPQMG---INQPQINPQFGPNPQQRIGFPMQPNMGMRPGFN--QMPGMPPNQMRPGFNQMP 202
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114289   493 aavngrGMPMVPGHNGPMPMYPGMPTQFPAGGPAPGYPGMNARGP-VPAQGRPMMMPGSVPSAGPAeaeavPAVPGMP 569
Cdd:pfam07271 203 ------GMPPRPGFPNPMPNMQPRPGFRPQPGPMGNRPGGGFPHPgTPMGPNRMPNPGMNQRPGMA-----PPRPGFP 269
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
363-425 3.57e-03

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 40.37  E-value: 3.57e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289   363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMN 425
Cdd:TIGR01648  58 GCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120
RRM_U2AF35 cd12538
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
234-332 3.58e-03

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.


Pssm-ID: 409954 [Multi-domain]  Cd Length: 104  Bit Score: 37.34  E-value: 3.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 234 NDKKVYVGHHVSRRERQskveaLKANFTNVYiknldteitEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHEC 313
Cdd:cd12538  15 NTPQSADGLKVKVSDVE-----LQEHFDEFY---------EDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80
                        90
                ....*....|....*....
gi 19114289 314 AQKAVDELNDKEYKGKKLY 332
Cdd:cd12538  81 AEKAVNDLNNRWFNGQPIY 99
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
264-321 3.72e-03

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 36.83  E-value: 3.72e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 264 YIKNLDTEITEQEFSDLFGQFGEITSLSLVKdqndKPRG-FGFVNYANHECAQKAVDEL 321
Cdd:cd12245   6 FVANLGPNVSEQELRQLFSRQPGFRRLRMHN----KGGGpVCFVEFEDVPFATQALNHL 60
RRM_TDRD10 cd21617
RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar ...
82-149 3.75e-03

RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins; TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM).


Pssm-ID: 410196 [Multi-domain]  Cd Length: 69  Bit Score: 36.24  E-value: 3.75e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVcrdavtRRSLG-YAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd21617   2 VYVGNLPLDISEEEILQLFKAFNPVLVKKI------RSGFKcFAFVDLGSDENVKLAIQQLNGTLFGGR 64
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
82-153 3.78e-03

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 36.53  E-value: 3.78e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALdELNYTLIKGRPCRI 153
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDLMRFPDSGNFRGIAFITFKTEEAAKRAL-ALDGEMLGNRFLKV 71
RRM_II_PABPN1L cd12551
RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2) ...
262-333 3.84e-03

RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2); This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain.


Pssm-ID: 409967 [Multi-domain]  Cd Length: 77  Bit Score: 36.73  E-value: 3.84e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 262 NVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12551   1 SVYVGNVDYGSTADELEAHFNGCGPINRVTILCDKfSGHPKGYAYIEFATRSSVQAAV-ALDESSFRGRVIKV 72
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
273-333 3.85e-03

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 36.89  E-value: 3.85e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 273 TEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12642  17 TERDLREVFSRYGPLAGVNVVYDQrTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRV 78
RRM1_DAZAP1 cd12574
RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
170-215 3.85e-03

RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409988 [Multi-domain]  Cd Length: 82  Bit Score: 36.94  E-value: 3.85e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHF 215
Cdd:cd12574   2 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNqSRGFGFVKF 48
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
170-241 3.86e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 36.78  E-value: 3.86e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILscKVAVDELGnaKGY-GFVHFDSVESANAAIEhvngmLLNDKKVYVG 241
Cdd:cd12422   4 VTVTNLLYPVTVDVLHQVFSPYGAVE--KIVIFEKG--TGVqALVQFDSVESAEAAKK-----ALNGRNIYDG 67
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
384-437 3.88e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 36.43  E-value: 3.88e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 384 FSAFGTI-TSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVA 437
Cdd:cd12515  21 FYGYRVIpDSVSIRYNDDGQPTGDARVAFPSPREARRAVRELNNRPLGGRKVKLF 75
RRM4_SHARP cd12351
RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
368-436 3.93e-03

RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409787 [Multi-domain]  Cd Length: 77  Bit Score: 36.58  E-value: 3.93e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 368 IKNLQDEVDDERLKAEFSAFGTITsaKIMTDEQgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12351  12 LDGLSENVTEQYLTRHFCRYGPVV--KVVIDRQ---KGMALVLYDEVECAQAAVKETKGRKIGGRKIQV 75
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
263-333 3.93e-03

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 36.53  E-value: 3.93e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQND-KPRGFGFVNYANHECAQKAVdELNDKEYKGKKLYV 333
Cdd:cd12271   1 VYVGGIPYYSTEAEIRSYFSSCGEVRSVDLMRFPDSgNFRGIAFITFKTEEAAKRAL-ALDGEMLGNRFLKV 71
RRM2_hnRNPA3 cd12582
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) ...
269-318 3.97e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409996 [Multi-domain]  Cd Length: 80  Bit Score: 36.85  E-value: 3.97e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 19114289 269 DTEitEQEFSDLFGQFGEITSLSLVKD-QNDKPRGFGFVNYANHECAQKAV 318
Cdd:cd12582  11 DTE--EYHLRDYFEKYGKIETIEVMEDrQSGKKRGFAFVTFDDHDTVDKIV 59
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
170-221 4.04e-03

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 36.40  E-value: 4.04e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESA 221
Cdd:cd12226   2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDRGFAYIDLRTSEAA 53
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
263-333 4.12e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 36.43  E-value: 4.12e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEI-TSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12515   3 VKMRNLPFKATIEDILDFFYGYRVIpDSVSIRYNDDGQPTGDARVAFPSPREARRAVRELNNRPLGGRKVKL 74
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
280-340 4.19e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 36.79  E-value: 4.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 280 LFGQFG--EITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNdkeykGKKLyvgraQKKH 340
Cdd:cd12278  27 IFSKFGsgKIVGIYMPVDETGKTKGFAFVEYATPEEAKKAVKALN-----GYKL-----DKKH 79
RRM1_DND1 cd12487
RNA recognition motif 1 (RRM1) found in vertebrate dead end protein homolog 1 (DND1); This ...
363-436 4.20e-03

RNA recognition motif 1 (RRM1) found in vertebrate dead end protein homolog 1 (DND1); This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409913 [Multi-domain]  Cd Length: 78  Bit Score: 36.66  E-value: 4.20e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 363 GVNLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQ-RMLAGKPLYV 436
Cdd:cd12487   1 GSEVFIGKIPQDVYEDKLIPLFQSVGQLYEFRLMMTFSGLNRGFAYAKYASRRSAQAAITTLNGyELQKGCPITV 75
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
171-247 4.22e-03

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 36.20  E-value: 4.22e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGkiLSCKvavDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHVSRR 247
Cdd:cd12358   2 YIGNLSSDVNESDLRQLFEEHK--IPVS---SVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPKK 73
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
257-317 4.23e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 36.76  E-value: 4.23e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 257 KANFTnVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKA 317
Cdd:cd12555   5 RANRT-LFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRA 64
RRM_RBM44 cd12248
RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; ...
170-240 4.27e-03

RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins; This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells.


Pssm-ID: 409694 [Multi-domain]  Cd Length: 77  Bit Score: 36.43  E-value: 4.27e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKalhDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12248   4 VHVGNLAPSVSEE---DLLMHFEKYHVSKISIQKLSMNYRYASLTFDDASDAQAAVKEMNGKDISGRKVKV 71
RRM_7 pfam16367
RNA recognition motif;
170-254 4.32e-03

RNA recognition motif;


Pssm-ID: 465106 [Multi-domain]  Cd Length: 91  Bit Score: 36.96  E-value: 4.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   170 VFIKNLDPAIDNKALHDTFSAFGkilscKVAVD---------ELGNAKGYGFVHFDSVESANAaiehvngmLLNDKKVYV 240
Cdd:pfam16367   4 VFVGGLPWDITEAELTATFGRFG-----PLLVDwpgkpespsYFPDVKGYVFLVFEDEKSVQA--------LLDACTQED 70
                          90
                  ....*....|....*...
gi 19114289   241 GHHV----SRRERQSKVE 254
Cdd:pfam16367  71 GKYYlklsSPRMKDKPVQ 88
RRM_AtC3H46_like cd12458
RNA recognition motif (RRM) found in Arabidopsis thaliana zinc finger CCCH domain-containing ...
269-322 4.36e-03

RNA recognition motif (RRM) found in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins; This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity.


Pssm-ID: 409891 [Multi-domain]  Cd Length: 70  Bit Score: 36.31  E-value: 4.36e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 19114289 269 DTEITEQEFSDLFGQFGEITSLSLVKDQNdkpRGFGFVNYANHECAQKAVDELN 322
Cdd:cd12458   8 ESSFTEEDVSTYFSSFGPVQDVRIPYQQK---RMFGFVTFANAETVKTILAEGN 58
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
462-586 4.44e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.35  E-value: 4.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  462 QQQVAAAAGIPAVQYGATGPliyGPGGYPIPAAVNGRGMPMVPGHNGPMPMYPGMPTQFPAGGPAPgypgmnARGPVPAQ 541
Cdd:PRK07764 412 PAAAAPAAAAAPAPAAAPQP---APAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAP------EPTAAPAP 482
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 19114289  542 GRPMMMPGSVPSAGPAEAEAVPAVPG--MPERFTAADLAAVPEESRK 586
Cdd:PRK07764 483 APPAAPAPAAAPAAPAAPAAPAGADDaaTLRERWPEILAAVPKRSRK 529
Epiglycanin_TR pfam05647
Tandem-repeating region of mucin, epiglycanin-like; The unusual mucin, epiglycanin, is ...
20-79 4.48e-03

Tandem-repeating region of mucin, epiglycanin-like; The unusual mucin, epiglycanin, is membrane-bound at the C-terminus but has a long region of this tandem-repeat at the N-terminus. It was the first mucin identified to be associated with the malignant behaviour of carcinoma cells. Mouse Muc21/epiglycanin is thought to be a highly glycosylated molecule, which makes it likely that its function is dependent on its glycoforms. Cells expressing Muc21 are significantly less adherent to each other and to extracellular matrix components than control cells, and this loss of adhesion is mediated by the TR portion of Muc21. This family also now contains the repeat that was the C. elegans protein of unknown function (DUF801).


Pssm-ID: 461702 [Multi-domain]  Cd Length: 68  Bit Score: 36.15  E-value: 4.48e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289    20 TNNE-AVESSTKEESSNTPSTETQPEKKAEEPEAAAEPSESTSTPTNASSVATPSGTAPTS 79
Cdd:pfam05647   1 SSTEsSTTSSGASTTSNTGSSTTSGGTSTTSNTGSSTTSSGTSTATNTGSSETSSGSSTTS 61
RRM3_MRD1 cd12568
RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 ...
261-336 4.50e-03

RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241012 [Multi-domain]  Cd Length: 72  Bit Score: 36.21  E-value: 4.50e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLvkdqndKPRG-FGFVNYANHECAQKAVDELNDKEYKGKKLYVGRA 336
Cdd:cd12568   1 TTILVKNFPYGTTAEELRDLFEPHGKLTRVLM------PPAGtIAIVEFANPQQARLAFKALAYRRFKDSILYLEKG 71
RRM5_MRD1 cd12570
RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 ...
82-156 4.51e-03

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241014 [Multi-domain]  Cd Length: 76  Bit Score: 36.33  E-value: 4.51e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDaVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWS 156
Cdd:cd12570   3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKK-FDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQYA 76
RRM3_TIAR cd12620
RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup ...
81-157 4.52e-03

RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 241064 [Multi-domain]  Cd Length: 73  Bit Score: 36.15  E-value: 4.52e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  81 SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd12620   2 TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK 72
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
170-230 4.52e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 36.19  E-value: 4.52e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAkgYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12338   2 IYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRRRGPP--FAFVEFEDPRDAEDAIRGRDG 60
RRM1_NCL cd12403
RNA recognition motif 1 (RRM1) found in vertebrate nucleolin; This subfamily corresponds to ...
365-434 4.60e-03

RNA recognition motif 1 (RRM1) found in vertebrate nucleolin; This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409837 [Multi-domain]  Cd Length: 75  Bit Score: 36.24  E-value: 4.60e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 365 NLFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKSKGFGFVCYTTPEEANKAVtEMNQRMLAGKPL 434
Cdd:cd12403   2 SLFVGNLNSNKSFEELKTAISEFFAKKDLAVVDVRIGSSKKFGYVDFESAEDLEKAL-ELNGKKVLGNEI 70
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
263-538 4.68e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 39.80  E-value: 4.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDkprgfGFVNYANHECAQKAVDELNDKE--YKGKKLYVGRAQKkh 340
Cdd:TIGR01649   5 VHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQ-----ALVEFEDEESAKACVNFATSVPiyIRGQPAFFNYSTS-- 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   341 ereeelrKRYEQMKLEKMNKyQGVN----LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTdeqgKSKGF-GFVCYTTPE 415
Cdd:TIGR01649  78 -------QEIKRDGNSDFDS-AGPNkvlrVIVENPMYPITLDVLYQIFNPYGKVLRIVTFT----KNNVFqALVEFESVN 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289   416 EANKAVTEMN-QRMLAG---------KPLYVALAQRKEVRRSQLEAQIQARNQFRLQQQVAAAAGIPAVQYGAT-GPLIY 484
Cdd:TIGR01649 146 SAQHAKAALNgADIYNGcctlkieyaKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSyGHDGY 225
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289   485 G-PGGYPIPAAVNGRGMPMVPGHNGPMPMYpgmpTQFPAGGPAPGY-PGMNARGPV 538
Cdd:TIGR01649 226 SsHGGPLAPLAGGDRMGPPHGPPSRYRPAY----EAAPLAPAISSYgPAGGGPGSV 277
RRM2_SRSF4_like cd12600
RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
265-331 4.71e-03

RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 410012 [Multi-domain]  Cd Length: 72  Bit Score: 36.29  E-value: 4.71e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 265 IKNLDTEITEQEFSDLFGQFGEITslslVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKL 331
Cdd:cd12600   5 VENLSSRVSWQDLKDYMRQAGEVT----YADAHKQRKNEGVVEFASYSDMKNAIEKLDGTELNGRKI 67
RRM3_NCL cd12405
RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to ...
366-434 4.74e-03

RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409839 [Multi-domain]  Cd Length: 72  Bit Score: 36.39  E-value: 4.74e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKaefSAFGTITSAKImTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPL 434
Cdd:cd12405   4 LVVNNLSYSATEESLQ---SVFEKATSIRI-PQNNGRPKGYAFVEFESVEDAKEALESCNNTEIEGRSI 68
RRM3_TIAR cd12620
RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup ...
263-335 4.79e-03

RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 241064 [Multi-domain]  Cd Length: 73  Bit Score: 36.15  E-value: 4.79e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDqndkpRGFGFVNYANHECAQKAVDELNDKEYKGK--KLYVGR 335
Cdd:cd12620   3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHvvKCYWGK 72
RRM1_RBM34 cd12394
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
170-244 4.81e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409828 [Multi-domain]  Cd Length: 91  Bit Score: 36.80  E-value: 4.81e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKI--------------LSCKVAV------DELGNAKGYgfVHFDSVESANAAIEHvN 229
Cdd:cd12394   3 VFVGNLPVTVKKKALKKLFKEFGKIesvrfrsvavanpkLPKKVAVikkkfhPKRDSMNAY--VVFKEEESAQKALKL-N 79
                        90
                ....*....|....*
gi 19114289 230 GMLLNdkkvyvGHHV 244
Cdd:cd12394  80 GTEFE------GHHI 88
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
366-424 4.87e-03

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 36.25  E-value: 4.87e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTItsaKIMTDEQGKSKGFGFVCYTTPEEANKAVTEM 424
Cdd:cd12404   6 LFVKNLPYSTTQDELKEVFEDAVDI---RIPMGRDGRSKGIAYIEFKSEAEAEKALEEK 61
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
366-441 4.91e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 36.14  E-value: 4.91e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMtdeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVALAQR 441
Cdd:cd12337   2 VYIGRLPYRARERDVERFFRGYGRIRDINLK-------NGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
394-428 5.18e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 36.00  E-value: 5.18e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 19114289 394 KIMTDEQGKSKGFGFVCYTTPEEANKAVTEMNQRM 428
Cdd:cd12254  31 HIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKM 65
RRM2_MSI cd12323
RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, ...
170-238 5.19e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 240769 [Multi-domain]  Cd Length: 74  Bit Score: 36.26  E-value: 5.19e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNA-KGYGFVHFDSVESANAAIEhVNGMLLNDKKV 238
Cdd:cd12323   2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRhRGFGFVTFESEDVVDKVCE-IHFHEINNKMV 70
RRM3_RBM45 cd12368
RNA recognition motif 3 (RRM3) found in RNA-binding protein 45 (RBM45) and similar proteins; ...
82-142 5.24e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 45 (RBM45) and similar proteins; This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409803 [Multi-domain]  Cd Length: 75  Bit Score: 36.12  E-value: 5.24e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  82 LYVgELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELN 142
Cdd:cd12368   3 LFV-VVRKSVTQEQLHRLFDLIPGLEYCDLKRDPYTGKSKGFAYVTYNNPASAIYAKEKLN 62
RRM1_hnRNPQ cd12483
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
261-330 5.31e-03

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409910 [Multi-domain]  Cd Length: 84  Bit Score: 36.48  E-value: 5.31e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQ-NDKPRGFGFVNYANHECAQKAVDELNDKEYKGKK 330
Cdd:cd12483   6 TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPlTGLNRGYAFVTFCTKEAAQEAVKLCNNHEIRPGK 76
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
84-146 5.41e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 36.14  E-value: 5.41e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19114289  84 VGELDPSVTEAMLFELFNSIGPVASIRV--CRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLI 146
Cdd:cd12259   4 VTNVSPQATEEQMRTLFGFIGKIEELRLypSEDDLAPVLSKVCFVKYEDPEDVAVALHLTNTVFI 68
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
366-436 5.47e-03

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 36.54  E-value: 5.47e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12237   7 LFVGRLSLQTTEEKLKEVFSRYGDIRRLRLVRDiVTGFSKRYAFIEYKEERDALHAYRDAKKLVIDQYEIFV 78
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
497-567 5.56e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 39.72  E-value: 5.56e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289  497 GRGMPMVPGHNGPMPMYPGMPTqfPAGGPAPGYPgmnaRGPVPAQGRPMMMPGSVPSAGPAEAEAVPAVPG 567
Cdd:PRK14965 380 GAPAPPSAAWGAPTPAAPAAPP--PAAAPPVPPA----APARPAAARPAPAPAPPAAAAPPARSADPAAAA 444
RRM_PPARGC1A_like cd12357
RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma ...
263-323 5.60e-03

RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators; This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing.


Pssm-ID: 409793 [Multi-domain]  Cd Length: 91  Bit Score: 36.64  E-value: 5.60e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLS-LVKDQNDKprgFGFVNYANHECAQKAVDELND 323
Cdd:cd12357   5 VYVGKLEQDTTRSELRRRFEVFGEIEECTvHFRERGDK---YGFVTYRYSEDAFLALENGHD 63
RRM3_Spen cd12310
RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily ...
170-240 5.72e-03

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409750 [Multi-domain]  Cd Length: 72  Bit Score: 36.11  E-value: 5.72e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCkvavDELGNAKgYGFVHFDSVESANAAIEHVNGMLL--NDKKVYV 240
Cdd:cd12310   1 LWVGGLGPWTSLAELEREFDRFGAIRKI----DYRKGDD-YAYILYESLDAAQAAVRALRGFPLggPDRRLRV 68
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
72-153 5.79e-03

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 36.43  E-value: 5.79e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  72 PSGTAPTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrRSLG--YAYVNFHNMEDGEKALDELNYTLIKGR 149
Cdd:cd12556   1 PEDDQRATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKRPA---RGQGgaYAFLKFQNLDMAHRAKVAMSGRVIGRN 77

                ....
gi 19114289 150 PCRI 153
Cdd:cd12556  78 PIKI 81
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
366-436 5.91e-03

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 36.06  E-value: 5.91e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQgkSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12241   5 LYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTKE--TRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVV 73
RRM1_CELF1_2_Bruno cd12631
RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-1, CELF-2, ...
82-141 6.10e-03

RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 410040 [Multi-domain]  Cd Length: 84  Bit Score: 36.34  E-value: 6.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVT--RRSLGYAYVNFHNMEDGEKALDEL 141
Cdd:cd12631   4 MFVGQIPRSWSEKELRELFEQYGAVYQINVLRDRSQnpPQSKGCCFVTFYTRKAALEAQNAL 65
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
79-150 6.25e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 36.05  E-value: 6.25e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  79 SASLYVGELDPSVTEAMLFELFNSIGPVAS-------IRVCRdavTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRP 150
Cdd:cd12239   1 SNRLYVKNLSKRVSEKDLKYIFGRFVDSSSeeknmfdIRLMT---EGRMKGQAFITFPSEELAEKALNLTNGYVLHGKP 76
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
209-244 6.33e-03

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 36.10  E-value: 6.33e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 19114289 209 GYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGHHV 244
Cdd:cd12409  47 GIAYAEFSSVEEAEKVVKDLNGKVFKGRKLFVKLHV 82
RRM5_MRD1 cd12570
RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 ...
168-230 6.42e-03

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241014 [Multi-domain]  Cd Length: 76  Bit Score: 35.95  E-value: 6.42e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 168 GNVFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNG 230
Cdd:cd12570   1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKD 63
RRM1_DAZAP1 cd12574
RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
366-414 6.54e-03

RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409988 [Multi-domain]  Cd Length: 82  Bit Score: 36.17  E-value: 6.54e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQ-GKSKGFGFVCYTTP 414
Cdd:cd12574   2 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTtNQSRGFGFVKFKDP 51
RRM1_hnRNPQ cd12483
RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
82-147 6.78e-03

RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409910 [Multi-domain]  Cd Length: 84  Bit Score: 36.10  E-value: 6.78e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIK 147
Cdd:cd12483   8 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLCNNHEIR 73
RRM1_RBM47 cd12485
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47); This ...
82-154 6.83e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47); This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 240929 [Multi-domain]  Cd Length: 78  Bit Score: 36.10  E-value: 6.83e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDaVTRRSLGYAYVNFHNMEDGEKALDELNYTLIkgRPCRIM 154
Cdd:cd12485   4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVRELNNYEI--RPGRLL 73
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
170-240 7.00e-03

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 35.50  E-value: 7.00e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 170 VFIKNLDP-AIDNKALHDTFSAFGKILSCKVAvdelgnaKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYV 240
Cdd:cd12233   2 LFVVGFDPgTTREEDIEKLFEPFGPLVRCDIR-------KTFAFVEFEDSEDATKALEALHGSRIDGSVLTV 66
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
366-436 7.05e-03

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 35.67  E-value: 7.05e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDeqgksKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYV 436
Cdd:cd12586   4 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI 69
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
263-337 7.07e-03

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 36.23  E-value: 7.07e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289 263 VYIKNLDTEITEQEF----SDLFGQFGEITSLSLVKDQNDKPrgFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQ 337
Cdd:cd12453   5 LFVASLSSARSDEELcaavTNHFSKWGELLNVKVLKDWSNRP--YAFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKAK 81
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
90-158 7.21e-03

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 35.76  E-value: 7.21e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  90 SVTEAMLFELFNSIGPVASIRVCRDavtrRSLGYayVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQR 158
Cdd:cd12305  13 GITEDVLKKAFSPFGNIINISMEIE----KNCAF--VTFEKMESADQAIAELNGTTVEGVQLKVSIARR 75
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
171-238 7.25e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 35.89  E-value: 7.25e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 171 FIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGN-AKGYGFVHF---DSVESANAAIEHVngmlLNDKKV 238
Cdd:cd12576   3 FIGGLSWQTTPEGLREYFSKFGEITECMVMRDPTTKrSRGFGFVTFsdpASVDKVLAQGPHE----LDGKKI 70
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
82-138 7.45e-03

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 35.49  E-value: 7.45e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVcrdAVTRRSLGYAYVNFHNMEDGEKAL 138
Cdd:cd12599   2 VYVGNLPMDIREREVEDLFSKYGPVVSIDL---KIPPRPPAYAFVEFEDARDAEDAI 55
RRM2_hnRNPM cd12659
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
261-333 7.65e-03

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410060 [Multi-domain]  Cd Length: 76  Bit Score: 35.79  E-value: 7.65e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 261 TNVYIKNLDTEITEQEFSDLFGQFGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12659   1 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHV 73
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
80-158 7.76e-03

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 36.19  E-value: 7.76e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  80 ASLYVGELDPSV--TEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMWSQ 157
Cdd:cd21622   4 CNLFVKNLDDTVitNKEDLEQLFSPFGQIVSSYLATYPGTGISKGFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYAE 83

                .
gi 19114289 158 R 158
Cdd:cd21622  84 R 84
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
367-439 7.92e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 35.66  E-value: 7.92e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 19114289 367 FIKNLQDEVDDERLkAEFSAFGTITSAKIMTD-EQGKSKGFGFVCYTTPEEANKAVTeMNQRMLAGKPLYVALA 439
Cdd:cd12402   6 YLGNLPYDVTEDDI-EDFFRGLNISSVRLPREnGPGRLRGFGYVEFEDRESLIQALS-LNEESLKNRRIRVDVA 77
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
366-434 7.97e-03

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409733 [Multi-domain]  Cd Length: 73  Bit Score: 35.64  E-value: 7.97e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 366 LFIKNLQDEVDDERLKAEFSAFGTITSAKIMTDEQGKS-KGFGFVCYTTPEEANKAVtEMNQRMLAGKPL 434
Cdd:cd12291   2 VYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDSKEfKGSVFVEFKTEEEAKKFL-EKEKLKYKGKEL 70
RRM1_RBM34 cd12394
RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
82-149 7.99e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409828 [Multi-domain]  Cd Length: 91  Bit Score: 36.03  E-value: 7.99e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIR-----VCRDAVTRR---SLGY---------AYVNFHNMEDGEKALdELNYT 144
Cdd:cd12394   3 VFVGNLPVTVKKKALKKLFKEFGKIESVRfrsvaVANPKLPKKvavIKKKfhpkrdsmnAYVVFKEEESAQKAL-KLNGT 81

                ....*
gi 19114289 145 LIKGR 149
Cdd:cd12394  82 EFEGH 86
RRM1_PSP1 cd12586
RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup ...
82-153 8.17e-03

RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1); This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 409999 [Multi-domain]  Cd Length: 71  Bit Score: 35.67  E-value: 8.17e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAvtrrslGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12586   4 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAELDGTILKSRPLRI 69
RRM2_La_like cd12292
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ...
172-237 8.32e-03

RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409734 [Multi-domain]  Cd Length: 74  Bit Score: 35.37  E-value: 8.32e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289 172 IKNLDPAIDNKALHDTFSAFGKILSckvaVDELGNAKgYGFVHFDSVESANAAIEHVNGMLLNDKK 237
Cdd:cd12292   6 ITGIGPSVSRDDLKELFKQFGEVEY----VDFTPGDD-EGHVRFKTSEAAQKARDAYTGKLELNGK 66
RRM4_NCL cd12406
RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to ...
263-339 8.36e-03

RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409840 [Multi-domain]  Cd Length: 78  Bit Score: 35.66  E-value: 8.36e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 263 VYIKNLDTEITEQEFSDLFGqfGEITSLSLVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYVGRAQKK 339
Cdd:cd12406   3 LFVKGLSEDTTEETLKEAFE--GAISARIATDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKPK 77
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
79-153 8.81e-03

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 36.06  E-value: 8.81e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  79 SASLYVGELDPSVTEAMLF-ELFNSIGPVASIRV-CRDAVtrrSLGYAYVNFHNMEDGEKALDELNYTLIKGRPCRI 153
Cdd:cd12390   2 SKCLFVDRLPKDFRDGSELrKLFSQVGKPTFCQLaMGNGV---PRGFAFVEFASAEDAEEAQQLLNGHDLQGSPIRV 75
RRM_Set1 cd12304
RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This ...
368-438 8.86e-03

RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo.


Pssm-ID: 409745 [Multi-domain]  Cd Length: 93  Bit Score: 36.17  E-value: 8.86e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19114289 368 IKNLQDEVDDERLKAEFSAFGTITSAKIM-TDEQGKSKGFGFVCYTTPEEANKAVTEMNQRMLAGKPLYVAL 438
Cdd:cd12304   7 FANLNDNINEGFLKDMCKKYGEVEEVKIYfHPKTGKHLGLARVVFDTTKGAKDCVEKLNQTSVMGNIIHVFL 78
RRM3_hnRNPM cd12661
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
263-333 9.16e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410062 [Multi-domain]  Cd Length: 77  Bit Score: 35.62  E-value: 9.16e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114289 263 VYIKNLDTEITEQEFSDLFGQFGEITSLSlVKDQNDKPRGFGFVNYANHECAQKAVDELNDKEYKGKKLYV 333
Cdd:cd12661   2 IFVRNLPFDFTWKMLKDKFNECGHVLYAD-IKMENGKSKGCGVVRFESPEVAERACRMMNGIKLNGREIDV 71
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
82-140 9.18e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 35.42  E-value: 9.18e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 19114289  82 LYVGELDPSVTEAMLFELFNSIGPVASIRVcrdAVTRRSLGYAYVNFHNMEDGEKALDE 140
Cdd:cd12338   2 IYVGNLPGDIRERDIEDLFYKYGPILAIDL---KNRRRGPPFAFVEFEDPRDAEDAIRG 57
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
170-242 9.26e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 35.99  E-value: 9.26e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAFGKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12555  10 LFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMSGKVIGRNPIKIGY 82
RRM_SRSF3 cd12645
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); ...
77-153 9.42e-03

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 241089 [Multi-domain]  Cd Length: 81  Bit Score: 35.79  E-value: 9.42e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289  77 PTSASLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVtrrslGYAYVNFHNMEDGEKALDELNYTLIKGrpCRI 153
Cdd:cd12645   2 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRELDGRTLCG--CRV 71
RRM4_NCL cd12406
RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to ...
170-238 9.78e-03

RNA recognition motif 4 (RRM4) found in vertebrate nucleolin; This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409840 [Multi-domain]  Cd Length: 78  Bit Score: 35.66  E-value: 9.78e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114289 170 VFIKNLDPAIDNKALHDTFSAfgkILSCKVAVD-ELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKV 238
Cdd:cd12406   3 LFVKGLSEDTTEETLKEAFEG---AISARIATDrDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKV 69
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
81-155 9.98e-03

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 35.11  E-value: 9.98e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114289  81 SLYVGELDPSVTEAMLFE-LFNSIGPVASIRVCRDavtrrslgYAYVNFHNMEDGEKALDELNYTLIKGRPCRIMW 155
Cdd:cd12233   1 TLFVVGFDPGTTREEDIEkLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALHGSRIDGSVLTVEF 68
RRM1_SNF cd12476
RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF ...
170-242 1.00e-02

RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 409905 [Multi-domain]  Cd Length: 85  Bit Score: 35.66  E-value: 1.00e-02
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19114289 170 VFIKNLDPAIDN----KALHDTFSAFGKILSCkVAVDELgNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVGH 242
Cdd:cd12476   9 IYINNLNEKVKKeelkKSLYAIFSQFGQILDI-VALKTL-KMRGQAFVIFKDISSATNALRSMQGFPFYDKPMRIAY 83
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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