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Conserved domains on  [gi|564341264|ref|XP_006234384|]
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lupus La protein homolog isoform X3 [Rattus norvegicus]

Protein Classification

RNA-binding protein( domain architecture ID 10168935)

RNA-binding protein containing an RNA recognition motif (RRM) similar to Homo sapiens Lupus La protein which binds to the 3' poly(U) terminus of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 10-91 8.86e-45

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


:

Pssm-ID: 153397  Cd Length: 82  Bit Score: 149.76  E-value: 8.86e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  10 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKANLMEVSADKTKI 89
Cdd:cd08028    1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKI 80


                 ..
gi 564341264  90 RR 91
Cdd:cd08028   81 RR 82
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 112-183 7.15e-29

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: 107.29  E-value: 7.15e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564341264 112 SVYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLH-KTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLLIL 183
Cdd:cd12291    1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDsKEFKGSVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
RRM2_La cd12541
RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup ...
 230-306 1.37e-28

RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup corresponds to the RRM2 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). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


:

Pssm-ID: 409957 [Multi-domain]  Cd Length: 77  Bit Score: 106.97  E-value: 1.37e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564341264 230 GCLLKFSGDLDdQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKE--KAKDALEKARSANNGnLLLRNKKVTWKVLE 306
Cdd:cd12541    1 GCILHFSGVGE-QTSREDLKEAFEKHGEVAWIDFARGQTEGYVRFKEedAAKEALEKAKEAKNG-LKIRGKEVTVKLLE 77
 
Name Accession Description Interval E-value
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 10-91 8.86e-45

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


Pssm-ID: 153397  Cd Length: 82  Bit Score: 149.76  E-value: 8.86e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  10 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKANLMEVSADKTKI 89
Cdd:cd08028    1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKI 80


                 ..
gi 564341264  90 RR 91
Cdd:cd08028   81 RR 82
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
13-92 2.01e-32

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 116.95  E-value: 2.01e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264    13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKanLMEVSADKTKIRRS 92
Cdd:smart00715   3 LKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSP--KLEVSEDGLKVRRR 80
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 112-183 7.15e-29

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: 107.29  E-value: 7.15e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564341264 112 SVYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLH-KTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLLIL 183
Cdd:cd12291    1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDsKEFKGSVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
RRM2_La cd12541
RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup ...
 230-306 1.37e-28

RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup corresponds to the RRM2 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). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409957 [Multi-domain]  Cd Length: 77  Bit Score: 106.97  E-value: 1.37e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564341264 230 GCLLKFSGDLDdQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKE--KAKDALEKARSANNGnLLLRNKKVTWKVLE 306
Cdd:cd12541    1 GCILHFSGVGE-QTSREDLKEAFEKHGEVAWIDFARGQTEGYVRFKEedAAKEALEKAKEAKNG-LKIRGKEVTVKLLE 77
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
 230-333 3.47e-25

RNA binding motif; This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.


Pssm-ID: 400913 [Multi-domain]  Cd Length: 102  Bit Score: 98.59  E-value: 3.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  230 GCLLKFSGdLDDQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFK--EKAKDALEKARSANNgnlLLRNKKVTWKVLEG 307
Cdd:pfam08777   1 GVILKFSG-LGKPLSREDIKEAFSQLGEVAYVDYLEGDKEGHVRFKtdEAAKKAIEKATEAKT---IIKDAEVTAELLEG 76

                          90       100
                  ....*....|....*....|....*.
gi 564341264  308 HAEKDAMKKITDDQQESLNKWKSKGG 333
Cdd:pfam08777  77 EEEKEYWKKIIEDQQAKLNNPRNKGR 102
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 17-74 2.94e-24

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 94.41  E-value: 2.94e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 564341264   17 ICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLETMIKFNRLNRLTTDFNVIVQALSK 74
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 20-284 6.60e-15

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 75.85  E-value: 6.60e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  20 QIEYYFG-----DFNLPRDKFLKEQ---IKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKAN-LMEVSADKTKIR 90
Cdd:COG5193   78 QVEFYFSgskdtDSNFPKDKFLKTTapkNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDArVLEVSSSGSNKN 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  91 RSPSRPLpevTDEYKNDVKNRSVYIKGFPTDATLD--------DIKEWLDDKGQ--ILNIQMRRTLH-KTFKGSIFAVFD 159
Cdd:COG5193  158 RTEKLIS---NNNKSTSQMQRDVYQNGFGKEDVNNasrpeqqeDLEIQFPPHYHapPSQIRNRRDWLnKNFRGSVFVEFK 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264 160 SIQSAKKFVD--TPGQKYKDTNLLILFK--EDYF----AKKNEERKQSKVEAKLKAKQEHEGRHKPGSTEtRALEGKMGC 231
Cdd:COG5193  235 YFREAQRFNNgfYRNKKYPNDPETVYYYsvEPILlsimAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIP-LSFIGKFYR 313

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564341264 232 LLKFSGD--LDDQTCREDLHFLFSNHGEIkwidfVRGAKEGIILFKEKAKDALEK 284
Cdd:COG5193  314 NLSFGGDknLILAAMKEVVQNKATNHLEI-----ALGSIEDAQKNEAKDFSPGKK 363
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 113-181 4.17e-09

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: 52.62  E-value: 4.17e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  113 VYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLHKTFKGSIFAVFDSIQSAKKFVDT-PGQKYKDTNLL 181
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 103-367 2.94e-04

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: 42.87  E-value: 2.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  103 EYKNDVKNRSVYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLHKTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLL- 181
Cdd:TIGR01628 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEg 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  182 -ILFKEDyfAKKNEERkQSKVEAKLKAKQEHEGRHKPGSTetralegkmgCLLKfsgDLDDQTCREDLHFLFSNHGEIKW 260
Cdd:TIGR01628 251 kKLYVGR--AQKRAER-EAELRRKFEELQQERKMKAQGVN----------LYVK---NLDDTVTDEKLRELFSECGEITS 314

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  261 IDFVRGAKE-----GIILFKEkaKDALEKARSANNGNLLlrNKKVTWKVLeghAEKDAMKKITDDQQESLNKWKSKGGHA 335
Cdd:TIGR01628 315 AKVMLDEKGvsrgfGFVCFSN--PEEANRAVTEMHGRML--GGKPLYVAL---AQRKEQRRAHLQDQFMQLQPRMRQLPM 387

                         250       260       270
                  ....*....|....*....|....*....|..
gi 564341264  336 ARRFKgrGKGNRPAYAGaPKGRGQFQGRRTRF 367
Cdd:TIGR01628 388 GSPMG--GAMGQPPYYG-QGPQQQFNGQPLGW 416
 
Name Accession Description Interval E-value
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 10-91 8.86e-45

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


Pssm-ID: 153397  Cd Length: 82  Bit Score: 149.76  E-value: 8.86e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  10 MAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKANLMEVSADKTKI 89
Cdd:cd08028    1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKI 80


                 ..
gi 564341264  90 RR 91
Cdd:cd08028   81 RR 82
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
13-92 2.01e-32

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 116.95  E-value: 2.01e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264    13 LEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKanLMEVSADKTKIRRS 92
Cdd:smart00715   3 LKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSP--KLEVSEDGLKVRRR 80
RRM1_La cd12291
RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily ...
 112-183 7.15e-29

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: 107.29  E-value: 7.15e-29
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 564341264 112 SVYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLH-KTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLLIL 183
Cdd:cd12291    1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDsKEFKGSVFVEFKTEEEAKKFLEKEKLKYKGKELTIM 73
RRM2_La cd12541
RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup ...
 230-306 1.37e-28

RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins; This subgroup corresponds to the RRM2 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). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.


Pssm-ID: 409957 [Multi-domain]  Cd Length: 77  Bit Score: 106.97  E-value: 1.37e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564341264 230 GCLLKFSGDLDdQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKE--KAKDALEKARSANNGnLLLRNKKVTWKVLE 306
Cdd:cd12541    1 GCILHFSGVGE-QTSREDLKEAFEKHGEVAWIDFARGQTEGYVRFKEedAAKEALEKAKEAKNG-LKIRGKEVTVKLLE 77
LAM cd07323
LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins ...
 15-91 1.01e-27

LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153396  Cd Length: 75  Bit Score: 104.54  E-value: 1.01e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564341264  15 AKICHQIEYYFGDFNLPRDKFLKEQIKlDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKanLMEVSADKTKIRR 91
Cdd:cd07323    2 EKIKKQVEYYFSDENLCKDRFLRSLMD-DDGWVPLSLLASFNRVKKLTTDVELILEALRDSS--VVEVSEDGTKVRR 75
RRM_3 pfam08777
RNA binding motif; This domain is found in protein La which functions as an RNA chaperone ...
 230-333 3.47e-25

RNA binding motif; This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif.


Pssm-ID: 400913 [Multi-domain]  Cd Length: 102  Bit Score: 98.59  E-value: 3.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  230 GCLLKFSGdLDDQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFK--EKAKDALEKARSANNgnlLLRNKKVTWKVLEG 307
Cdd:pfam08777   1 GVILKFSG-LGKPLSREDIKEAFSQLGEVAYVDYLEGDKEGHVRFKtdEAAKKAIEKATEAKT---IIKDAEVTAELLEG 76

                          90       100
                  ....*....|....*....|....*.
gi 564341264  308 HAEKDAMKKITDDQQESLNKWKSKGG 333
Cdd:pfam08777  77 EEEKEYWKKIIEDQQAKLNNPRNKGR 102
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 17-74 2.94e-24

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 94.41  E-value: 2.94e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 564341264   17 ICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLETMIKFNRLNRLTTDFNVIVQALSK 74
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKDpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
RRM2_La_like cd12292
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ...
 230-306 7.57e-18

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: 77.36  E-value: 7.57e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 564341264 230 GCLLKFSGDLDdQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKEkaKDALEKARSANNGNLLLRNKKVTWKVLE 306
Cdd:cd12292    1 GLILKITGIGP-SVSRDDLKELFKQFGEVEYVDFTPGDDEGHVRFKT--SEAAQKARDAYTGKLELNGKEWKLEILE 74
LA_like_fungal cd08029
La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in ...
 14-91 1.67e-16

La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153398  Cd Length: 76  Bit Score: 73.87  E-value: 1.67e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 564341264  14 EAKICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLETMIKFNRLNRLtTDFNVIVQALSKSKanLMEVSADKTKIRR 91
Cdd:cd08029    1 PEEIRKQVEFYFSDSNLPTDKFLWTLTgGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRESE--LLEVSEDGENVRR 76
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 20-284 6.60e-15

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 75.85  E-value: 6.60e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  20 QIEYYFG-----DFNLPRDKFLKEQ---IKLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKAN-LMEVSADKTKIR 90
Cdd:COG5193   78 QVEFYFSgskdtDSNFPKDKFLKTTapkNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDArVLEVSSSGSNKN 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  91 RSPSRPLpevTDEYKNDVKNRSVYIKGFPTDATLD--------DIKEWLDDKGQ--ILNIQMRRTLH-KTFKGSIFAVFD 159
Cdd:COG5193  158 RTEKLIS---NNNKSTSQMQRDVYQNGFGKEDVNNasrpeqqeDLEIQFPPHYHapPSQIRNRRDWLnKNFRGSVFVEFK 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264 160 SIQSAKKFVD--TPGQKYKDTNLLILFK--EDYF----AKKNEERKQSKVEAKLKAKQEHEGRHKPGSTEtRALEGKMGC 231
Cdd:COG5193  235 YFREAQRFNNgfYRNKKYPNDPETVYYYsvEPILlsimAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIP-LSFIGKFYR 313

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 564341264 232 LLKFSGD--LDDQTCREDLHFLFSNHGEIkwidfVRGAKEGIILFKEKAKDALEK 284
Cdd:COG5193  314 NLSFGGDknLILAAMKEVVQNKATNHLEI-----ALGSIEDAQKNEAKDFSPGKK 363
LARP_6 cd08033
La RNA-binding domain of La-related protein 6; This domain is found in animal and plant ...
 15-91 1.97e-14

La RNA-binding domain of La-related protein 6; This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153402  Cd Length: 77  Bit Score: 68.08  E-value: 1.97e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 564341264  15 AKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLETMIKFNRLNRLTTDFNVIVQALSKSkaNLMEVSADKTKIRR 91
Cdd:cd08033    2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNkEGYVPIKLIASFKKVKALTRDWRVVAAALRRS--SKLVVSEDGKKVRR 77
LARP_7 cd08032
La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key ...
 9-91 5.33e-13

La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.


Pssm-ID: 153401  Cd Length: 82  Bit Score: 64.19  E-value: 5.33e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264   9 KMAALEAKICHQIEYYFGDFNLPRDKFLKEQI-KLDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSkaNLMEVSADKT 87
Cdd:cd08032    1 RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIeKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNS--SVVELNLEGT 78


                 ....
gi 564341264  88 KIRR 91
Cdd:cd08032   79 RIRR 82
LARP_4_5_like cd08031
La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found ...
 19-90 1.83e-12

La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153400  Cd Length: 75  Bit Score: 62.46  E-value: 1.83e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564341264  19 HQIEYYFGDFNLPRDKFLKEQIKLDEgWVPLETMIKFNRLNRLTTDFNVIVQALSKSKanLMEVSADKTKIR 90
Cdd:cd08031    6 RQLEYYFSRENLANDAYLLSQMDSDQ-YVPIWTIANFNKIKKLTTDIDLIVEALRESP--NVQVDEKGEKVR 74
LARP_1_2 cd08034
La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in ...
 17-91 3.38e-12

La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153403  Cd Length: 73  Bit Score: 61.67  E-value: 3.38e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564341264  17 ICHQIEYYFGDFNLPRDKFLKEQIKlDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKanlmEVSADKTKIRR 91
Cdd:cd08034    4 IKKQIEYYFSVDNLEKDFFLRRKMD-PEGYLPIALIASFHRVQALTTDVNLILEALKDST----VVELVDEKVRC 73
LA_like_plant cd08030
La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant ...
 15-91 1.26e-11

La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153399  Cd Length: 90  Bit Score: 60.48  E-value: 1.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  15 AKICHQIEYYFGDFNLPRDKFLKEQIKLD-EGWVPLETMIKFNRLNRL-------TTDFNV-----IVQALSKSKanLME 81
Cdd:cd08030    3 EKVLRQVEFYFSDSNLPRDDFLLEEVEEDpDGMVSLALICSFSRMRSLlglgggkPEDVPEdtlkaVAEALRTST--LLK 80

                         90
                 ....*....|
gi 564341264  82 VSADKTKIRR 91
Cdd:cd08030   81 VSEDGKRVGR 90
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 113-181 4.17e-09

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: 52.62  E-value: 4.17e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  113 VYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLHKTFKGSIFAVFDSIQSAKKFVDT-PGQKYKDTNLL 181
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
LARP_1 cd08037
La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related ...
 17-91 5.76e-09

La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153406  Cd Length: 73  Bit Score: 52.21  E-value: 5.76e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564341264  17 ICHQIEYYFGDFNLPRDKFLKEQIKlDEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSKAnlmeVSADKTKIRR 91
Cdd:cd08037    4 IKRQIEYYFSVDNLERDFFLRRKMD-EDGFLPVTLIASFHRVQALTTDISLIIKALKDSKV----VEIIDMKIRR 73
LARP_2 cd08038
La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related ...
 17-91 6.57e-09

La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153407  Cd Length: 73  Bit Score: 52.26  E-value: 6.57e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 564341264  17 ICHQIEYYFGDFNLPRDKFLKEQIKLdEGWVPLETMIKFNRLNRLTTDFNVIVQALSKSkanlMEVSADKTKIRR 91
Cdd:cd08038    4 IKRQIEYYFSTENLERDFFLRRKMDL-QGFLPISLIAGFYRVQALTTNVDLILEALKDS----TEVEIVDQKIRR 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 113-169 1.78e-07

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: 48.05  E-value: 1.78e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 564341264 113 VYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLHKTFKGSIFAVFDSIQSAKKFVD 169
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALE 57
LARP_4 cd08035
La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related ...
 20-90 1.82e-04

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153404  Cd Length: 75  Bit Score: 39.64  E-value: 1.82e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 564341264  20 QIEYYFGDFNLPRDKFLKEQIKLDEgWVPLETMIKFNRLNRLTTDFNVIVQALSKSKanLMEVSADKTKIR 90
Cdd:cd08035    7 QLEFCFSRENLSKDLYLISQMDSDQ-FVPIWTVANMEGIKKLTTDMDLILDVLRSSP--MVQVDETGEKVR 74
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 103-367 2.94e-04

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: 42.87  E-value: 2.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  103 EYKNDVKNRSVYIKGFPTDATLDDIKEWLDDKGQILNIQMRRTLHKTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLL- 181
Cdd:TIGR01628 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEg 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  182 -ILFKEDyfAKKNEERkQSKVEAKLKAKQEHEGRHKPGSTetralegkmgCLLKfsgDLDDQTCREDLHFLFSNHGEIKW 260
Cdd:TIGR01628 251 kKLYVGR--AQKRAER-EAELRRKFEELQQERKMKAQGVN----------LYVK---NLDDTVTDEKLRELFSECGEITS 314

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264  261 IDFVRGAKE-----GIILFKEkaKDALEKARSANNGNLLlrNKKVTWKVLeghAEKDAMKKITDDQQESLNKWKSKGGHA 335
Cdd:TIGR01628 315 AKVMLDEKGvsrgfGFVCFSN--PEEANRAVTEMHGRML--GGKPLYVAL---AQRKEQRRAHLQDQFMQLQPRMRQLPM 387

                         250       260       270
                  ....*....|....*....|....*....|..
gi 564341264  336 ARRFKgrGKGNRPAYAGaPKGRGQFQGRRTRF 367
Cdd:TIGR01628 388 GSPMG--GAMGQPPYYG-QGPQQQFNGQPLGW 416
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 237-303 9.12e-04

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: 37.65  E-value: 9.12e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564341264 237 GDLDDQTCREDLHFLFSNHGEIKWIDFVRGAKE-----GIILFKEkaKDALEKARSANNGNlLLRNKKVTWK 303
Cdd:cd00590    4 GNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEFES--PEDAEKALEALNGT-ELGGRPLKVS 72
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
 110-169 2.94e-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: 36.45  E-value: 2.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 564341264 110 NRSVYIKGFPTDATLDDIKEWLDDKGQIlnIQMRRTLHKTFKGSIFAVFDSIQSAKKFVD 169
Cdd:cd12241    2 NRILYVRNLPYKISSEELYDLFGKYGAI--RQIRIGNTKETRGTAFVVYEDIFDAKNACD 59
 
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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