RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580583  498 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 571
Cdd:cd12349    1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580583  670 FGKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 746
Cdd:cd12351    1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583   3520 PTASQNAMPQASTPKQGPITPQQAIRTQSLIMQPPTISIPEQTPHFAVPQmvlSPQSHHPQQPGTYMVGIRAPSPHSPLH 3599
Cdd:pfam03154  184 PSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQ---TPTLHPQRLPSPHPPLQPMTQPPPPSQ 260

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583   3600 SPGRGVAQSRLVGQLSPVGRPMVSQPSPQQQVQQTQQQHALITSPQsSNISPLASPTTRVLSSSNS---PTTSKVNSYQP 3676
Cdd:pfam03154  261 VSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQ-SQVPPGPSPAAPGQSQQRIhtpPSQSQLQSQQP 339

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580583   3677 RNQQvPQQPSPKSVAEVQTTPqlmTIPLQKMTPIQVPHHPTIISKVVTVQpqqaTQSQVASSP---PLGSLPPH 3747
Cdd:pfam03154  340 PREQ-PLPPAPLSMPHIKPPP---TTPIPQLPNPQSHKHPPHLSGPSPFQ----MNSNLPPPPalkPLSSLSTH 405

Cytochrome b6-f complex subunit petO; Chloroplastic cytochrome b6-f complex subunit petO (or PETO), also called cytochrome b6-f complex subunit V (suV) or cytochrome b6-f-associated phosphoprotein, is a novel cytochrome b6-f subunit specific in green algae that is predicted by sequence analysis and biochemical characterization to have a one transmembrane alpha-helix topology with two large hydrophilic domains extending on the stromal and lumenal side of the thylakoid membranes, with a lumenal location of the N-terminus. It is reversibly phosphorylated upon state transition, and may have a possible role in signal transduction during redox-controlled short term and long term adaptation of the eukaryotic photosynthetic apparatus. PetO has been shown to contribute to the cyclic electron flow (CEF) around photosystem I (PSI) and cytochrome b6-f that generates ATP.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 4530 IEEVTASNATVAASHL--APPEGAGVESHVPQLDAkevepvsvVTPISTPAPVSVAAPVTVPVPAMVPVKPTmPQHPKKK 4607
Cdd:cd22950   12 AEEQAQAAAAAAAAALltASPANAGVVLQQPELKK--------VFQDDSPAAAAPKREFKGPPALPAPTAAA-PAAAKEK 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 24580583 4608 AiaAAEIESyqainssiPSGGLPMHQTAAPATQKITGGVADAVSK 4652
Cdd:cd22950   83 K--AEVVES--------SSGGLDPRSVALPAALVFVIGGAFAASK 117

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580583  498 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 571
Cdd:cd12349    1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580583  670 FGKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 746
Cdd:cd12351    1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    499 IRVRNLPARSSDTSLKDglfhEYKKHGKVTWVKVV----GQnSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEPYQ 574
Cdd:TIGR01628   91 IFVKNLDKSVDNKALFD----TFSKFGNILSCKVAtdenGK-SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFI 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    575 gydvedNEFRPYEAELDEYhpkstRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLN---AYAFCQYSDIVSVVK 651
Cdd:TIGR01628  166 ------KKHEREAAPLKKF-----TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGrsrGFAFVNFEKHEDAAK 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    652 AMRKMDGEHLG----SNRIKLG-----------------------FGKSMPTNcVWIDGVDEKVSESFLQSQFTRFGAVT 704
Cdd:TIGR01628  235 AVEEMNGKKIGlakeGKKLYVGraqkraereaelrrkfeelqqerKMKAQGVN-LYVKNLDDTVTDEKLRELFSECGEIT 313

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 24580583    705 --KVSID---RNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDFASR 749
Cdd:TIGR01628  314 saKVMLDekgVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    601 LFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA---YAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 667
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRskgFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    600 TLFIGNLEKDITAGELRSHFEAFGEIIEI----DIKKQGLNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG---- 671
Cdd:TIGR01628    2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVrvcrDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSqrdp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    672 ---KSMPTNcVWIDGVDEKVSESFLQSQFTRFGAVT--KVSIDRN---RQLALVLYDQVQNAQAAVKDMRGTILRRKKLQ 743
Cdd:TIGR01628   82 slrRSGVGN-IFVKNLDKSVDNKALFDTFSKFGNILscKVATDENgksRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY 160

                   .
gi 24580583    744 V 744
Cdd:TIGR01628  161 V 161

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580583  598 TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI-------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNRIK 667
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLitdretgRSRG---FGFVEMPDDEEAQAAIEALNGAELMGRTLK 74

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).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    598 TRTLFIGN-LEKDITAGELRSHFEAFGEI-----IEIDIKKQGLnAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 671
Cdd:TIGR01661    2 SKTNLIVNyLPQTMTQEEIRSLFTSIGEIescklVRDKVTGQSL-GYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24580583    672 K----SMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSI------DRNRQLALVLYDQVQNAQAAVKDMRGTI 736
Cdd:TIGR01661   81 RpssdSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIlsdnvtGLSKGVGFIRFDKRDEADRAIKTLNGTT 155

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 1881 LRKQVEREEKDRKAQQEERekedrkakeeekererekkaqedrekkereerELREKEQRDKEQKEKEIREKDLREKEQRE 1960
Cdd:COG1196  293 LLAELARLEQDIARLEERR--------------------------------RELEERLEELEEELAELEEELEELEEELE 340

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24580583 1961 RDNREKELRDKDLREKEMREKEQREKELHREKDQREREHREKEQSRRAMDVEQE 2014
Cdd:COG1196  341 ELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRA 394

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583   1940 DKEQKEKEIREKDL-REKE-QRERDNREKELRDKD-LREKEMREKEQREKELHREkdqREREHREKEQSRRAMDVEQEGR 2016
Cdd:TIGR01622   18 DRDRRRDKGRERSRdRSRDrERSRSRRRDRHRDRDyYRGRERRSRSRRPNRRYRP---REKRRRRGDSYRRRRDDRRSRR 94

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24580583  498 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTWVKVVGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVE 571
Cdd:cd12349    1 GIKVRNLPVRSSDTSLKDGLFHEFKKHGKVTSVKVHGQGEERYAIVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24580583  670 FGKSMPTNCVWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRRKKLQVDF 746
Cdd:cd12351    1 FGKSMPTNCVWLDGLSENVTEQYLTRHFCRYGPVVKVVIDRQKGMALVLYDEVECAQAAVKETKGRKIGGRKIQVDF 77

SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 (RBM15) and similar proteins; This subfamily includes RBM15, RBM15B, and similar proteins found in metazoans. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as a 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). RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein that shares 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 of this family have 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 domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 5320 WQGLLALKTDQAAVQMHFVHGNPNVARASLPSLVETNTPLLRIAQRMRLEQTQLEGVAKKMQV--DKEHCMLLALP---C 5394
Cdd:cd21544    2 WSGALVLKNSAFPVRMHLLRGDVQLADTLLPNPTSGEQPVLRITQRLRLDPPKLDDVSRRISSagSSGYCVLLAVPgsgA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 5395 GRDHADVLQHS--RNLqtgfITYLQQKMAAGIVNIP---IPGSEQAAYVVHIFPSCDFANENLERAAPDLKNRVAELAHL 5469
Cdd:cd21544   82 NSEADASTQQRplRNL----VSYLKQKEAAGVVSLPpngSVGEKKVTGVLHAFPPCDFSQQLLRRLAPSLSLESLKDDHL 157

                 ....
gi 24580583 5470 LIVI 5473
Cdd:cd21544  158 VIVL 161

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583   5312 LLQRYPVMWQGLLALKT-DQAAVQMHFVHGNPNVARASLpslvetntplLRIAQRMRLEQTQ--LEGVAKKMqvdkeHCM 5388
Cdd:pfam07744    1 SLQDLEVIWQGTLAMKGvAEFSVRAHLVSGDIDSLLPSL----------LRITGRIRLDAVWkyLDEVRRSI-----TRD 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583   5389 LLAL-PCGRDHADVLQhsrnlQTGFITYLQQKMAAGIVNipiPGSEQaAYVVHIFPSCDFAnENLERAAPDLKNRVAEla 5467
Cdd:pfam07744   66 VLVVrFFPSSESDESA-----FDELIDYLQSKQRAGVIH---AKSAD-VKDLYLFPPCEFL-ELLLPVGLSLEVSEPN-- 133

                   ....*....
gi 24580583   5468 HLLIVIATV 5476
Cdd:pfam07744  134 LLLGVVVRK 142

SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15); RBM15, also called 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 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. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 5320 WQGLLALKTDQAAVQMHFVHGNPNVARaSLpsLVETNT----PLLRIAQRMRLEQTQLEGVAKKMQV--DKEHCMLLALP 5393
Cdd:cd21549    2 WQGMLLLKNSNFPSNMHLLEGDLSVAS-SL--LVDGSTggkvAQLKITQRLRLDQPKLDEVTRRIKVagPNGYAVLLAVP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 5394 CGRDHADVLQHSRNLQ---TGFITYLQQKMAAGIVNIPIPGSEQA--AYVVHIFPSCDFANENLERAAPDLKNrvAELAH 5468
Cdd:cd21549   79 GSSEVSSVSDQATSTQrplRNLVSYLKQKQAAGVISLPVGGSKDKdnTGVLHAFPPCDFSQQFLDSSAKALAK--SEEDY 156

                 ....*
gi 24580583 5469 LLIVI 5473
Cdd:cd21549  157 LVMII 161

RNA recognition motif;

                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24580583     600 TLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQGLNA----YAFCQYSDIVSVVKAMRKMDGEHLGSNRIKL 668
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGkskgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    517 LFHEYKKHGKVTWVKV----VGQNSERYALVCFKKPDDVEKALEVSHDKHFFGCKIEVEpyqgYDVEDNEFRpyeaelde 592
Cdd:TIGR01628   17 LYDLFKPFGPVLSVRVcrdsVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIM----WSQRDPSLR-------- 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    593 yhpKS-TRTLFIGNLEKDITAGELRSHFEAFGEIIEIDI------KKQGlnaYAFCQYSDIVSVVKAMRKMDGEHLGSNR 665
Cdd:TIGR01628   85 ---RSgVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVatdengKSRG---YGFVHFEKEESAKAAIQKVNGMLLNDKE 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    666 IKLgfGKSMP------------TNcVWIDGVDEKVSESFLQSQFTRFGAVT--KVSIDRNRQ---LALVLYDQVQNAQAA 728
Cdd:TIGR01628  159 VYV--GRFIKkhereaaplkkfTN-LYVKNLDPSVNEDKLRELFAKFGEITsaAVMKDGSGRsrgFAFVNFEKHEDAAKA 235

                   ....*..
gi 24580583    729 VKDMRGT 735
Cdd:TIGR01628  236 VEEMNGK 242

SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein 15B (RBM15B); RBM15B, also called one-twenty two 3 (OTT3), is a paralog of RNA binding motif protein 15 (RBM15), which is also known as one-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein that shares 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 contains 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 domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 5320 WQGLLALKTDQAAVQMHFVHGNPNVARASLPSLVE-TNTPLLRIAQRMRLEQTQLEGVAKKMQVDKE--HCMLLALPCGR 5396
Cdd:cd21550    2 WNGVLVLKNSCFPTNMHILEGDLGVVNILLKDYTSgGKLTQLKIAQRLRLDQPKLDEVTRRIKQGSPdgYAVLLATQAPQ 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583 5397 DHADV--------LQhsRNLQTGFITYLQQKMAAGIVNIPIPGSEQAAY--VVHIFPSCDFANENLERAAPDLKNRVAEl 5466
Cdd:cd21550   82 GGEGGgappvepgLQ--RRLLRNLVSYLKQKQAAGVISLPVGGSKDRDNtgMLYAFPPCDFSQQYLQSALRTLGKLEEE- 158

                 ....*..
gi 24580583 5467 aHLLIVI 5473
Cdd:cd21550  159 -HMVIVI 164

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583  596 KSTRTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKK----QGlNAYAFCQYSDIVSVVKAMRKMDGEHLGSNRIKLGFG 671
Cdd:cd12556    6 RATRNLFIGNLDHNVSEVELRRAFEKYGIIEEVVIKRpargQG-GAYAFLKFQNLDMAHRAKVAMSGRVIGRNPIKIGYG 84

                 .
gi 24580583  672 K 672
Cdd:cd12556   85 K 85

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    501 VRNLPARSSDTSLKDglFheYKKHGKVTWVKVV-GQNSER---YALVCFKKPDDVEKALEVSHDKhFFGCKIEVEPYQGy 576
Cdd:TIGR01622  119 VQQLAARARERDLYE--F--FSKVGKVRDVQIIkDRNSRRskgVGYVEFYDVDSVQAALALTGQK-LLGIPVIVQLSEA- 192

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24580583    577 dvEDNEFRPYEAELDEYHPKST--RTLFIGNLEKDITAGELRSHFEAFGEIIEIDIKKQG----LNAYAFCQYSDIVSVV 650
Cdd:TIGR01622  193 --EKNRAARAATETSGHHPNSIpfHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPetgrSKGYGFIQFRDAEQAK 270

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24580583    651 KAMRKMDGEHLGSNRIKLGFG-KSMPTNcvwiDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLA 715
Cdd:TIGR01622  271 EALEKMNGFELAGRPIKVGLGnDFTPES----DANLAQRFQDQDGSAFSGAGLNTPARSQLMRKLA 332

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24580583  679 VWIDGVDEKVSESFLQSQFTRFGAVTKVSIDRNRQLALVLYDQVQNAQAAVKDMRGTILRR--KKLQVDFA 747
Cdd:cd12310    1 LWVGGLGPWTSLAELEREFDRFGAIRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGpdRRLRVDFA 71

RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM1 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 contains 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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24580583  498 AIRVRNLPARSSDTSLKDGLFHEYKKHGKVTwVKVVGQNSERYALVCFKKPDDVEKA 554
Cdd:cd12553    3 TLKISELGSQLSDEAVEDGLFHEFKKFGDVS-VKISRLGDERVAFVNFRRPEDARAA 58