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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980  98 EFSVFVGDLTSEVDDYQLHQFFLKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEEFQNASGLGGKPIRISIAV 177
Cdd:cd12612    1 EFSLFVGDLTPEVDDGMLYEFFLKRYPSCKGAKVVLDQLGNSRGYGFVRFSDENEQKRALTECQGASGLGGKPIRLSVAI 80

                 ..
gi 157384980 178 NK 179
Cdd:cd12612   81 PK 82

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980  98 EFSVFVGDLTSEVDDYQLHQFFLKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEEFQNASGLGGKPIRISIAV 177
Cdd:cd12612    1 EFSLFVGDLTPEVDDGMLYEFFLKRYPSCKGAKVVLDQLGNSRGYGFVRFSDENEQKRALTECQGASGLGGKPIRLSVAI 80

                 ..
gi 157384980 178 NK 179
Cdd:cd12612   81 PK 82

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 157384980    7 SLWMGDLDPYMDENFIKQAFSTMGETAfGVKIITHRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVpGSNPPRKFKLNY 86
Cdd:TIGR01628   2 SLYVGDLDPDVTEAKLYDLFKPFGPVL-SVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRL-GGKPIRIMWSQR 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157384980   87 ATYGKRPEPGpefSVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEE 159
Cdd:TIGR01628  80 DPSLRRSGVG---NIFVKNLDKSVDNKALFDTF-SKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148

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 157384980  101 VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEEFQNASgLGGKPIR 172
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLF-SKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKE-LGGRELK 70

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157384980 100 SVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEFQNASgLGGKPIRISIA 176
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELF-SEYGEVTSVKLITDREtGRSRGFGFVEMPDDEEAQAAIEALNGAE-LMGRTLKVNEA 78

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157384980    8 LWMGDLDPYMDENFIKQAFSTMGETAfGVKIIThRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVPG 75
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIK-SIRLVR-DETGRSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

glycine-rich RNA-binding protein 4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980 101 VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTD-PYGNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPIRISIAVNK 179
Cdd:PLN03134  37 LFIGGLSWGTDDASLRDAF-AHFGDVVDAKVIVDrETGRSRGFGFVNFNDEGAATAAISEM-DGKELNGRHIRVNPANDR 114

                 ....*..
gi 157384980 180 GNKASTY 186
Cdd:PLN03134 115 PSAPRAY 121

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980  98 EFSVFVGDLTSEVDDYQLHQFFLKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEEFQNASGLGGKPIRISIAV 177
Cdd:cd12612    1 EFSLFVGDLTPEVDDGMLYEFFLKRYPSCKGAKVVLDQLGNSRGYGFVRFSDENEQKRALTECQGASGLGGKPIRLSVAI 80

                 ..
gi 157384980 178 NK 179
Cdd:cd12612   81 PK 82

Selenocysteine tRNA 1 associated proteins; This entry represents the C-terminal region of Selenocysteine tRNA 1 associated proteins (Trnau1ap also known as Secp43). Family members found in Eukaryotes have been shown to serve an essential role in the synthesis of selenoproteins, which have critical functions in numerous biological processes. Selenium deficiency results in a variety of diseases, including cardiac disease. Trnau1ap proteins harbor RNA recognition motifs (RRM) pfam00076 and Tyr-rich region found in the C-terminal. The Tyr-rich region (amino acids 185-225) is conserved among several mammals, including human, chimp, dog, cattle, mouse and rat. Furthermore, constitutive deletion of exons corresponding to the Tyr-rich region in mouse resulted in embryonic lethality.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980  211 PQWGYDQYSG-YNYGYNPYaapppmmgppppmgmppmpPDMQGSTEAHdgTEEVEEDPSEDPNPQVDVEELNRQYMERSE 289
Cdd:pfam17654  21 SQWGYDQYNGyYSYSYPQY-------------------GYTPAPTTQE--AEQQDEDPLEDPNLELDVEELNKEFMERSE 79

                          90       100
                  ....*....|....*....|..
gi 157384980  290 ELYDSLMECHWLPMDTITSDIS 311
Cdd:pfam17654  80 ELYDALMNCHWQPLDSVTSEIP 101

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980  98 EFSVFVGDLTSEVDDYQLHQFFLKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEFQnasGL--GGKPIRIS 174
Cdd:cd12613    1 EYSIFVGDLSPTTNESDLVSLFQSRFPSCKSAKIMTDPVtGVSRGYGFVRFSDENDQQRALIEMQ---GKycQGRPLRIS 77

                 ..
gi 157384980 175 IA 176
Cdd:cd12613   78 YA 79

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 157384980    7 SLWMGDLDPYMDENFIKQAFSTMGETAfGVKIITHRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVpGSNPPRKFKLNY 86
Cdd:TIGR01628   2 SLYVGDLDPDVTEAKLYDLFKPFGPVL-SVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRL-GGKPIRIMWSQR 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157384980   87 ATYGKRPEPGpefSVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEE 159
Cdd:TIGR01628  80 DPSLRRSGVG---NIFVKNLDKSVDNKALFDTF-SKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148

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).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157384980  98 EFSVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGN-SRGYGFVKFSDENEQKKALEEFqNASGLGGKPIRIS 174
Cdd:cd12383    6 DFRIFCGDLGNEVTDEVLARAF-SKYPSFQKAKVIRDKRTGkSKGYGFVSFKDPNDYLKALREM-NGKYVGNRPIKLR 81

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 157384980   13 LDPYMDENFIKQAFSTMGETAfGVKIITHRVTGGSAGYCFVEMADEASVDRCVQrLNGKLVPGSnpPRKFKLNYA----- 87
Cdd:TIGR01622 122 LAARARERDLYEFFSKVGKVR-DVQIIKDRNSRRSKGVGYVEFYDVDSVQAALA-LTGQKLLGI--PVIVQLSEAeknra 197

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980   88 ------TYGKRPEPGPEFSVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEF 160
Cdd:TIGR01622 198 araateTSGHHPNSIPFHRLYVGNLHFNITEQDLRQIF-EPFGEIEFVQLQKDPEtGRSKGYGFIQFRDAEQAKEALEKM 276

                         170
                  ....*....|....*.
gi 157384980  161 qNASGLGGKPIRISIA 176
Cdd:TIGR01622 277 -NGFELAGRPIKVGLG 291

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157384980   100 SVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEFQNASgLGGKPIRI 173
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELF-SKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKE-LDGRPLKV 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 157384980   12 DLDPYMDENFIKQAFSTMGeTAFGVKIITHrVTGGSAGYCFVEMADEASVDRCVQRLNGKLVPGSNpprkfkLNYATYGK 91
Cdd:TIGR01628  95 NLDKSVDNKALFDTFSKFG-NILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKE------VYVGRFIK 166

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157384980   92 RPE----PGPEFS-VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEE 159
Cdd:TIGR01628 167 KHEreaaPLKKFTnLYVKNLDPSVNEDKLRELF-AKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE 238

RNA recognition motif;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157384980     7 SLWMGDLDPYMDENFIKQAFSTMGETAFgVKIITHRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVPG 75
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES-VRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDG 68

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157384980 101 VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPIR 172
Cdd:cd12353    2 IFVGDLSPEIETEDLKEAF-APFGEISDARVVKDTQtGKSKGYGFVSFVKKEDAENAIQGM-NGQWLGGRNIR 72

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157384980 100 SVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDP-YGNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPIRI 173
Cdd:cd21601    2 ALFIGDLDKDVTEEMLRDIF-SKYKSLVSVKICLDSeTKKSLGYGYLNFSDKEDAEKAIEEF-NYTPIFGKEVRI 74

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157384980 100 SVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTD-PYGNSRGYGFVKFSDENEQKKALEEFQNASgLGGKPIRISIA 176
Cdd:cd12447    1 TLFVGGLSWNVDDPWLKKEF-EKYGGVISARVITDrGSGRSKGYGYVDFATPEAAQKALAAMSGKE-IDGRQINVDFS 76

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157384980 101 VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPIRISIA 176
Cdd:cd21608    2 LYVGNLSWDTTEDDLRDLF-SEFGEVESAKVITDREtGRSRGFGFVTFSTAEAAEAAIDAL-NGKELDGRSIVVNEA 76

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157384980    8 LWMGDLDPYMDENFIKQAFSTMGETAfGVKIIThRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVPG 75
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIK-SIRLVR-DETGRSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

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).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157384980   8 LWMGDLDPYMDENFIKQAFSTMGEtAFGVKIITHRvTGGSAGYCFVEMADEASVDRCVQRLNGKLVPG 75
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGE-VVSVRIVRDR-DGKSKGFAFVEFESPEDAEKALEALNGTELGG 66

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157384980 101 VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPI 171
Cdd:cd12380    4 VYVKNFGEDVDDDELKELF-EKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEEL-NGKELNGKKL 72

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980 100 SVFVGDLTSEVDDYQLHQFFLKKFPsCKGAKVVTDP-YGNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPIRISIAVN 178
Cdd:cd12413    1 TLFVRNLPYDTTDEQLEELFSDVGP-VKRCFVVKDKgKDKCRGFGYVTFALAEDAQRALEEV-KGKKFGGRKIKVELAKK 78

                 .
gi 157384980 179 K 179
Cdd:cd12413   79 K 79

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157384980 101 VFVGDLTSEVDDYQLHQFFLK--KFPSCKgakVVTDPYGNSRGYGFVKFSDENEQKKALEEFqNASGLGGK 169
Cdd:cd12379    5 IFIKNLDKSIDNKALYDTFSAfgNILSCK---VATDENGGSKGYGFVHFETEEAAERAIEKV-NGMLLNGK 71

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980   37 KIITHRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVPGsnppRKFKLNYAtygkRP--EPGPEFSVFVGDLTSEVDDYQ 114
Cdd:TIGR01659 138 RIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN----KRLKVSYA----RPggESIKDTNLYVTNLPRTITDDQ 209

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157384980  115 LHQFFlKKFPSCKGAKVVTDPY-GNSRGYGFVKFSDENEQKKALEEFQNASGLGG-KPIRISIAVNKGnKASTYH 187
Cdd:TIGR01659 210 LDTIF-GKYGQIVQKNILRDKLtGTPRGVAFVRFNKREEAQEAISALNNVIPEGGsQPLTVRLAEEHG-KAKAHH 282

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157384980  99 FSVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTD-PYGNSRGYGFVKFSDENEQKKALEEFqNASGLGGKPIR 172
Cdd:cd12618    3 FHVFVGDLSPEITTEDIKAAF-APFGRISDARVVKDmATGKSKGYGFVSFFNKWDAENAIQQM-GGQWLGGRQIR 75

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157384980  99 FSVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDP-YGNSRGYGFVKFSDENEQKKALEEFQNASGLGG 168
Cdd:cd12415    1 KTVFIRNLSFDTTEEDLKEFF-SKFGEVKYARIVLDKdTGHSKGTAFVQFKTKESADKCIEAANDESEDGG 70

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980   7 SLWMGDLDPYMDENFIKQAFSTMGETAfGVKIITHRVTGGSAGYCFVEMADEASVDRCVQRLNGKLVPGS 76
Cdd:cd12417    1 NLWISGLSDTTKAADLKKIFSKYGKVV-SAKVVTSARTPGSRCYGYVTMASVEEADLCIKSLNKTELHGR 69

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).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980 101 VFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTD-PYGNSRGYGFVKFSDENEQKKALEE 159
Cdd:cd12384    3 IFVGGLPYHTTDDSLREYF-EQFGEIEEAVVITDrQTGKSRGYGFVTMADREAAERACKD 61

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157384980 100 SVFVGDLTSEVDDYQLHQFFlKKFPSCKGAKVVTDPYGNSRGYGFVKFSDENEQKKALEE 159
Cdd:cd12673    4 RIFVGGIDFKTNENDLRKFF-AQYGSVKEVKIVNDRAGVSKGYGFITFETQEDAQKILQE 62