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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 661 EKHKLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKVAISNP 740
Cdd:cd12392     1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISNP 80

                  .
gi 1720414289 741 P 741
Cdd:cd12392    81 P 81

LSM-interacting associated unstructured; LSM_int_assoc is a family found largely on eukaryotic SART3 proteins just upstream of their C-terminal LSM-interacting domain. This region is natively unstructured.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720414289 739 NPPQRKVPEKPEVRTAPGaPMLPRQMYGARGKGRTQLSLLPRALQRQGA-APQAENGPAPGP 799
Cdd:pfam16605   1 NPPQRKVPDKPEASRALG-AMVPRQVYGARGKGRTQLSLLPRALHRQSApVAKAENGTAAAP 61

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 661 EKHKLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKVAISNP 740
Cdd:cd12392     1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISNP 80

                  .
gi 1720414289 741 P 741
Cdd:cd12392    81 P 81

LSM-interacting associated unstructured; LSM_int_assoc is a family found largely on eukaryotic SART3 proteins just upstream of their C-terminal LSM-interacting domain. This region is natively unstructured.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720414289 739 NPPQRKVPEKPEVRTAPGaPMLPRQMYGARGKGRTQLSLLPRALQRQGA-APQAENGPAPGP 799
Cdd:pfam16605   1 NPPQRKVPDKPEASRALG-AMVPRQVYGARGKGRTQLSLLPRALHRQSApVAKAENGTAAAP 61

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 1720414289 665 LFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIK 734
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

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 1720414289 560 DSSKDSVTVFVSNLPYSIEEPEVKlrPLFEVCGEVVQIRPIFS-NRGDFRGYCYVEFGEEKSAQQALELDRKIVEGRPMF 638
Cdd:TIGR01622 109 EDERDRRTVFVQQLAARARERDLY--EFFSKVGKVRDVQIIKDrNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVI 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 639 VSPCvDKSKNpdfKVFRYSTTLE--------KHKLFISGLPFSCTKEELEDICKAHGTVKDLRLVTN-RAGKPKGLAYVE 709
Cdd:TIGR01622 187 VQLS-EAEKN---RAARAATETSghhpnsipFHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDpETGRSKGYGFIQ 262

                         170       180       190
                  ....*....|....*....|....*....|
gi 1720414289 710 YENESQASQAVMKMDGMTIRENVIKVAISN 739
Cdd:TIGR01622 263 FRDAEQAKEALEKMNGFELAGRPIKVGLGN 292

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 565 SVTVFVSNLPYSIEEPEvkLRPLFEVCGEVVQIRpIFSNR--GDFRGYCYVEFGEEKSAQQALE-LDRKIVEGRPMFVSP 641
Cdd:COG0724     1 SMKIYVGNLPYSVTEED--LRELFSEYGEVTSVK-LITDRetGRSRGFGFVEMPDDEEAQAAIEaLNGAELMGRTLKVNE 77

                  ....*...
gi 1720414289 642 CVDKSKNP 649
Cdd:COG0724    78 ARPREERP 85

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289   1 MSELFPLTEELWLEWLHDEISMAmdglDREHVYELFERAVKDYICPNIWLEYGQY----SVGGIGQKGGleKVRSVFERA 76
Cdd:COG5107    68 LSSPFPIMEHAWRLYMSGELARK----DFRSVESLFGRCLKKSLNLDLWMLYLEYirrvNNLITGQKRF--KIYEAYEFV 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289  77 LSSVGLHMTKGlAIWEAYREFE------SAIVEAARLEKVHSLFRRQLAIPLYEMEATFAEYEEWSEE------------ 138
Cdd:COG5107   142 LGCAIFEPQSE-NYWDEYGLFLeyieelGKWEEQQRIDKIRNGYMRALQTPMGNLEKLWKDYENFELElnkitarkfvge 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 139 --PMPESVLQSYQKALGQLEKYKPYEEALLQA--EAPRLAE--YQAYIDFEMK-----IGDP--ARIQLIFERALVENCL 205
Cdd:COG5107   221 tsPIYMSARQRYQEIQNLTRGLSVKNPINLRTanKAARTSDsnWLNWIKWEMEnglklGGRPheQRIHYIHNQILDYFYY 300

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 206 VPDLWIRYSQYL----DRQlKVKDLVLsvhsRAVRNCP-WTVALWSRYLLAMerhglDHQTISATFENALSA-------- 272
Cdd:COG5107   301 AEEVWFDYSEYLigisDKQ-KALKTVE----RGIEMSPsLTMFLSEYYELVN-----DEEAVYGCFDKCTQDlkrkysmg 370

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1720414289 273 ------------------GFIQATDYVEIWQVYLDYLRRRvdfrqdssKELEELRSMFT--RALEYLQQEV 323
Cdd:COG5107   371 esesaskvdnnfeyskelLLKRINKLTFVFCVHLNYVLRK--------RGLEAARKLFIklRKEGIVGHHV 433

glycine-rich RNA-binding protein 4; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 565 SVTVFVSNLPYSIEEPEvkLRPLFEVCGEVVQIRPIFSNR-GDFRGYCYVEFGEEKSAQQAL-ELDRKIVEGRPMFVSPC 642
Cdd:PLN03134   34 STKLFIGGLSWGTDDAS--LRDAFAHFGDVVDAKVIVDREtGRSRGFGFVNFNDEGAATAAIsEMDGKELNGRHIRVNPA 111

                  ....*..
gi 1720414289 643 VDKSKNP 649
Cdd:PLN03134  112 NDRPSAP 118

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 661 EKHKLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKVAISNP 740
Cdd:cd12392     1 EKNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISNP 80

                  .
gi 1720414289 741 P 741
Cdd:cd12392    81 P 81

LSM-interacting associated unstructured; LSM_int_assoc is a family found largely on eukaryotic SART3 proteins just upstream of their C-terminal LSM-interacting domain. This region is natively unstructured.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720414289 739 NPPQRKVPEKPEVRTAPGaPMLPRQMYGARGKGRTQLSLLPRALQRQGA-APQAENGPAPGP 799
Cdd:pfam16605   1 NPPQRKVPDKPEASRALG-AMVPRQVYGARGKGRTQLSLLPRALHRQSApVAKAENGTAAAP 61

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720414289  664 KLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKV 735
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 664 KLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKVAISNPPQ 742
Cdd:COG0724     3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDREtGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82

                  ..
gi 1720414289 743 RK 744
Cdd:COG0724    83 ER 84

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 1720414289 560 DSSKDSVTVFVSNLPYSIEEPEVKlrPLFEVCGEVVQIRPIFS-NRGDFRGYCYVEFGEEKSAQQALELDRKIVEGRPMF 638
Cdd:TIGR01622 109 EDERDRRTVFVQQLAARARERDLY--EFFSKVGKVRDVQIIKDrNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVI 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 639 VSPCvDKSKNpdfKVFRYSTTLE--------KHKLFISGLPFSCTKEELEDICKAHGTVKDLRLVTN-RAGKPKGLAYVE 709
Cdd:TIGR01622 187 VQLS-EAEKN---RAARAATETSghhpnsipFHRLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDpETGRSKGYGFIQ 262

                         170       180       190
                  ....*....|....*....|....*....|
gi 1720414289 710 YENESQASQAVMKMDGMTIRENVIKVAISN 739
Cdd:TIGR01622 263 FRDAEQAKEALEKMNGFELAGRPIKVGLGN 292

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720414289 567 TVFVSNLPYSIEEPEvkLRPLFEVCGEVVQIRpIFSNRGD--FRGYCYVEFGEEKSAQQALELDRKIVEGRPMFV 639
Cdd:cd12450     1 TLFVGNLSWSATQDD--LENFFSDCGEVVDVR-IAMDRDDgrSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720414289 665 LFISGLPFSCTKEELEDICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKV 735
Cdd:cd12398     3 VFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDReTGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRV 74

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 1720414289 568 VFVSNLPYSIEEPEvkLRPLFEVCGEVVQIRPIFSNRGDFRGYCYVEFGEEKSAQQALE-LDRKIVEGRPM 637
Cdd:pfam00076   1 LFVGNLPPDTTEED--LKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEaLNGKELGGREL 69

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720414289 664 KLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKV 735
Cdd:cd12414     1 RLIVRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPVAV 72

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720414289 568 VFVSNLPYSIEEPEvkLRPLFEVCGEVVQIR-PIFS--NRGDF-RGYCYVEFGEEKSAQQALELDRKIVEGRPMFVS 640
Cdd:cd12298     3 IRVRNLDFELDEEA--LRGIFEKFGEIESINiPKKQknRKGRHnNGFAFVTFEDADSAESALQLNGTLLDNRKISVS 77

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720414289 568 VFVSNLPYSIEEPEVklRPLFEVCGEVVQIR-PIFSNRGDFRGYCYVEFGEEKSAQQALELDRKIVEGRPMFV 639
Cdd:cd12271     1 VYVGGIPYYSTEAEI--RSYFSSCGEVRSVDlMRFPDSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 568 VFVSNLPYSIEEPEvkLRPLFEVCGEVVQIRPIFSNRGDFRGYCYVEFGEEKSAQQALEL--DRKIVEGRPMFVSPCVDK 645
Cdd:TIGR01648  61 VFVGKIPRDLYEDE--LVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLlnNYEIRPGRLLGVCISVDN 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720414289 646 SknpdfkvfrysttlekhKLFISGLPFSCTKEE-LEDICKAHGTVKDLRLVTNRAGKPK--GLAYVEYENESQASQAVMK 722
Cdd:TIGR01648 139 C-----------------RLFVGGIPKNKKREEiLEEFSKVTEGVVDVIVYHSAADKKKnrGFAFVEYESHRAAAMARRK 201

                         170       180
                  ....*....|....*....|
gi 1720414289 723 -MDG-MTIRENVIKVAISNP 740
Cdd:TIGR01648 202 lMPGrIQLWGHVIAVDWAEP 221

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.

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gi 1720414289 665 LFISGLPFSCTKEELEDICKahgTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTI 728
Cdd:cd12404     6 LFVKNLPYSTTQDELKEVFE---DAVDIRIPMGRDGRSKGIAYIEFKSEAEAEKALEEKQGTEV 66

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

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gi 1720414289 663 HKLFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKVAisnPPQ 742
Cdd:cd12412     3 NRIFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNVG---PAI 79

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gi 1720414289 743 RK 744
Cdd:cd12412    80 RK 81

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

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gi 1720414289 665 LFISGLPFSCTKEELEDICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMD-----GMTIREN 731
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDReTKRPRGFGFVELQEEESAEKAIAKLDgtdfmGRTIRVN 73

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

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gi 1720414289 664 KLFISGLPFSCTKEELEDICKAHGTVKDLRLvtnrAGKPKGLAYVEYENESQASQAVMKMDGMTIRENVIKVAISNP 740
Cdd:cd12373     1 KVYVGNLGPRVTKRELEDAFEKYGPLRNVWV----ARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73

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

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gi 1720414289 564 DSVTVFVSNLPYSIEEPEvkLRPLFEVCGEVVQIR-PIFSNRGDFRGYCYVEFGEEKSAQQAL-ELDRKIVEGRPMFVSP 641
Cdd:cd12566     1 ETGRLFLRNLPYSTKEDD--LQKLFSKFGEVSEVHvPIDKKTKKSKGFAYVLFLDPEDAVQAYnELDGKVFQGRLIHILP 78

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

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gi 1720414289 665 LFISGLPFSCTKEELEDICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENeSQASQAVMKMDGMTIRENVIKV 735
Cdd:cd12400     3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDKKtGKSKGCAFVEFDN-QKALQKALKLHHTSLGGRKINV 73

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

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gi 1720414289 567 TVFVSNLPYSIEEPEvkLRPLFEVCGEVVQIRpIFSNRGDFRgYCYVEFGEEKSAQQALELDRKIVEGRPMFVSPcvdkS 646
Cdd:cd12225     2 TIHVGGIDGSLSEDE--LADYFSNCGEVTQVR-LCGDRVHTR-FAWVEFATDASALSALNLDGTTLGGHPLRVSP----S 73

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gi 1720414289 647 KNP 649
Cdd:cd12225    74 KTA 76

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

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gi 1720414289 665 LFISGLPFSCTKEELEDICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK----MDGMTIR 729
Cdd:cd12450     2 LFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRdDGRSKGFGHVEFASAESAQKALEKsgqdLGGREIR 71

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.