RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 76559935  54 GLRSVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGVFAIVEMGDISAREAVLSQPKHSLGGHTLRVRPRE 127
Cdd:cd12279   1 EERSVFVSGFKRGTSELELSDYFQAFGPVASVVMDKDKGVYAIVEMDSTETVEKVLSQPQHCLNGQRLRVKPRE 74

DNA polymerase sigma [Replication, recombination and repair];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935 358 RVQTVPSARRPVVKFCHRPSGLHGDISLSNRLALYNSRFLNLCSEMDSRVRPLVYTLRCWA---QHNGLSGGGplLNNYA 434
Cdd:COG5260 147 EVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLkrrALNDVATGT--LSSYT 224

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935 435 LTLLVIYFLQTRDPPVLptvaqltqrsgegeqvevdgwdcsFPK-DASRLEPSTNVEPLSSLLAQFFSCVS-CWDLSGSL 512
Cdd:COG5260 225 ISCMVLSFLQMHPPFLF------------------------FDNgLLSPLKYNKNIDNLGVLFDDFFELYGkSFNYSLVV 280

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 76559935 513 LSLREGQALmvaggLPSDLWEGL---RLGPMNLQDPF-DLSHNVAAnvTSRVAKRLQS 566
Cdd:COG5260 281 LSINSGDFY-----LPKYEKGWLkpsKPNSLSIQDPGtDRNNDISA--VSFNIKDIKA 331

RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 76559935  54 GLRSVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGVFAIVEMGDISAREAVLSQPKHSLGGHTLRVRPRE 127
Cdd:cd12279   1 EERSVFVSGFKRGTSELELSDYFQAFGPVASVVMDKDKGVYAIVEMDSTETVEKVLSQPQHCLNGQRLRVKPRE 74

DNA polymerase sigma [Replication, recombination and repair];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935 358 RVQTVPSARRPVVKFCHRPSGLHGDISLSNRLALYNSRFLNLCSEMDSRVRPLVYTLRCWA---QHNGLSGGGplLNNYA 434
Cdd:COG5260 147 EVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLkrrALNDVATGT--LSSYT 224

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935 435 LTLLVIYFLQTRDPPVLptvaqltqrsgegeqvevdgwdcsFPK-DASRLEPSTNVEPLSSLLAQFFSCVS-CWDLSGSL 512
Cdd:COG5260 225 ISCMVLSFLQMHPPFLF------------------------FDNgLLSPLKYNKNIDNLGVLFDDFFELYGkSFNYSLVV 280

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 76559935 513 LSLREGQALmvaggLPSDLWEGL---RLGPMNLQDPF-DLSHNVAAnvTSRVAKRLQS 566
Cdd:COG5260 281 LSINSGDFY-----LPKYEKGWLkpsKPNSLSIQDPGtDRNNDISA--VSFNIKDIKA 331

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 76559935   491 PLSSLLAQFFSCVS-CWDLSGSLLSLREGQALMVAGgLPSDLWEGLRLGPMNLQDPFDLSH 550
Cdd:pfam03828   1 SLGELLIGFFEYYGrEFDYENVVISIRTGGILSKKE-KGWLRNEGRRPFLLCIEDPFDLDN 60

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.

                          10        20
                  ....*....|....*....|....*
gi 76559935    16 FRCCLCDVTTANRPSLDAHLKGRKH 40
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 76559935    58 VFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGVfAIVEMGDI-SAREAV 108
Cdd:TIGR01649   5 VHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQ-ALVEFEDEeSAKACV 55

RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins; This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 76559935  54 GLRSVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGVFAIVEMGDISAREAVLSQPKHSLGGHTLRVRPRE 127
Cdd:cd12279   1 EERSVFVSGFKRGTSELELSDYFQAFGPVASVVMDKDKGVYAIVEMDSTETVEKVLSQPQHCLNGQRLRVKPRE 74

DNA polymerase sigma [Replication, recombination and repair];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935 358 RVQTVPSARRPVVKFCHRPSGLHGDISLSNRLALYNSRFLNLCSEMDSRVRPLVYTLRCWA---QHNGLSGGGplLNNYA 434
Cdd:COG5260 147 EVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLkrrALNDVATGT--LSSYT 224

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935 435 LTLLVIYFLQTRDPPVLptvaqltqrsgegeqvevdgwdcsFPK-DASRLEPSTNVEPLSSLLAQFFSCVS-CWDLSGSL 512
Cdd:COG5260 225 ISCMVLSFLQMHPPFLF------------------------FDNgLLSPLKYNKNIDNLGVLFDDFFELYGkSFNYSLVV 280

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 76559935 513 LSLREGQALmvaggLPSDLWEGL---RLGPMNLQDPF-DLSHNVAAnvTSRVAKRLQS 566
Cdd:COG5260 281 LSINSGDFY-----LPKYEKGWLkpsKPNSLSIQDPGtDRNNDISA--VSFNIKDIKA 331

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 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPV--ANIVMDKDKG---VFAIVEMGDISAREAVLSQP-KHSLGGHTLRVRP 125
Cdd:cd21608   2 LYVGNLSWDTTEDDLRDLFSEFGEVesAKVITDRETGrsrGFGFVTFSTAEAAEAAIDALnGKELDGRSIVVNE 75

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPV--ANIVMDKDKGV---FAIVEMGDISAREAVLSQPKHSLGGHTLRVRPREQK 129
Cdd:cd12330   2 IFVGGLAPDVTEEEFKEYFEQFGTVvdAVVMLDHDTGRsrgFGFVTFDSESAVEKVLSKGFHELGGKKVEVKRATPK 78

RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins; This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 76559935  57 SVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKG-------VFaiVEMGDISAREAVLSQPKHSLGGHTLRV 123
Cdd:cd12291   1 TVYVKGFPLDATLDDIQEFFEKKGKVENVRMRRDLDskefkgsVF--VEFKTEEEAKKFLEKEKLKYKGKELTI 72

Cid1 family poly A polymerase; This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 76559935   491 PLSSLLAQFFSCVS-CWDLSGSLLSLREGQALMVAGgLPSDLWEGLRLGPMNLQDPFDLSH 550
Cdd:pfam03828   1 SLGELLIGFFEYYGrEFDYENVVISIRTGGILSKKE-KGWLRNEGRRPFLLCIEDPFDLDN 60

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPVAN--IVMDKDKGV---FAIVEMGDI-SAREAVLSQPKHSLGGHTLRVR 124
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIaeVMYDRYTGRsrgFGFVTMGSVeDAKAAIEKLNGTEVGGREIKVN 74

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 76559935  56 RSVFVSGFPRDVGSAQLSEYFQTFGPVAN--IVMDKDKG---VFAIVEMGDI-SAREAVLSQPKHSLGGHTLRV 123
Cdd:cd12398   1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSfrLVTDRETGkpkGYGFCEFRDAeTALSAVRNLNGYELNGRPLRV 74

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 76559935  57 SVFVSGFPRDVGSAQLSEYFQTFGPV--ANIVMDKDKG--------VFAIVEmgdiSAREAVLSQPKHSLGGHTLRV 123
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEELFSDVGPVkrCFVVKDKGKDkcrgfgyvTFALAE----DAQRALEEVKGKKFGGRKIKV 73

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.

                          10        20
                  ....*....|....*....|....*
gi 76559935    16 FRCCLCDVTTANRPSLDAHLKGRKH 40
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 76559935  56 RSVFVSGFPRDVGSAQLSEYFQTFGPVAN--IVMDKDKGVFAIVEMGDISAREAVLSQPKHSLGGHTLRVRP 125
Cdd:cd12225   1 RTIHVGGIDGSLSEDELADYFSNCGEVTQvrLCGDRVHTRFAWVEFATDASALSALNLDGTTLGGHPLRVSP 72

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPV--ANIVMDKDKGV---FAIVEMGD-ISAREAVLSQpKHSLGGHTLRVRPREQKE 130
Cdd:cd12579   2 LFVGGLKGDVGEGDLVEHFSQFGTVekVEVIADKDTGKkrgFGFVYFEDhDSADKAAVVK-FHSINGHRVEVKKAVPKE 79

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGV-----FAIVEMGDISAREAVLSQPKHSLGGHTLRVR 124
Cdd:cd12329   2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTnkrrgFCFITFDSEEPVKKILETQFHVIGGKKVEVK 73

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 76559935  56 RSVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGV-----FAIVEMGDISAREAVLSQPKHSLGGHTLRVR 124
Cdd:cd12580   1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSgkkrgFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 74

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGV-----FAIVEMGDISAREAVLS-QPKHSLGGHTLRVRPR 126
Cdd:cd12229   6 LFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGgrlpnFGFVVFDDPEAVQKILAnKPIMFRGEHRLNVEEK 80

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPV--ANIVMDKD---KGvFAIVEMGDISAREAVLS-QPKHSLGGHTLRVRPREQK 129
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVkdVKIIKDRAgvsKG-YGFVTFETQEDAEKIQKwGANLVFKGKKLNVGPAIRK 81

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 76559935  56 RSVFVSGFPRDVGSAQLSEYFQTFGPV--ANIVMD----KDKGvFAIVEMGDIS-AREAVLSQPKHSLGGHTLRV 123
Cdd:cd12674   1 TTLFVRNLPFDVTLESLTDFFSDIGPVkhAVVVTDpetkKSRG-YGFVSFSTHDdAEEALAKLKNRKLSGHILKL 74

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPVAN--IVMDKDKGV---FAIVEMGDISAREAVLSQPKHSLGGHTL 121
Cdd:cd12757   7 MFVGGLSWDTSKKDLKDYFTKFGEVVDctIKMDPNTGRsrgFGFILFKDAASVDKVLEQKEHRLDGRVI 75

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM1 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 76559935  57 SVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGV-FAIVEMGDISAREAVLSQPKHSLGGHTLRV 123
Cdd:cd12296   2 TVLVKNLPKSITENKIRQFFKDCGEIREVKILESGNGlVAVIEFETEDEALAALTKDHKRIGGNEISV 69

RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 76559935  56 RSVFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGVFAIVEMGDISAREAVLSQpKHSLGGHTLRV 123
Cdd:cd12322   1 RKVFVGRCTEDMTEDDLRQYFSQFGEVTDVFIPKPFRAFAFVTFADDEVAQSLCGE-DHIIKGVSVHI 67

RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76559935  58 VFVSGFPRDVGSAQLSEYFQTFGPVANIVMDKDKGV-----FAIVEMGDISAREAVLSQPKHSLGGHTLRVRPREQKEFQ 132
Cdd:cd12574   2 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTnqsrgFGFVKFKDPNCVGTVLASRPHNLDGRNIDPKPCTPRGMQ 81

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.

                          10        20
                  ....*....|....*....|....*..
gi 76559935    15 RFRCCLCDVTTANRPSLDAHLKGRKHR 41
Cdd:pfam12171   1 QFYCVLCDKYFKSENALQNHLKSKKHK 27