RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 178 DEIRRTVYVGNLNSqTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHSN 257
Cdd:cd12260     1 EEIRRTVYVGNLDP-STTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSN 79

                  ....*.
gi 1021311773 258 NAIVKP 263
Cdd:cd12260    80 NAIVKP 85

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 178 DEIRRTVYVGNLNSqTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHSN 257
Cdd:cd12260     1 EEIRRTVYVGNLDP-STTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSN 79

                  ....*.
gi 1021311773 258 NAIVKP 263
Cdd:cd12260    80 NAIVKP 85

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1021311773 183 TVYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGD-ET-QPTRFAFVEFADQNSVPRAL-AFNGVMFGDRPLKIN 254
Cdd:COG0724     3 KIYVGNL-PYSVTEEDLRELFSEYGEVTSVKLITDrETgRSRGFGFVEMPDDEEAQAAIeALNGAELMGRTLKVN 76

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1021311773 181 RRTVYVGNLNSQTTTADqLLEFFKQVGEVKFVRMAGDET--QPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHS 256
Cdd:TIGR01622 114 RRTVFVQQLAARARERD-LYEFFSKVGKVRDVQIIKDRNsrRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQLS 190

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1021311773   20 VIQVTNLSSAVTSEQMRTLFSFLGEIEELRLYPpdNAPLAFSSKVCYVKFRDPSSVGVAQHLTNTVFID-RALIV 93
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVR--DKETGKSKGFAFVEFESEEDAEKALEALNGKELDgRPLKV 73

nucleic acid binding protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 182 RTVYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGDeTQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHSNNAIV 261
Cdd:PLN03120    5 RTVKVSNV-SLKATERDIKEFFSFSGDIEYVEMQSE-NERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDYQL 82

                          90       100
                  ....*....|....*....|....*....
gi 1021311773 262 KPPEMTPQAAAKELEEVMKRVREAQSFIS 290
Cdd:PLN03120   83 PPEALAPLSSNSPASGAESAVKKAEDVVS 111

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 178 DEIRRTVYVGNLNSqTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHSN 257
Cdd:cd12260     1 EEIRRTVYVGNLDP-STTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSN 79

                  ....*.
gi 1021311773 258 NAIVKP 263
Cdd:cd12260    80 NAIVKP 85

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1021311773  20 VIQVTNLSSAVTSEQMRTLFSFLGEIEELRLYPPDNAPLAFSSKVCYVKFRDPSSVGVAQHLTNTVFIDRALIVVP 95
Cdd:cd12259     1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPSEDDLAPVLSKVCFVKYEDPEDVAVALHLTNTVFIDRALIVIP 76

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM2 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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 178 DEIRRTVYVGNLNSQTTTaDQLLEFFKQV-GEVKFVRMAGDETQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHS 256
Cdd:cd12460     1 EMCARTIYCTNIDKKVTQ-DDVKAFFESLcGEVHRLRLLGDYVHSTRIAFVEFVMAESAIAALNCSGALLGSLPIRVSPS 79

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 1021311773 182 RTVYVGNLNSQTTTADqLLEFFKQVGEVKFVRMAGDETQpTRFAFVEFADQNSVPRALAFNGVMFGDRPLKINHSNNA 259
Cdd:cd12225     1 RTIHVGGIDGSLSEDE-LADYFSNCGEVTQVRLCGDRVH-TRFAWVEFATDASALSALNLDGTTLGGHPLRVSPSKTA 76

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1021311773 183 TVYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGD-ET-QPTRFAFVEFADQNSVPRAL-AFNGVMFGDRPLKIN 254
Cdd:COG0724     3 KIYVGNL-PYSVTEEDLRELFSEYGEVTSVKLITDrETgRSRGFGFVEMPDDEEAQAAIeALNGAELMGRTLKVN 76

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are 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. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1021311773 184 VYVGNLNsQTTTADQLLEFFKQVGEVKFVRMAGDET--QPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKI 253
Cdd:cd12306     2 IYVGNVD-YGTTPEELQAHFKSCGTINRVTILCDKFtgQPKGFAYIEFVDKSSVENALLLNESEFRGRQIKV 72

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 1021311773 184 VYVGNLNsQTTTADQLLEFFKQVGEVKFVRMAGDET-QPTRFAFVEFADQNSVPRAL-AFNGVMFGDRPLK 252
Cdd:pfam00076   1 LFVGNLP-PDTTEEDLKDLFSKFGPIKSIRLVRDETgRSKGFAFVEFEDEEDAEKAIeALNGKELGGRELK 70

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 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 1021311773 185 YVGNLNSQTTTaDQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPRAL-AFNGVMFGDRPLKIN 254
Cdd:cd12352     2 YVGNLDRQVTE-DLILQLFSQIGPCKSCKMITEHGGNDPYCFVEFYEHNHAAAALqAMNGRKILGKEVKVN 71

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1021311773 184 VYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGDET--QPTRFAFVEFADQNSVPRALAFNGVMFGDRplKIN 254
Cdd:cd12400     3 LFVGNL-PYDTTAEDLKEHFKKAGEPPSVRLLTDKKtgKSKGCAFVEFDNQKALQKALKLHHTSLGGR--KIN 72

RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins; This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1021311773 184 VYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGDETQ--PTRFAFVEFADQNSVPRALAF-NGVMFGDRPLKI 253
Cdd:cd12240     1 LYVGNL-SFYTTEEQIYELFSKCGDIKRIIMGLDKFKktPCGFCFVEYYSREDAENAVKYlNGTKLDDRIIRV 72

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1021311773 183 TVYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGD-ETQPTR-FAFVEFADQNSVPRALAFNGVMFGDRPLKI 253
Cdd:cd12395     1 SVFVGNL-PFDIEEEELRKHFEDCGDVEAVRIVRDrETGIGKgFGYVLFKDKDSVDLALKLNGSKLRGRKLRV 72

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 1021311773 183 TVYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGD-ETQPTR-FAFVEFADQNSVPRALAF-NGVMFGDRPLKIN 254
Cdd:cd21608     1 KLYVGNL-SWDTTEDDLRDLFSEFGEVESAKVITDrETGRSRgFGFVTFSTAEAAEAAIDAlNGKELDGRSIVVN 74

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1021311773 182 RTVYVGNLNSQTTTaDQLLEFFKQVGEVKFVRMAGD-ETQPTRFAFVEFADQNSVPRALA-FNGVMFGDRPLKI 253
Cdd:cd12592     2 RTLFVGNLDTKVTE-ELLFELFLQAGPVIKVKIPKDkDGKPKQFAFVNFKHEVSVPYAMNlLNGIKLYGRPLKI 74

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 184 VYVGNLNSQTTTADqLLEFFKQVGEVKFVRMAGD-ETQPTR-FAFVEFADQNSVprALA---FNGVMFGDRPLKINHSNN 258
Cdd:cd12411    12 IYIGGLPYELTEGD-ILCVFSQYGEIVDINLVRDkKTGKSKgFAFLAYEDQRST--ILAvdnLNGIKLLGRTIRVDHVEN 88

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 1021311773 184 VYVGNLNSQTTTADqLLEFFKQVGEVKFVRMA--GDETQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKI 253
Cdd:cd12271     1 VYVGGIPYYSTEAE-IRSYFSSCGEVRSVDLMrfPDSGNFRGIAFITFKTEEAAKRALALDGEMLGNRFLKV 71

RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins; This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1021311773 183 TVYVGNLNSQTTtADQLLEFFKQVGEVKFVRMAGDE--TQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKIN 254
Cdd:cd12550     1 SVYVGNVDYGAT-AEELEAHFHGCGSVNRVTILCDKfsGHPKGFAYIEFADKESVRTALALDESLFRGRQIKVM 73

RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 182 RTVYVGNLNsQTTTADQLLEFFKQVgevkfVRMAGDETQP------------TRFAFVEFADQNSVPRALAFNGVMFGDR 249
Cdd:cd12230     2 RRLYVGNIP-PGITEEELMDFFNQA-----MRAAGLTQAPgnpvlavqinpdKNFAFVEFRSVEETTAALALDGIIFKGQ 75

                  ....
gi 1021311773 250 PLKI 253
Cdd:cd12230    76 PLKI 79

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1021311773 182 RTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPRA-LAFNGVMFGDRPLKI 253
Cdd:cd12390     3 KCLFVDRLPKDFRDGSELRKLFSQVGKPTFCQLAMGNGVPRGFAFVEFASAEDAEEAqQLLNGHDLQGSPIRV 75

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1021311773  21 IQVTNLSSAVTSEQMRTLFSFLGEIEELRLYPPDNAPlafSSKVCYVKFRDPSSVGVA-QHLTNTVFIDRALIV 93
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGK---SKGFAFVEFESPEDAEKAlEALNGTELGGRPLKV 71

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three 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 1021311773 182 RTVYVGNLNSqTTTADQLLEFFKQVGEVKFVRMAGDET----QPTRFAFVEFADQNSVPRAL-AFNGVMFGDRPLKI 253
Cdd:cd21619     2 NTIYVGNIDM-TINEDALEKIFSRYGQVESVRRPPIHTdkadRTTGFGFIKYTDAESAERAMqQADGILLGRRRLVV 77

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1021311773 184 VYVGNLNSqTTTADQLLEFFKQVGEVKFVRMAGDETQPTR-FAFVEFADQNSVPRALA-FNGVMFGDRPLKIN 254
Cdd:TIGR01628 288 LYVKNLDD-TVTDEKLRELFSECGEITSAKVMLDEKGVSRgFGFVCFSNPEEANRAVTeMHGRMLGGKPLYVA 359

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 1021311773 183 TVYVGNLNSqTTTADQLLEFFKQVGEVKFVRMAGDETQpTRF---AFVEFADQNSVPRALAFNGVMFGDRPLKI 253
Cdd:cd12291     1 TVYVKGFPL-DATLDDIQEFFEKKGKVENVRMRRDLDS-KEFkgsVFVEFKTEEEAKKFLEKEKLKYKGKELTI 72

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1021311773   20 VIQVTNLSSAVTSEQMRTLFSFLGEIEELRLYPpdNAPLAFSSKVCYVKFRDPSSVGVAQHLTNTVFID-RALIV 93
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVR--DKETGKSKGFAFVEFESEEDAEKALEALNGKELDgRPLKV 73

RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2); This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1021311773 183 TVYVGNLNsQTTTADQLLEFFKQVGEVKFVRMAGDE--TQPTRFAFVEFADQNSVPRALAFNGVMFGDRPLKI 253
Cdd:cd12551     1 SVYVGNVD-YGSTADELEAHFNGCGPINRVTILCDKfsGHPKGYAYIEFATRSSVQAAVALDESSFRGRVIKV 72

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 183 TVYVGNLNSQTTTAD---QLLEFFKQVGEV------KFVRMAGdetQptrfAFVEFADQNSVPRAL-AFNGVMFGDRPLK 252
Cdd:cd12246     1 TLYINNLNEKIKKDElkrSLYALFSQFGPVldivasKSLKMRG---Q----AFVVFKDVESATNALrALQGFPFYGKPMR 73

                  ....
gi 1021311773 253 INHS 256
Cdd:cd12246    74 IQYA 77

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM1 of Nop12p which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 182 RTVYVGNLNSQTTTADQLLEFFK----QVGEVKFVR---MAGDETQPTRFAFVE---------------FADQNSVPRAL 239
Cdd:cd12669     1 RTIFVGNLPAEVVTSKSVYKNFKklfnQFGKIQSIRfrsISFSDALPRKVAFIQkkfhssrdtvnayivFKEQSSAKSAL 80

                          90
                  ....*....|....*.
gi 1021311773 240 AFNGVMFGDRPLKINH 255
Cdd:cd12669    81 SLNGTVFMDRHLRVDS 96

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1021311773 183 TVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGD-ETQPTR-FAFVEFADQNSVPRALA-FNGVMFGDRPLKI 253
Cdd:cd12613     3 SIFVGDLSPTTNESDLVSLFQSRFPSCKSAKIMTDpVTGVSRgYGFVRFSDENDQQRALIeMQGKYCQGRPLRI 76

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 1021311773 181 RRTVYVGNLnSQTTTADQLLEFFKQVGEVKFVRMAGDET-QPTRFAFVEFADQNSVPRA-LAFNGVMFGDRPLKInhsnn 258
Cdd:cd12392     2 KNKLFVKGL-PFSCTKEELEELFKQHGTVKDVRLVTYRNgKPKGLAYVEYENEADASQAvLKTDGTEIKDHTISV----- 75

                  ....*.
gi 1021311773 259 AIVKPP 264
Cdd:cd12392    76 AISNPP 81

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 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 1021311773 183 TVYVGNLNS---QTTTADQLLEFFKQVGEVKFVRMAGD-ETQPTR-FAFVEFADQNSVPRALAFNGVMFGDRPLKIN 254
Cdd:cd12451     1 TIFVKGFDAslgEDTIRDELREHFGECGEVTNVRIPTDrETGELKgFAYIEFSTKEAKEKALELNGSDIAGGNLVVD 77

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and 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. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1021311773 183 TVYVGNLNSQTTTADqLLEFFKQVGEVKFVRMAGDETqptrFAFVEFADQNSVPRA-LAFNGVMFGDRPLK 252
Cdd:cd12354     2 TVYVGNITKGLTEAL-LQQTFSPFGQILEVRVFPDKG----YAFIRFDSHEAATHAiVSVNGTIINGQAVK 67

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is 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. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 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. NAM8 also contains three RRMs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021311773 183 TVYVGNLNSQTTTAdQLLEFFKQV-GEVKFVRMAGDetQPTR----FAFVEFADQNSVPRALA-FNGVMFGDRPLKINHS 256
Cdd:cd12345     3 SLFVGDLAPDVTDY-QLYETFSARyPSVRGAKVVMD--PVTGrskgYGFVRFGDESEQDRALTeMQGVYLGSRPIRVSPA 79