RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 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 79325059 148 IRRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLRFAFIEFTDEVGARTALNLSGTMLGFYPVKVMPSKTAI 227
Cdd:cd12459   1 IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAALSLSGTMLGFYPVRVLPSKTAI 80

Ataxin-2 C-terminal region; The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for pfam00658. It has been found in a wide range of eukaryotic proteins. Strikingly, this motif appears to occur solely outside of globular domains.

                          10
                  ....*....|....*
gi 79325059    74 SKLNPMAKEFIPPSL 88
Cdd:pfam07145   3 SKLNPNAKEFVPSFK 17

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 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 79325059 148 IRRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLRFAFIEFTDEVGARTALNLSGTMLGFYPVKVMPSKTAI 227
Cdd:cd12459   1 IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAALSLSGTMLGFYPVRVLPSKTAI 80

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79325059    151 TVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVL--RFAFIEFTDEVGARTALN-LSGTMLGFYPVKV 220
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKskGFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79325059   152 VYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTAL-NLSGTMLG 214
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKgFAFVEFEDEEDAEKAIeALNGKELG 65

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79325059 151 TVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNS--VLRFAFIEFTDEVGARTALN-LSGTMLG 214
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETgrSRGFGFVEMPDDEEAQAAIEaLNGAELM 69

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059 248 TIYCTNIDKKLTQTDIKLFFESvCGEVYRLRLLGDYH--HPTRIGFVEFV---MAESAIAALNcsGVLLGSLPIR-SKNK 321
Cdd:COG0724   3 KIYVGNLPYSVTEEDLRELFSE-YGEVTSVKLITDREtgRSRGFGFVEMPddeEAQAAIEALN--GAELMGRTLKvNEAR 79

                .
gi 79325059 322 P 322
Cdd:COG0724  80 P 80

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM1 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 79325059 148 IRRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLRFAFIEFTDEVGARTALNLSGTMLGFYPVKVMPSKTAI 227
Cdd:cd12459   1 IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRICGDPNSVLRFAFIEFTDEEGARAALSLSGTMLGFYPVRVLPSKTAI 80

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 79325059 150 RTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPnSVLRFAFIEFTDEVGARTALNLSGTMLGFYPVKVMPSKTA 226
Cdd:cd12225   1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDR-VHTRFAWVEFATDASALSALNLDGTTLGGHPLRVSPSKTA 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 79325059 146 EIIRRTVYVSDIDQQVTEEQLAGLFIGF-GQVVDCRICGDPNSVLRFAFIEFTDEVGARTALNLSGTMLGFYPVKVMPSK 224
Cdd:cd12460   1 EMCARTIYCTNIDKKVTQDDVKAFFESLcGEVHRLRLLGDYVHSTRIAFVEFVMAESAIAALNCSGALLGSLPIRVSPSK 80

                .
gi 79325059 225 T 225
Cdd:cd12460  81 T 81

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 79325059 152 VYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTALN-LSGTMLGFYPVKVM 221
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEaLNGTELGGRPLKVS 72

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 79325059   122 RRKKSFGQQGKRRMNPRTSLAQREEII-----RRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR--FAFI 194
Cdd:TIGR01622  82 SYRRRRDDRRSRREKPRARDGTPEPLTederdRRTVFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRNSRRSkgVGYV 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059   195 EFTDEVGARTALNLSGTMLGFYPVKVMPSKTA--IAPVNPTFLPRTEdEREMCARTIYCTNIDKKLTQTDIKLFFESVcG 272
Cdd:TIGR01622 162 EFYDVDSVQAALALTGQKLLGIPVIVQLSEAEknRAARAATETSGHH-PNSIPFHRLYVGNLHFNITEQDLRQIFEPF-G 239

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059   273 EVYRLRL-LGDYHHPTR-IGFVEFVMAESAIAALN-CSGVLLGSLPIR----SKNKPTLT 325
Cdd:TIGR01622 240 EIEFVQLqKDPETGRSKgYGFIQFRDAEQAKEALEkMNGFELAGRPIKvglgNDFTPESD 299

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059   152 VYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTAL-NLSGTMLGfypvKVMPSKtaIAP 229
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRgFAFVNFEKHEDAAKAVeEMNGKKIG----LAKEGK--KLY 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059   230 VNPtFLPRTEDEREMCAR---------------TIYCTNIDKKLTQTDIKLFFESvCGEVYRLRLLGDYHHPTR-IGFVE 293
Cdd:TIGR01628 255 VGR-AQKRAEREAELRRKfeelqqerkmkaqgvNLYVKNLDDTVTDEKLRELFSE-CGEITSAKVMLDEKGVSRgFGFVC 332

                         170       180
                  ....*....|....*....|....
gi 79325059   294 FVMAESAIAALN-CSGVLLGSLPI 316
Cdd:TIGR01628 333 FSNPEEANRAVTeMHGRMLGGKPL 356

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an 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. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and 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. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain 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. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 79325059 149 RRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTALNL 208
Cdd:cd12336   1 DRTLFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKnFAFVTFKHEVSVPYAIQL 61

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 79325059 249 IYCTNIDKKLTQTDIKLFFESvCGEVYRLRLLGDYH-HPTRIGFVEFVMAESAIAALN-CSGVLLGSLPIR 317
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSK-FGEVVSVRIVRDRDgKSKGFAFVEFESPEDAEKALEaLNGTELGGRPLK 70

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059   124 KKSFGQQGKRRMNPRTSlAQREE---IIRRtVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR--FAFIEFTD 198
Cdd:TIGR01645  81 KQTKAHQQQQLENQQRQ-QQRQQalaIMCR-VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHkgFAFVEYEV 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059   199 EVGARTAL-NLSGTMLGFYPVKV-MPSKtaIAPVNPTFLPRTEDEREMcaRTIYCTNIDKKLTQTDIKLFFESVcGEVYR 276
Cdd:TIGR01645 159 PEAAQLALeQMNGQMLGGRNIKVgRPSN--MPQAQPIIDMVQEEAKKF--NRIYVASVHPDLSETDIKSVFEAF-GEIVK 233

                         170       180       190
                  ....*....|....*....|....*....|....
gi 79325059   277 LRLLGD--YHHPTRIGFVEFVMAES---AIAALN 305
Cdd:TIGR01645 234 CQLARAptGRGHKGYGFIEYNNLQSqseAIASMN 267

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 79325059 153 YVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLRFAFIEFTDEVGARTALN-LSGTMLGFYPVKV 220
Cdd:cd12352   2 YVGNLDRQVTEDLILQLFSQIGPCKSCKMITEHGGNDPYCFVEFYEHNHAAAALQaMNGRKILGKEVKV 70

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79325059 152 VYVSDIDQQVTEEQLAGLFIGFGQVVDC-----RICGDPNSvlrFAFIEFTDEVGARTALN-LSGTMLGFYPVKV 220
Cdd:cd12334   1 VYVGNLDEKVTEELLWELFIQAGPVVNVhmpkdRVTQQHQG---YGFVEFLSEEDADYAIKiMNMIKLYGKPIRV 72

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 79325059 151 TVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTALNLSGTMLGFYPVKV 220
Cdd:cd12391   1 TVFVSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKGKSKgYCYVEFKDEESAQKALKLDRQPVEGRPMFV 71

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 79325059 149 RRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTA-LNLSGTMLG 214
Cdd:cd12392   2 KNKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKgLAYVEYENEADASQAvLKTDGTEIK 69

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 79325059 152 VYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR--FAFIEFTDEVGARTALNLSGTMLGFYPVKV 220
Cdd:cd12306   2 IYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFTGQPkgFAYIEFVDKSSVENALLLNESEFRGRQIKV 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 79325059 150 RTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR--FAFIEFTDEVGARTAL-NLSGTMLGFYPVKV 220
Cdd:cd12398   1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDRETGKPkgYGFCEFRDAETALSAVrNLNGYELNGRPLRV 74

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79325059 151 TVYVSDIDQQVTEEQLAGLFIGFGQVVDCRIC--GDPNSVLRFAFIEFTDEVGARTALNLSGTMLG 214
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAmdRDDGRSKGFGHVEFASAESAQKALEKSGQDLG 66

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 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 RRMs, which may play an important structural role in organizing specific rRNA processing events.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 79325059 160 QVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGARTALN-LSGTML 213
Cdd:cd12320  11 EATRKEIRELFSPFGQLKSVRLPKKFDGSHRgFAFVEFVTKQEAQNAMEaLKSTHL 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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 79325059 148 IRRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTDEVGA 202
Cdd:cd12412   1 IPNRIFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKgYGFVTFETQEDA 56

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 79325059   249 IYCTNIDKKLTQTDIKLFFESvCGEVYRLRLLGDYHHPTR-IGFVEFVMAESAIAAL-NCSGVLLGSLPIR 317
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSK-FGPIKSIRLVRDETGRSKgFAFVEFEDEEDAEKAIeALNGKELGGRELK 70

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 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 79325059 151 TVYVSDIDQQVTEEQLAGLFIGFGQVVDCRI-----CGdpnsvlrfaFIEFTDEVGARTALN-LSGTMLG 214
Cdd:cd12346   3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIppgkgCG---------FVQFVNRASAEAAIQkLQGTPIG 63

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79325059 152 VYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR--FAFIEFTDEVGARTALN-LSGTMLG 214
Cdd:cd12353   2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKDTQTGKSkgYGFVSFVKKEDAENAIQgMNGQWLG 67

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 79325059 246 ARTIYCTNIDKKLTQTDIKLFF------ESvcgeVYRLRLLGDYHHPTR-IGFVEFVMAESAIAALN-CSGVLLG 312
Cdd:cd21619   1 SNTIYVGNIDMTINEDALEKIFsrygqvES----VRRPPIHTDKADRTTgFGFIKYTDAESAERAMQqADGILLG 71

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 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 79325059 151 TVYVSDIDQQVTEEQLAGLFIGFGQVVDCRIcgdP----NSVLRFAFIEFTDEVGARTALNLSGTMLG 214
Cdd:cd12297   2 TLWVTNFPPSYDERSIRDLFGDYGVILSVRL---PslryNTSRRFCYIDFTSPESARAAVELLNGLLE 66

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 79325059 150 RTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRIC-----GDPNSvlrFAFIEFTDEVGARTAL-NLSGTMLG 214
Cdd:cd12671   7 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVydretGKPKG---YGFCEYQDQETALSAMrNLNGYELN 74

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 79325059 150 RTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR-FAFIEFTD-EVGARTALNLSGTMLGFYPVKV 220
Cdd:cd12309   3 RTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNaYAFVKFLNlDMAHRAKVAMSGQYIGRNQIKI 75

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 79325059 152 VYVSDIDQQVTEEQLAGLFIGFGQVVDCricgdpnSVLR-FAFIEFTDEVGARTAL-NLSGTML 213
Cdd:cd12608   3 IFVGNVDEDTSQEELSALFEPYGAVLSC-------AVMKqFAFVHMRGEAAADRAIrELNGREL 59

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 79325059 150 RTVYVSDIDQQVTEEQL----------AGLFIGFGQ-VVDCRICGDPNsvlrFAFIEFTDEVGARTALNLSGTMLGFYPV 218
Cdd:cd12230   2 RRLYVGNIPPGITEEELmdffnqamraAGLTQAPGNpVLAVQINPDKN----FAFVEFRSVEETTAALALDGIIFKGQPL 77

                ..
gi 79325059 219 KV 220
Cdd:cd12230  78 KI 79

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79325059 133 RRMNPRTSLAQREEIIRRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGDPNSVLR--FAFIEFTDEVGARTALNLSG 210
Cdd:cd21615   2 REWNPEEDPHIADGDPYKTLFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDKETGKSrgYAFIVFKSESDAKNAFKEGN 81

                ....
gi 79325059 211 TMLG 214
Cdd:cd21615  82 GLRG 85

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 79325059 248 TIYCTNIDKKLTQTDIKLFFESvCGEVYRLRLLGDYHHPTRIGF--VEFVMAESAIAALNCSGVLLGSLPIR 317
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSD-CGEVVDVRIAMDRDDGRSKGFghVEFASAESAQKALEKSGQDLGGREIR 71