RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126 144 DVYVGNLPGDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 215
Cdd:cd12270     1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126 144 DVYVGNLPGDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 215
Cdd:cd12270     1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72

5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2217307126   7 AVSKETPVVTIVHDCQVVD-IPeelVEEHDITVDYILTPTRV 47
Cdd:COG0212   148 RLRPRPLTIGLAFDCQLVDeLP---VEPHDVPLDAIVTEKGV 186

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217307126 146 YVGNLPGDARVSDLKRALRELGSV------PLRLTwQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 219
Cdd:COG0724     5 YVGNLPYSVTEEDLRELFSEYGEVtsvkliTDRET-GRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83

                  .
gi 2217307126 220 K 220
Cdd:COG0724    84 R 84

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2217307126 183 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 219
Cdd:TIGR01661  49 FVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD 85

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126 144 DVYVGNLPGDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 215
Cdd:cd12270     1 TVYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126  145 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 211
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVesvrlVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2217307126   7 AVSKETPVVTIVHDCQVVD-IPeelVEEHDITVDYILTPTRV 47
Cdd:COG0212   148 RLRPRPLTIGLAFDCQLVDeLP---VEPHDVPLDAIVTEKGV 186

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 2217307126 145 VYVGNLPGDARVSDLKRALRELGSV-PLRL-----TWQgPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 214
Cdd:cd12398     3 VFVGNIPYDATEEQLKEIFSEVGPVvSFRLvtdreTGK-PKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217307126 140 PLAADVYVGNLPGDARVSDLKRALRELGsvPLRLTW--QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 217
Cdd:cd12645     2 PLDCKVYVGNLGNNGNKTELERAFGYYG--PLRSVWvaRNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 79

                  .
gi 2217307126 218 R 218
Cdd:cd12645    80 K 80

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126 145 VYVGNLPGDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 211
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVfdvklPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72

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 2217307126 145 VYVGNLPGDARVSDLKRALRELGSV-PLRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 211
Cdd:cd12671     9 VFVGNIPYEATEEQLKDIFSEVGPVvSFRLVYDretgKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRV 80

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7); This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126 145 VYVGNLPGDARVSDLKRALRELGsvPLRLTW--QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 214
Cdd:cd12646     2 VYVGNLGTGAGKGELERAFSYYG--PLRTVWiaRNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 71

RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family; This subfamily corresponds to the RRM3 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 is a novel 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 shares 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2217307126 145 VYVGNLPGDARVSDLKRALRELGSvPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 211
Cdd:cd12310     1 LWVGGLGPWTSLAELEREFDRFGA-IRKIDYRKGDDYAYILYESLDAAQAAVRALRGFPLGGPDRRL 66

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2217307126 182 AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 215
Cdd:cd12771    49 GFVNYIEPKDAEKAINTLNGLRLQTKTIKVSYAR 82

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217307126 106 QTVPLSVGR------RPPDTPGPET-NSMEAAPGSPPGEGAPLAAD----VYVGNLPGDARVSDLKRALRELGsvPLR-- 172
Cdd:TIGR01642 248 SNVFLKIRRphdyipVPQITPEVSQkNPDDNAKNVEKLVNSTTVLDskdrIYIGNLPLYLGEDQIKELLESFG--DLKaf 325

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2217307126 173 -----LTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 216
Cdd:TIGR01642 326 nlikdIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV 374

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217307126 145 VYVGNLPGDARVSDLKRALRELGSV-PLRLTWQGPRRR----AFLHYPDSAAAQQAVSCLQGLRLGTDTLRV 211
Cdd:cd12370     3 VYVGSIYFELGEDTIRQAFAPFGPIkSIDMSWDPVTMKhkgfAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2217307126 159 LKRALRELGSVpLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 215
Cdd:cd12305    19 LKKAFSPFGNI-INISMEIEKNCAFVTFEKMESADQAIAELNGTTVEGVQLKVSIAR 74

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2217307126 146 YVGNLPGDARVSDLKRALRELGSVPLRL----TWQGPRRRAFLHYPDSAAAQQAVScLQGLRLGTDTLRVALARQQR 218
Cdd:cd12402     6 YLGNLPYDVTEDDIEDFFRGLNISSVRLprenGPGRLRGFGYVEFEDRESLIQALS-LNEESLKNRRIRVDVAGQAQ 81