RNA recognition motif;

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50949388    196 RIYVKNLAKHVQEKDLKYIFGRYVDFSSEtqRIMFDirlMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVV 273
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESV--RLVRD---KETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50949388 197 IYVKNLAKHVQEKDLK----YIFGRYvdfssetQRIMfDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV 272
Cdd:cd12246   2 LYINNLNEKIKKDELKrslyALFSQF-------GPVL-DIVASKSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMR 73

                ....*
gi 50949388 273 VQFAR 277
Cdd:cd12246  74 IQYAK 78

RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50949388 193 PNCRIYVKNLAKHVQEKDLKYIFgrYVDFSSETQriMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV 272
Cdd:cd12476   5 PNQTIYINNLNEKVKKEELKKSL--YAIFSQFGQ--ILDIVALKTLKMRGQAFVIFKDISSATNALRSMQGFPFYDKPMR 80

                ....*
gi 50949388 273 VQFAR 277
Cdd:cd12476  81 IAYSK 85

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50949388 195 CRIYVKNLAKHVQEKDLKYIFGRYvdFSSETQRIMFDirlmKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQ 274
Cdd:cd12418   1 TRVRVSNLHPDVTEEDLRELFGRV--GPVKSVKINYD----RSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKVE 74

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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50949388 196 RIYVKNLAKHVQEKDLKYIFGRYVDFSSetQRIMFDirlMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQF 275
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVES--AKVITD---RETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNE 75

                .
gi 50949388 276 A 276
Cdd:cd21608  76 A 76

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.

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                ....*....|....*....|....*....|....*....|....*....|....
gi 50949388 196 RIYVKNLAKHVQEKDLKYIFgryvdfssETQRIMFDIRLMK--EGRMKGQAFIG 247
Cdd:cd12565   2 RIIVKNLPKYVTEKRLKEHF--------SKKGEITDVKVMRtkDGKSRRFGFIG 47

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50949388   153 KEDSDEMPSECIS----RRELEKGRISREEMETLSVFRSYEPGEPNcrIYVKNLAKHVQEKDLKYIFGRYVDFSSetQRI 228
Cdd:TIGR01628 242 KKIGLAKEGKKLYvgraQKRAEREAELRRKFEELQQERKMKAQGVN--LYVKNLDDTVTDEKLRELFSECGEITS--AKV 317

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 50949388   229 MFDirlmKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA 276
Cdd:TIGR01628 318 MLD----EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 50949388 191 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDfssetqriMFDIRLMKE---GRMKGQAFI 246
Cdd:cd12237   1 GDPRLTLFVGRLSLQTTEEKLKEVFSRYGD--------IRRLRLVRDivtGFSKRYAFI 51