RNA recognition motif;

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gi 386770785    95 LYVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFENRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQAPVV 168
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFG--KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386770785   95 LYVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFeNRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHG 163
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFG--PIKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGG 66

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins; This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping.

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gi 386770785  92 RYQLYVGNLTWWTTDQDIANSLRDIGVSDLQEVKFFENRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQAPVVTYP 171
Cdd:cd12644    1 RAAVYVGNFSWWTTDQDLINLIRSLGVKDVVELKFAENRANGQSKGYAEVVVASENSVHLLLELLPGKKLNGEKVDVRLA 80

                         90
                 ....*....|
gi 386770785 172 SKQALTQFES 181
Cdd:cd12644   81 TRQNLSQFEA 90

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 386770785  94 QLYVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFENRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQAPVVTY 170
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFG--EVESAKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNE 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).

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gi 386770785  95 LYVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFENRaNGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQ 164
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFG--EVVSVRIVRDR-DGKSKGFAFVEFESPEDAEKALEALNGTELGGR 67

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).

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gi 386770785  95 LYVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFENRANGQSKGFSVISLGSESSLRAVLdqlpkkEMHGQ 164
Cdd:cd12450    2 LFVGNLSWSATQDDLENFFSDCG--EVVDVRIAMDRDDGRSKGFGHVEFASAESAQKAL------EKSGQ 63

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

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gi 386770785  94 QLYVGNLTWWTTDQDIANSLRDIGVSDLQEVKFfeNRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQAPVVTYPSK 173
Cdd:cd21609    1 RLYVGNIPRNVTSEELAKIFEEAGTVEIAEVMY--DRYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITEK 78

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.

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gi 386770785  95 LYVGNLTWWTTDQDIANSLRDIGVsdLQEVKFFENRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQAPVVT 169
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGA--VFDVKLPMDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVN 73

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.

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gi 386770785  95 LYVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFENRANGQSKGFSVISLGSESSLRAVLDQLPKKEMHGQ 164
Cdd:cd12447    2 LFVGGLSWNVDDPWLKKEFEKYG--GVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGR 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.

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gi 386770785  96 YVGNLTWWTTDQDIANSLRDIGvsDLQEVKFFENRANGQSKGFSVISLGSESSLRAVLdQLPKKEMHGQAPVVT 169
Cdd:cd12306    3 YVGNVDYGTTPEELQAHFKSCG--TINRVTILCDKFTGQPKGFAYIEFVDKSSVENAL-LLNESEFRGRQIKVT 73