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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGKSNlensIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKGYLKLRERELRIS 360
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDCGD----VEAVRIVRDRETGIGKGFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGKSNlensIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKGYLKLRERELRIS 360
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDCGD----VEAVRIVRDRETGIGKGFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73

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 15237960   115 KRKKRKRDEIENEYETKKYGS-VEMKEKKVGEKRKKADEVADTMVSKEGFDDESKLLRTVFVGNLPLKVKKKVILKEFSK 193
Cdd:TIGR01622  58 ERRSRSRRPNRRYRPREKRRRrGDSYRRRRDDRRSRREKPRARDGTPEPLTEDERDRRTVFVQQLAARARERDLYEFFSK 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960   194 FGEVESVRirsvpivdskrtrkgaiMLKQINEKASSVHAYVVFETEQSAAASLAHNMSLIDGNHVRV-------DRACPP 266
Cdd:TIGR01622 138 VGKVRDVQ-----------------IIKDRNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVqlseaekNRAARA 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960   267 RKKQKGHDDTHLydPKRTVFMGNLPFDVKDEEVYQLFtgksNLENSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLK 346
Cdd:TIGR01622 201 ATETSGHHPNSI--PFHRLYVGNLHFNITEQDLRQIF----EPFGEIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALE 274

                         250       260
                  ....*....|....*....|..
gi 15237960   347 K-GYLKLRERELRISRVKPDTP 367
Cdd:TIGR01622 275 KmNGFELAGRPIKVGLGNDFTP 296

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 15237960   285 VFMGNLPFDVKDEEVYQLFTGKsnleNSIEAVRVIRDPHLNiGKGIAYVLFKTREAANLVLKK--GYlKLRERELR 358
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKF----GPIKSIRLVRDETGR-SKGFAFVEFEDEEDAEKAIEAlnGK-ELGGRELK 70

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 15237960   173 VFVGNLPLKVKKKVILKEFSKFGEVESVRIrsvpIVDSKRTRKGaimlkqinekassvHAYVVFETEQSAAASLA 247
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRL----VRDETGRSKG--------------FAFVEFEDEEDAEKAIE 57

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGKSNlensIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKGYLKLRERELRIS 360
Cdd:cd12395   1 SVFVGNLPFDIEEEELRKHFEDCGD----VEAVRIVRDRETGIGKGFGYVLFKDKDSVDLALKLNGSKLRGRKLRVK 73

RNA recognition motif;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15237960    284 TVFMGNLPFDVKDEEVYQLFT--GKsnlensIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKK-GYLKLRERELRI 359
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSkfGK------VESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAlNGKELDGRPLKV 73

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 15237960 285 VFMGNLPFDVKDEEVYQLFT--GKsnlensIEAVRVIRDPHlNIGKGIAYVLFKTREAANLVLKK-GYLKLRERELRIS 360
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSkfGE------VVSVRIVRDRD-GKSKGFAFVEFESPEDAEKALEAlNGTELGGRPLKVS 72

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 283 RTVFMGNLPFDVKDEEVYQLFT--GKsnlensIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLK-------KGYLKLR 353
Cdd:cd12415   1 KTVFIRNLSFDTTEEDLKEFFSkfGE------VKYARIVLDKDTGHSKGTAFVQFKTKESADKCIEaandeseDGGLVLD 74

                ....*...
gi 15237960 354 ERELRISR 361
Cdd:cd12415  75 GRKLIVSL 82

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 15237960   115 KRKKRKRDEIENEYETKKYGS-VEMKEKKVGEKRKKADEVADTMVSKEGFDDESKLLRTVFVGNLPLKVKKKVILKEFSK 193
Cdd:TIGR01622  58 ERRSRSRRPNRRYRPREKRRRrGDSYRRRRDDRRSRREKPRARDGTPEPLTEDERDRRTVFVQQLAARARERDLYEFFSK 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960   194 FGEVESVRirsvpivdskrtrkgaiMLKQINEKASSVHAYVVFETEQSAAASLAHNMSLIDGNHVRV-------DRACPP 266
Cdd:TIGR01622 138 VGKVRDVQ-----------------IIKDRNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVqlseaekNRAARA 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960   267 RKKQKGHDDTHLydPKRTVFMGNLPFDVKDEEVYQLFtgksNLENSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLK 346
Cdd:TIGR01622 201 ATETSGHHPNSI--PFHRLYVGNLHFNITEQDLRQIF----EPFGEIEFVQLQKDPETGRSKGYGFIQFRDAEQAKEALE 274

                         250       260
                  ....*....|....*....|..
gi 15237960   347 K-GYLKLRERELRISRVKPDTP 367
Cdd:TIGR01622 275 KmNGFELAGRPIKVGLGNDFTP 296

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 15237960 281 PKRTVFMGNLPFDVKDEEVYQLFTGKsnlenSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKGYLKLRERELRI 359
Cdd:cd12402   1 PPYTAYLGNLPYDVTEDDIEDFFRGL-----NISSVRLPRENGPGRLRGFGYVEFEDRESLIQALSLNEESLKNRRIRV 74

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 285 VFMGNLPFDVKDEEVYQLFTGksnlENSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLK-KGYLKLRERELRIS 360
Cdd:cd12448   1 LFVGNLPFSATQDALYEAFSQ----HGSIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDaLGGEYIDGRPIRLD 73

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15237960 280 DPKRTVFMGNLPFDVKDEEVYQLFTGKSnlenSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKG 348
Cdd:cd21615  16 DPYKTLFVGRLDYSLTELELQKKFSKFG----EIEKIRIVRDKETGKSRGYAFIVFKSESDAKNAFKEG 80

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 172 TVFVGNLPLKVKKKVILKEFSKFGEVESVRIrsvpIVDSKRTRkgaimlkqinekaSSVHAYVVFETEQSAAASL-AHNM 250
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKV----ITDRETGR-------------SRGFGFVTFSTAEAAEAAIdALNG 63

                        90
                ....*....|...
gi 15237960 251 SLIDGNHVRVDRA 263
Cdd:cd21608  64 KELDGRSIVVNEA 76

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFT--GKsnlensIEAVRVIRDpHLNIGKGIAYVLFKTREAANLVLKKG-YLKLRERELRIS 360
Cdd:cd12412   4 RIFVGGIDWDTTEEELREFFSkfGK------VKDVKIIKD-RAGVSKGYGFVTFETQEDAEKIQKWGaNLVFKGKKLNVG 76

                ..
gi 15237960 361 RV 362
Cdd:cd12412  77 PA 78

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 286 FMGNLPFDVKDEEVYQLFTGKSNlensIEAVRVIRDPHLNIGKGIAYVLFKTREAAN 342
Cdd:cd12361   3 FVGMIPKTASEEDVRPLFEQFGN----IEEVQILRDKQTGQSKGCAFVTFSTREEAL 55

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 172 TVFVGNLPLKVKKKVILKEFSKFGEVESVRIrsvpIVDSKRTRkgaimlkqinekaSSVHAYVVFETEQSAAASLAH-NM 250
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARV----ITDRGSGR-------------SKGYGYVDFATPEAAQKALAAmSG 63

                        90
                ....*....|...
gi 15237960 251 SLIDGNHVRVDRA 263
Cdd:cd12447  64 KEIDGRQINVDFS 76

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 172 TVFVGNLPLKVKKKVILKEFSKFGEVESVRIRSVpiVDSKRTRKgaimlkqinekassvHAYVVFETEQSAAASLAHNMS 251
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAMD--RDDGRSKG---------------FGHVEFASAESAQKALEKSGQ 63

                        90
                ....*....|..
gi 15237960 252 LIDGNHVRVDRA 263
Cdd:cd12450  64 DLGGREIRLDLA 75

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237960 282 KRTVFMGNLPFDVKDEEVYQLFT--GKsnlensIEAVRVIRDPHLNIGKGIAYVLFKTREAA 341
Cdd:cd12393   1 KSTVYVSNLPFSLTNNDLHQIFSkyGK------VVKVTILKDKETRKSKGVAFVLFLDRESA 56

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGksnlENSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLK 346
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSE----FGEVESAKVITDRETGRSRGFGFVTFSTAEAAEAAID 59

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 283 RTVFMGNLPFDVKDEEVYQLFTGKSNLENsieaVRVIRDPHLNIGKGIAYVLFKTREAA-----NLvlkKGYlKLREREL 357
Cdd:cd12398   1 RSVFVGNIPYDATEEQLKEIFSEVGPVVS----FRLVTDRETGKPKGYGFCEFRDAETAlsavrNL---NGY-ELNGRPL 72

                ..
gi 15237960 358 RI 359
Cdd:cd12398  73 RV 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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGKSnlenSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKGYLKLRERELRI 359
Cdd:cd12450   1 TLFVGNLSWSATQDDLENFFSDCG----EVVDVRIAMDRDDGRSKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGKSNlenSIEAVRVIRDPHLNIGKGIAYVLF 335
Cdd:cd12345   3 SLFVGDLAPDVTDYQLYETFSARYP---SVRGAKVVMDPVTGRSKGYGFVRF 51

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237960 171 RTVFVGNLPLKVKKKVILKEFSKFGEVESVRirsvpIVDSKRTRKgaimlkqinekaSSVHAYVVFETEQSA 242
Cdd:cd21615  19 KTLFVGRLDYSLTELELQKKFSKFGEIEKIR-----IVRDKETGK------------SRGYAFIVFKSESDA 73

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237960 285 VFMGNLPFDVKDEEVYQLFTGKSNLEnsiEAVRVIRDPHlNIGKGIAYVLFKTREAANLVLKKGYLKLRERE 356
Cdd:cd12514   2 IRITNLPYDATPVDIQRFFEDHGVRP---EDVHLLRNKK-GRGNGEALVTFKSEGDAREVLKLNGKKLGKRE 69

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 284 TVFMGNLPFDVKDEEVYQLFTGKSnlenSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKKGYLKLRERELRIS 360
Cdd:cd12272   1 TVYIGNLAWDIDEDDLRELFAECC----EITNVRLHTDKETGEFKGYGHVEFADEESLDAALKLAGTKLCGRPIRVD 73

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 172 TVFVGNLPLKVKKKVILKEFSKFGEVESVRirsvPIVDSKRTRKGaimlkqinekassvHAYVVFETEQSAAASLAHNMS 251
Cdd:cd12391   1 TVFVSNLDYSVPEDKIREIFSGCGEITDVR----LVKNYKGKSKG--------------YCYVEFKDEESAQKALKLDRQ 62

                ....
gi 15237960 252 LIDG 255
Cdd:cd12391  63 PVEG 66

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15237960 286 FMGNLPFDVKDEEVYQLFTGKSNlensIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLK 346
Cdd:cd12637   3 FVGSLPKTATEQEVRDLFEAYGE----VEEVYLMKDPVTQQGTGCAFVKFAYKEEALAAIR 59

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Mug28 is a meiosis-specific protein that regulates spore wall formation. 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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 171 RTVFVGNLPLKVKKKVILKEFSKFGEVesvrIRSVPIVDSKRtrkgaimlKQINEKASSVHAYVVFETEQSAAASLAH-N 249
Cdd:cd21620   2 RSLYVGNLPQTCQSEDLIILFEPYGNV----CGAHIASRKKV--------KVSWVKPSKLFAFVEFETKEAATTAIVLlN 69

                        90
                ....*....|.
gi 15237960 250 MSLIDGNHVRV 260
Cdd:cd21620  70 GITYMGCQLKV 80

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 285 VFMGNLPFDVKDEEVYQLFT--GksnlenSIEAVRVIRDPHLNIGKGIAYVLFKTREAANLVLKK--GYLkLRERELRIS 360
Cdd:cd12370   3 VYVGSIYFELGEDTIRQAFApfG------PIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQmnGVM-LGGRNIKVG 75

                .
gi 15237960 361 R 361
Cdd:cd12370  76 R 76

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15237960 285 VFMGNLPFDVKDEEVYQLFT--GKsnlensIEAVRVIRDPHLNIGKGIAYVLFKTREAA-NLVLKKGYLKLRERELR 358
Cdd:cd12397   1 LFVGNLSFETTEEDLRKHFApaGK------IRKVRMATFEDSGKCKGFAFVDFKEIESAtNAVKGPINHSLNGRDLR 71

RNA recognition motif (RRM) found in plant proteins related to the La autoantigen; This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15237960 171 RTVFVGNLPLKVKKKVILKEFSKFGEVESVRIRsvpivDSKRTRKGAIMLKQINEKASSVHAYVVFET-EQS--AAASLA 247
Cdd:cd12288   1 RTVVVENLPEDHSIQNLREIFGTVGSVKNVRVC-----DPGRVGSGEKAKKPDTFVSNKLHALVEYETvEAAekAVTELN 75

                        90
                ....*....|...
gi 15237960 248 HNMSLIDGNHVRV 260
Cdd:cd12288  76 NEGNWRNGLRVRL 88

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15237960 285 VFMGNLPFDVKDEEVYQLFTGKSNLEnsiEAVrVIRDPHLNIGKGIAYVLFKTREAANLVLK 346
Cdd:cd12384   3 IFVGGLPYHTTDDSLREYFEQFGEIE---EAV-VITDRQTGKSRGYGFVTMADREAAERACK 60

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15237960 285 VFMGNLPFDVKDEEVYQLFTGKSNLENsieaVRVIRDPHLNIGKGIAYVLFKTREAANLVLKK 347
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEI----AEVMYDRYTGRSRGFGFVTMGSVEDAKAAIEK 60