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 676388591   23 AQKSGKFWDGFRWVEHTPASQMPSNP----ATRKERRLYVGNLPQTFDSEQLRIFLNEALRACGAIPAGVDEVVVSSWVS 98
Cdd:TIGR01642 141 APRPAMTDPEKLLAEGSIITPLPVLPyqqqATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN 220

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 676388591   99 PDKKFAFVELSTVEAATTSLGLSGITCMGCQLKICHPNNYV 139
Cdd:TIGR01642 221 KEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYI 261

RNA recognition motif;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676388591    55 RLYVGNLPQTFDSEQLRiflnEALRACGAIpagvdevvVSSWVSPDKK------FAFVELSTVEAATTSL-GLSGITCMG 127
Cdd:smart00360   1 TLFVGNLPPDTTEEELR----ELFSKFGKV--------ESVRLVRDKEtgkskgFAFVEFESEEDAEKALeALNGKELDG 68

                   ....*
gi 676388591   128 CQLKI 132
Cdd:smart00360  69 RPLKV 73

RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 676388591  54 RRLYVGNLPQTFDSEQLRIFLNEALRACGAIPAGVDEVVvSSWVSPDKKFAFVELSTVEAATTSLGLSGITCMGCQLKI 132
Cdd:cd12230    2 RRLYVGNIPPGITEEELMDFFNQAMRAAGLTQAPGNPVL-AVQINPDKNFAFVEFRSVEETTAALALDGIIFKGQPLKI 79

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 676388591  55 RLYVGNLPQTFDSEQLRIFLNEalraCGAIPagVDEVVVSSWVSPDKKFAFVELSTVEAATTSL 118
Cdd:cd21609    1 RLYVGNIPRNVTSEELAKIFEE----AGTVE--IAEVMYDRYTGRSRGFGFVTMGSVEDAKAAI 58

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676388591  55 RLYVGNLPQTFDSEQLRiflnEALRACGAipagvdevVVSSWVSPDKK------FAFVELSTVEAATTSL-GLSGITCMG 127
Cdd:COG0724    3 KIYVGNLPYSVTEEDLR----ELFSEYGE--------VTSVKLITDREtgrsrgFGFVEMPDDEEAQAAIeALNGAELMG 70

                 ....*
gi 676388591 128 CQLKI 132
Cdd:COG0724   71 RTLKV 75

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 676388591  56 LYVGNLPQTFDSEQLRiflnEALRACGAIPAgvDEVVVSSWVSPDKKFAFVELSTVEAATTSLG-LSGITCMGCQLKI 132
Cdd:cd12399    1 LYVGNLPYSASEEQLK----SLFGQFGAVFD--VKLPMDRETKRPRGFGFVELQEEESAEKAIAkLDGTDFMGRTIRV 72

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676388591  54 RRLYVGNLPQTFDSEQLRIFLNEA-----LRACGaipagvDEvvvsswvSPDKKFAFVELSTVEAATTSLGLSGITCMGC 128
Cdd:cd12260    5 RTVYVGNLDPSTTADQLLEFFSQAgevkyVRMAG------DE-------TQPTRYAFVEFAEQTSVINALKLNGKMFGGR 71

                         90
                 ....*....|..
gi 676388591 129 QLKICHPNNYVV 140
Cdd:cd12260   72 PLKVNHSNNAIV 83

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676388591  54 RRLYVGNLPQTFDSEQLR-IFLNE----ALRACGaipagvdevvvsswVSPDKKFAFVELSTVEAATTSLGLSGITCMGC 128
Cdd:cd12225    1 RTIHVGGIDGSLSEDELAdYFSNCgevtQVRLCG--------------DRVHTRFAWVEFATDASALSALNLDGTTLGGH 66

                 ....*.
gi 676388591 129 QLKICH 134
Cdd:cd12225   67 PLRVSP 72

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 676388591  56 LYVGNLPQTFDSEQLRIFLNEalraCGaipaGVDEVVVSSWVSPD--KKFAFVELSTVEAATTSLGLSGITCMGCQLKI 132
Cdd:cd12450    2 LFVGNLSWSATQDDLENFFSD----CG----EVVDVRIAMDRDDGrsKGFGHVEFASAESAQKALEKSGQDLGGREIRL 72

RNA recognition motif 1 (RRM1) found in vertebrate nucleolin; This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 676388591  56 LYVGNLPQTFDSEQLRIFLNEALracgaipAGVDEVVVSSWVSPDKKFAFVELSTVEAATTSLGLSGITCMGCQLKI 132
Cdd:cd12403    3 LFVGNLNSNKSFEELKTAISEFF-------AKKDLAVVDVRIGSSKKFGYVDFESAEDLEKALELNGKKVLGNEIKL 72

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 676388591  56 LYVGNLPQTFDSEQLRIFLNEALRACGAipagvdEVVVSSWVSPDKKFAFVELSTVEAA 114
Cdd:cd12417    2 LWISGLSDTTKAADLKKIFSKYGKVVSA------KVVTSARTPGSRCYGYVTMASVEEA 54