RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914684911  43 SQTILCPNMYKNPIHEPNGK-----KFTQRELAEQFDAFYEDMFCEFS-KYGEVEQLVVCDNVGDHLVGNVYVRFKYEES 116
Cdd:cd12538    1 SQTILLQNLYQNPQNTPQSAdglkvKVSDVELQEHFDEFYEDVFVELEeKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80

                         90       100
                 ....*....|....*....|....
gi 914684911 117 AQNAIDDLNSRWYSQRPVYAELSP 140
Cdd:cd12538   81 AEKAVNDLNNRWFNGQPIYAELSP 104

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                          10        20
                  ....*....|....*....|....*
gi 914684911  143 DFREACCRQHETSECQRGGLCNFMH 167
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAH 25

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914684911  43 SQTILCPNMYKNPIHEPNGK-----KFTQRELAEQFDAFYEDMFCEFS-KYGEVEQLVVCDNVGDHLVGNVYVRFKYEES 116
Cdd:cd12538    1 SQTILLQNLYQNPQNTPQSAdglkvKVSDVELQEHFDEFYEDVFVELEeKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80

                         90       100
                 ....*....|....*....|....
gi 914684911 117 AQNAIDDLNSRWYSQRPVYAELSP 140
Cdd:cd12538   81 AEKAVNDLNNRWFNGQPIYAELSP 104

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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 914684911   78 EDMFCEFSKYGEVEQLVVCDNVGDHLVGNVYVRFKYEESAQNAIDDLNSRWYSQRPVY 135
Cdd:pfam00076  13 EDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                          10        20
                  ....*....|....*....|....*..
gi 914684911   13 QDKVNCSFYYKIGACRHGERCSRKHVK 39
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914684911  43 SQTILCPNMYKNPIHEPNGK-----KFTQRELAEQFDAFYEDMFCEFS-KYGEVEQLVVCDNVGDHLVGNVYVRFKYEES 116
Cdd:cd12538    1 SQTILLQNLYQNPQNTPQSAdglkvKVSDVELQEHFDEFYEDVFVELEeKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80

                         90       100
                 ....*....|....*....|....
gi 914684911 117 AQNAIDDLNSRWYSQRPVYAELSP 140
Cdd:cd12538   81 AEKAVNDLNNRWFNGQPIYAELSP 104

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914684911  45 TILCPNMYKNP-----IHEPNGKKFTQRELAEQFDAFYEDMFCEFSKYGEVEQLVVCDNVGDHLVGNVYVRFKYEESAQN 119
Cdd:cd12287    1 TLLLKNMYPNPdnfisSLDDGSLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVCSNLNDHLLGNVYVKFESEEDAEA 80

                         90       100
                 ....*....|....*....|.
gi 914684911 120 AIDDLNSRWYSQRPVYAELSP 140
Cdd:cd12287   81 ALQALNGRYYAGRPLYPELSP 101

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 914684911  78 EDMFCEFSKYGEVEQLVVCDNVGDhlvGNVYVRFKYEESAQNAIDDLNSRWYSQRPVYAELSP 140
Cdd:cd12285   26 EDVIEECSKYGPVLHIYVDKNSPQ---GNVYVKFKTIEAAQKCVQAMNGRWFDGRQITAAYVP 85

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 914684911  78 EDMFCEFSKYGEVEQLVVCDNVGDHLVGNVYVRFKYEESAQNAIDDLNSRWYSQRPVYAE 137
Cdd:cd00590   13 EDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 914684911  77 YEDMFCEFSKYGEVEQLVVCDnvgDHLVGNVYVRFKYEESAQNAIDDLNSRWYSQRPVYAEL-SPVTDF 144
Cdd:cd12282   26 KEDLREECEKFGQVKKVVVFD---RHPDGVASVKFKEPEEADKCIQALNGRWFAGRKLEAETwDGKTDY 91

RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins; This subgroup corresponds to the RRM3 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), 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. The 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914684911  83 EFSKYGEVEQLVVC------DNVGDHLVgNVYVRFKYEESAQNAIDDLNSRWYSQRPVYAELSPVTDF 144
Cdd:cd12648   26 ECGKFGAVNRVIIYqekqgeEEDAEIIV-KIFVEFSMPSEAEKAIQALNGRWFGGRKVVAELYDQTRF 92

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 914684911  71 EQFDAFYEDMFCEFSKYGEVEQLVV--CDNVGDHLVGNVYVRFKYEESAQNAIDDLNSRWYSQRPVYAELSP 140
Cdd:cd12374   14 EIDEDLKDEIKEECSKYGKVLNVIIheVASSEADDAVRVFVEFEDADEAIKAFRALNGRFFGGRKVKARFYD 85

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
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 914684911  84 FSKYGEVEQL-VVCDNVGDHLVGNVYVRFKYEESAQNAIDDLNSRWY---SQRPV 134
Cdd:cd12637   20 FEAYGEVEEVyLMKDPVTQQGTGCAFVKFAYKEEALAAIRSLNGTVTfdgCSRPV 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 914684911  73 FDAFYEDMFCEFSKYGEVEQLVV-CDNVGDHLVGNVYVRFKYEESAQNAIDDLNSRWYSQRPV 134
Cdd:cd12448    8 FSATQDALYEAFSQHGSIVSVRLpTDRETGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRPI 70

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                          10        20
                  ....*....|....*....|....*..
gi 914684911   13 QDKVNCSFYYKIGACRHGERCSRKHVK 39
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27

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
                 ....*....|....*....|....*....|....*....|....*....|
gi 914684911  73 FDAFYEDMFCEFSKYGEVEQ-LVVCDNVGDHLVGNVYVRFKYEESAQNAI 121
Cdd:cd12415   10 FDTTEEDLKEFFSKFGEVKYaRIVLDKDTGHSKGTAFVQFKTKESADKCI 59

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein 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 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        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914684911  62 KKFTQRELaeqfdafyEDMFcefSKYGEV-EQLVVCDNVGDHLVGNVYVRFKYEESAQNAIDDLN 125
Cdd:cd12652   10 KTMTQKEL--------EQLF---SQFGRIiTSRILCDNVTGLSRGVGFIRFDKRVEAERAIKALN 63

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
                 ....*....|....*....|....*....|....*....|....*
gi 914684911  84 FSKYGEVEQL-VVCDNVGDHLVGNVYVRFKYEESAQNAIDDLNSR 127
Cdd:cd21615   39 FSKFGEIEKIrIVRDKETGKSRGYAFIVFKSESDAKNAFKEGNGL 83