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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPTDVLGFLGPECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12740    1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKK 80

                         90       100
                 ....*....|....*....|..
gi 755527422 412 HKGMLGKRYIELFRSTAAEVQQ 433
Cdd:cd12740   81 HKGILGKRYIELFRSTAAEVQQ 102

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422  82 LSPQCREASGLSADSLARAESLDKVLQQFSQLVSGDvallggGPYVLCTDGQQLLRQVLHPEASRKNLVLPDTFFSFYDL 161
Cdd:cd06133   54 LSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKN------GKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDL 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 755527422 162 RREF--HMQHPstcsaRDLTVGTMAQDLGLETDATEDDfGVWEVKTMVAVILHLL 214
Cdd:cd06133  128 KKEFakFYGLK-----KRTGLSKALEYLGLEFEGRHHR-GLDDARNIARILKRLL 176

RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and similar proteins; This subgroup corresponds to the RRM2 of ESRP2, also termed RNA-binding motif protein 35B (RBM35B), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. ESRP2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPTDVLGFLGPECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12740    1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKK 80

                         90       100
                 ....*....|....*....|..
gi 755527422 412 HKGMLGKRYIELFRSTAAEVQQ 433
Cdd:cd12740   81 HKGILGKRYIELFRSTAAEVQQ 102

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422  82 LSPQCREASGLSADSLARAESLDKVLQQFSQLVSGDvallggGPYVLCTDGQQLLRQVLHPEASRKNLVLPDTFFSFYDL 161
Cdd:cd06133   54 LSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKN------GKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDL 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 755527422 162 RREF--HMQHPstcsaRDLTVGTMAQDLGLETDATEDDfGVWEVKTMVAVILHLL 214
Cdd:cd06133  128 KKEFakFYGLK-----KRTGLSKALEYLGLEFEGRHHR-GLDDARNIARILKRLL 176

RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and similar proteins; This subgroup corresponds to the RRM2 of ESRP2, also termed RNA-binding motif protein 35B (RBM35B), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. ESRP2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPTDVLGFLGPECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12740    1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKK 80

                         90       100
                 ....*....|....*....|..
gi 755527422 412 HKGMLGKRYIELFRSTAAEVQQ 433
Cdd:cd12740   81 HKGILGKRYIELFRSTAAEVQQ 102

RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and similar proteins; This subgroup corresponds to the RRM1 of ESRP2, also termed RNA-binding motif protein 35B (RBM35B), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. ESRP2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVYKATGEEF 327
Cdd:cd12737    1 VIRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEEF 80

RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and similar proteins; This subgroup corresponds to the RRM2 of ESRP1, also termed RNA-binding motif protein 35A (RBM35A), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. Additional research indicated that ESRP1 functions as a tumor suppressor in colon cancer cells. It may be involved in posttranscriptional regulation of various genes by exerting a differential effect on protein translation via 5' untranslated regions (UTRs) of mRNAs. ESRP1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPTDVLGFLGPECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12739    1 GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVLAFFGQHCPVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKK 80

                         90       100
                 ....*....|....*....|..
gi 755527422 412 HKGMLGKRYIELFRSTAAEVQQ 433
Cdd:cd12739   81 HKDLLGKRYIELFRSTAAEVQQ 102

RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM2 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli.Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. It shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 347 QVILRLRGLPFSAGPTDVLGFLGPECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12508    1 QVIVRMRGLPFSATAADILAFFGGECPVTGGKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 755527422 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. Members in this family have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. They also include a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. They may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 248 VVRARGLPWQSSDQDVARFFKGLNIARG--GVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12503    1 VVRARGLPWSATAEDVLNFFTDCRIKGGenGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFR 76

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. Members in this family have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. They also include a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. They may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755527422 349 ILRLRGLPFSAGPTDVLGFLgPECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12503    1 VVRARGLPWSATAEDVLNFF-TDCRIKGGENGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 77

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Currently, little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock. In addition, the typical hnRNP H proteins contain contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, like other hnRNP H protein family members, hnRNP H3 has an extensive glycine-rich region near the C-terminus, which may allow it to homo- or heterodimerize.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 234 TGPCSKADVVDneTVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMG 313
Cdd:cd12732    8 NGPTDTENSSD--GTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIG 85

                         90
                 ....*....|
gi 755527422 314 VRYIEVYKAT 323
Cdd:cd12732   86 HRYIEIFKSS 95

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 249 VRARGLPWQSSDQDVARFFKGL--NIARGGVALCLNAQGRRNGEALIRFVDSEQ-RDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12509    4 IRLRGLPYSATVEDILNFLGEFakHIAPQGVHMVINAQGRPSGDAFIQMLSAEFaRLAAQKRHKHHMGERYIEVFQ 79

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM2 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 349 ILRLRGLPFSAGPTDVLGFL-GPECPvtggADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRST 427
Cdd:cd12731   10 FVRLRGLPFGCSKEEIVQFFsGLEIV----PNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 85

                 ....*
gi 755527422 428 AAEVQ 432
Cdd:cd12731   86 RAEVR 90

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM1 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical. Both of them have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755527422 349 ILRLRGLPFSAGPTDVLGFLGpECPVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12729    3 VVKVRGLPWSCSADEVQNFFS-DCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79

RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 248 VVRARGLPWQSSDQDVARFFKGLNIARG--GVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12730    3 IVRARGLPWSCTAEDVLSFFSDCRIRNGedGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVFE 78

RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM2 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 346 DQVILRLRGLPFSAGPTDVLGFLGPECpvtggADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFR 425
Cdd:cd12746    1 DDVYLFLRGMPYSATEDDVRNFFSGLK-----VDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTR 75

                 ..
gi 755527422 426 ST 427
Cdd:cd12746   76 TT 77

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 350 LRLRGLPFSAGPTDVLGFLGpECPVTGGADGLLFVRHPDGRPTGDAF-ALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12509    4 IRLRGLPYSATVEDILNFLG-EFAKHIAPQGVHMVINAQGRPSGDAFiQMLSAEFARLAAQKRHKHHMGERYIEVF 78

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755527422 349 ILRLRGLPFSAGPTDVLGFLGPECPVTggadgllfVR---HPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12506    2 TVHMRGLPYRATENDIFEFFSPLNPVN--------VRiryNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELF 72

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 and similar proteins; This subgroup corresponds to the RRM3 of ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B). These are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 249 VRARGLPWQSSDQDVARFFK--GLNIARGGVALCLNAQGRRNGEALIRFVDSEQRDLALQR-HKHHMGVRYIEVYK 321
Cdd:cd12742    4 IRLRGLPYAATIEDILEFLGefAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVFQ 79

RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 and similar proteins; This subgroup corresponds to the RRM3 of ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B). These are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 350 LRLRGLPFSAGPTDVLGFLGpECPVTGGADGLLFVRHPDGRPTGDAF-ALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12742    4 IRLRGLPYAATIEDILEFLG-EFAADIRPHGVHMVLNHQGRPSGDAFiQMKSADRAFLAAQKCHKKTMKDRYVEVF 78

RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755527422 351 RLRGLPFSAGPTDVLGFLGPECPVTggadgLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12502    4 KLRGAPFNVKEKQIREFFSPLKPVA-----IRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) and similar proteins; This subgroup corresponds to the RRM3 of hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Currently, little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock. In addition, the typical hnRNP H proteins contain contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, like other hnRNP H protein family members, hnRNP H3 has an extensive glycine-rich region near the C-terminus, which may allow it to homo- or heterodimerize.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755527422 249 VRARGLPWQSSDQDVARFFKGLNIARggVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12735    3 VHMRGLPFRATESDIANFFSPLNPIR--VHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELF 72

RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM2 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which 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. The biological role of RBM12 remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755527422 249 VRARGLPWQSSDQDVARFFKGLNIArgGVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVYKA 322
Cdd:cd12747    4 VHLHGMPFSATEADVRDFFHGLRID--AIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVSPA 75

RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM2 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 shows 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 755527422 350 LRLRGLPFSAGPTDVLGFLGPECpvtggADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12511    2 LSLHGMPYSAMENDVRDFFHGLR-----VDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71

RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM3 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 249 VRARGLPWQSSDQDVARFFK--GLNIARGGVALCLNAQGRRNGEALIRfVDSEQ--RDLALQRHKHHMGV----RYIEVY 320
Cdd:cd12743    4 IRLRGLPYEAQVEHILEFLGdfAKMIVFQGVHMVYNAQGQPSGEAFIQ-MDSEQsaSACAQQRHNRYMVFgkkqRYIEVF 82

                 ...
gi 755527422 321 KAT 323
Cdd:cd12743   83 QCS 85

RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM3 of G-rich sequence factor 1 (GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755527422 249 VRARGLPWQSSDQDVARFFKGLNIARggVALCLNAQGRRNGEALIRFVDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12733    3 VHMRGLPFQANGQDIINFFAPLKPVR--ITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELF 72

RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM3 of G-rich sequence factor 1 (GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 755527422 352 LRGLPFSAGPTDVLGFLGPECPVTggadgLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12733    5 MRGLPFQANGQDIINFFAPLKPVR-----ITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELF 72

RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM1 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALClnaqGRRNGEALIRFVDSEQRDLALQR 307
Cdd:cd12510    3 VIRLQGLPWEAGSLDIRRFFSGLTIPDGGVHII----GGEKGEAFIIFATDEDARLAMMR 58

RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM5 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 755527422 348 VILRLRGLPFSAGPTDVLGFLGpECPVTggADGLLFVRHPDGRPTGDAFALFACEELAQAALR-RHKGMLGKRYIELF 424
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFY-GYRVI--PDSVSIRYNDDGQPTGDARVAFPSPREARRAVReLNNRPLGGRKVKLF 75

RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM2 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which 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. The biological role of RBM12 remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755527422 350 LRLRGLPFSAGPTDVLGFLgpecpvTG-GADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12747    4 VHLHGMPFSATEADVRDFF------HGlRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422  82 LSPQCREASGLSADSLARAESLDKVLQQFSQLVSGDvallggGPYVLCTDGQQLLRQVLHPEASRKNLVLPDTFFSFYDL 161
Cdd:cd06133   54 LSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKN------GKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDL 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 755527422 162 RREF--HMQHPstcsaRDLTVGTMAQDLGLETDATEDDfGVWEVKTMVAVILHLL 214
Cdd:cd06133  128 KKEFakFYGLK-----KRTGLSKALEYLGLEFEGRHHR-GLDDARNIARILKRLL 176

RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM3 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 350 LRLRGLPFSAGPTDVLGFLGpECPVTGGADGLLFVRHPDGRPTGDAFALFACEELA-QAALRRHKG--MLGK--RYIELF 424
Cdd:cd12743    4 IRLRGLPYEAQVEHILEFLG-DFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSAsACAQQRHNRymVFGKkqRYIEVF 82

                 ...
gi 755527422 425 RST 427
Cdd:cd12743   83 QCS 85

RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; This subfamily corresponds to the RRM3 of RBM12. 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. The biological role of RBM12 remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755527422 352 LRGLPFSAGPTDVLGFLGPECPVTggaDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIEL 423
Cdd:cd12512   14 LKGLPYEAENKHVIEFFKKLDIVE---DSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82

RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM1 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755527422 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALClnaqGRRNGEALIRFVDSEQRDLALQR 307
Cdd:cd12744    3 VIRLQGLPVVAGSTDIRHFFTGLTIPDGGVHII----GGELGEAFIIFATDEDARRAMSR 58

RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM3 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755527422 350 LRLRGLPFSAGPTDVLGFLGPecpVTGGADGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12513    3 VHLKNLSYSVDKRDIRNFFRD---LDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIY 74

RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM4 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755527422 252 RGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFVDSEQ--RDLALQRHKH 310
Cdd:cd12748    6 RNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEamKAERLNGQRF 66

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755527422 354 GLPFSAGPTDVLGFLGPECPVTGgadgLLFVRHPD-GRPTGDAFALFACEELAQAALRRHKGMLGKRYI 421
Cdd:cd12271    5 GIPYYSTEAEIRSYFSSCGEVRS----VDLMRFPDsGNFRGIAFITFKTEEAAKRALALDGEMLGNRFL 69