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Conserved domains on  [gi|157818053|ref|NP_001100893|]
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epithelial splicing regulatory protein 2 [Rattus norvegicus]

Protein Classification

RNA-binding protein( domain architecture ID 10295279)

RNA-binding protein containing a DnaQ-like (or DEDD) 3'-5' exonuclease domain and RNA recognition motif(s) (RRM), with similarity to epithelial splicing regulatory protein 1

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
332-438 1.98e-68

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).


The actual alignment was detected with superfamily member cd12740:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 107  Bit Score: 219.47  E-value: 1.98e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPADVLDFLGPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12740    1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKK 80
                         90       100
                 ....*....|....*....|....*..
gi 157818053 412 HKGMLGKRYIELFRSTAAEVQQVLNRY 438
Cdd:cd12740   81 HKGILGKRYIELFRSTAAEVQQVLNRY 107
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
238-330 2.13e-54

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).


The actual alignment was detected with superfamily member cd12736:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 93  Bit Score: 181.37  E-value: 2.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 238 SKADVVDNETVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYI 317
Cdd:cd12736    1 SKMEIIDDNTVIRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYI 80
                         90
                 ....*....|...
gi 157818053 318 EVYKATGEEFVKI 330
Cdd:cd12736   81 EVYKATGEDFLKI 93
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
464-544 2.28e-53

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).


:

Pssm-ID: 410138 [Multi-domain]  Cd Length: 81  Bit Score: 178.07  E-value: 2.28e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 464 RDCVRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEVVPC 543
Cdd:cd12742    1 RDCIRLRGLPYAATIEDILEFLGEFAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKCHKKTMKDRYVEVFQC 80

                 .
gi 157818053 544 S 544
Cdd:cd12742   81 S 81
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
82-214 2.83e-06

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.


The actual alignment was detected with superfamily member cd06133:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 176  Bit Score: 47.99  E-value: 2.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  82 LSPQCREASGLSADSLARAESLDKVLQQFSQLVSGDvallggGPYVLCTDGQQLLRQVLHPEASRKNLVLPDTFFSFYDL 161
Cdd:cd06133   54 LSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKN------GKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDL 127
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 162 RREF--HVQHPstcsaRDLTVGTMAQDLGLETDATEDDfGVWEVKTMVAVILHLL 214
Cdd:cd06133  128 KKEFakFYGLK-----KRTGLSKALEYLGLEFEGRHHR-GLDDARNIARILKRLL 176
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
664-693 1.14e-05

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).


The actual alignment was detected with superfamily member cd12515:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 75  Bit Score: 43.75  E-value: 1.14e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 157818053 664 ALVRMQGVPYTAGMKDLLSVFQAYQLAPDD 693
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFYGYRVIPDS 30
PHA03247 super family cl33720
large tegument protein UL36; Provisional
555-678 6.61e-04

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 6.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  555 GSLSRSGLSPPPCKLPCLSPPTYATFQASPALIPTETTALYPSSALLPAARVPAAATPLAYYPGPATQlymnyTAYYPSP 634
Cdd:PHA03247 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP-----PAASPAG 2826
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 157818053  635 PVSPTTVGYLTTPPTALASTPTSMLSQ----PGALVRMQGVPYTAGMK 678
Cdd:PHA03247 2827 PLPPPTSAQPTAPPPPPGPPPPSLPLGgsvaPGGDVRRRPPSRSPAAK 2874
 
Name Accession Description Interval E-value
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
332-438 1.98e-68

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).


Pssm-ID: 241184 [Multi-domain]  Cd Length: 107  Bit Score: 219.47  E-value: 1.98e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPADVLDFLGPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12740    1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKK 80
                         90       100
                 ....*....|....*....|....*..
gi 157818053 412 HKGMLGKRYIELFRSTAAEVQQVLNRY 438
Cdd:cd12740   81 HKGILGKRYIELFRSTAAEVQQVLNRY 107
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
238-330 2.13e-54

RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and similar proteins; This subgroup corresponds to the RRM1 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 (p120-Catenin) and ENAH (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).


Pssm-ID: 410134 [Multi-domain]  Cd Length: 93  Bit Score: 181.37  E-value: 2.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 238 SKADVVDNETVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYI 317
Cdd:cd12736    1 SKMEIIDDNTVIRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYI 80
                         90
                 ....*....|...
gi 157818053 318 EVYKATGEEFVKI 330
Cdd:cd12736   81 EVYKATGEDFLKI 93
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
464-544 2.28e-53

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).


Pssm-ID: 410138 [Multi-domain]  Cd Length: 81  Bit Score: 178.07  E-value: 2.28e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 464 RDCVRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEVVPC 543
Cdd:cd12742    1 RDCIRLRGLPYAATIEDILEFLGEFAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKCHKKTMKDRYVEVFQC 80

                 .
gi 157818053 544 S 544
Cdd:cd12742   81 S 81
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
82-214 2.83e-06

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.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 47.99  E-value: 2.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  82 LSPQCREASGLSADSLARAESLDKVLQQFSQLVSGDvallggGPYVLCTDGQQLLRQVLHPEASRKNLVLPDTFFSFYDL 161
Cdd:cd06133   54 LSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKN------GKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDL 127
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 162 RREF--HVQHPstcsaRDLTVGTMAQDLGLETDATEDDfGVWEVKTMVAVILHLL 214
Cdd:cd06133  128 KKEFakFYGLK-----KRTGLSKALEYLGLEFEGRHHR-GLDDARNIARILKRLL 176
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
664-693 1.14e-05

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.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 43.75  E-value: 1.14e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 157818053 664 ALVRMQGVPYTAGMKDLLSVFQAYQLAPDD 693
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFYGYRVIPDS 30
RRM smart00360
RNA recognition motif;
466-540 1.25e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.65  E-value: 1.25e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053   466 CVRLRGLPYTATIEDILSFLGEaAADIRphGVHMVLNQQ-GRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSK-FGKVE--SVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PHA03247 PHA03247
large tegument protein UL36; Provisional
555-678 6.61e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 6.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  555 GSLSRSGLSPPPCKLPCLSPPTYATFQASPALIPTETTALYPSSALLPAARVPAAATPLAYYPGPATQlymnyTAYYPSP 634
Cdd:PHA03247 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP-----PAASPAG 2826
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 157818053  635 PVSPTTVGYLTTPPTALASTPTSMLSQ----PGALVRMQGVPYTAGMK 678
Cdd:PHA03247 2827 PLPPPTSAQPTAPPPPPGPPPPSLPLGgsvaPGGDVRRRPPSRSPAAK 2874
 
Name Accession Description Interval E-value
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
332-438 1.98e-68

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).


Pssm-ID: 241184 [Multi-domain]  Cd Length: 107  Bit Score: 219.47  E-value: 1.98e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPADVLDFLGPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12740    1 GGTSNEVAQFLSKENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKK 80
                         90       100
                 ....*....|....*....|....*..
gi 157818053 412 HKGMLGKRYIELFRSTAAEVQQVLNRY 438
Cdd:cd12740   81 HKGILGKRYIELFRSTAAEVQQVLNRY 107
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
238-330 2.13e-54

RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and similar proteins; This subgroup corresponds to the RRM1 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 (p120-Catenin) and ENAH (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).


Pssm-ID: 410134 [Multi-domain]  Cd Length: 93  Bit Score: 181.37  E-value: 2.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 238 SKADVVDNETVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYI 317
Cdd:cd12736    1 SKMEIIDDNTVIRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQRHKHHMGNRYI 80
                         90
                 ....*....|...
gi 157818053 318 EVYKATGEEFVKI 330
Cdd:cd12736   81 EVYKATGEDFLKI 93
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
248-327 1.25e-53

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).


Pssm-ID: 410135 [Multi-domain]  Cd Length: 80  Bit Score: 179.04  E-value: 1.25e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKATGEEF 327
Cdd:cd12737    1 VIRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALERHKHHMGSRYIEVYKATGEEF 80
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
464-544 2.28e-53

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).


Pssm-ID: 410138 [Multi-domain]  Cd Length: 81  Bit Score: 178.07  E-value: 2.28e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 464 RDCVRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEVVPC 543
Cdd:cd12742    1 RDCIRLRGLPYAATIEDILEFLGEFAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKCHKKTMKDRYVEVFQC 80

                 .
gi 157818053 544 S 544
Cdd:cd12742   81 S 81
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
332-441 1.34e-52

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).


Pssm-ID: 410136 [Multi-domain]  Cd Length: 111  Bit Score: 177.16  E-value: 1.34e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 332 GGTSLEVARFLSREDQVILRLRGLPFSAGPADVLDFLGPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRR 411
Cdd:cd12739    1 GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVLAFFGQHCPVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKK 80
                         90       100       110
                 ....*....|....*....|....*....|
gi 157818053 412 HKGMLGKRYIELFRSTAAEVQQVLNRYAAS 441
Cdd:cd12739   81 HKDLLGKRYIELFRSTAAEVQQVLNRYSSA 110
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
248-322 1.38e-50

RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM1 of ESRPs and Fusilli. 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). 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 fibroblast growth factor receptor 2 (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.


Pssm-ID: 240951 [Multi-domain]  Cd Length: 75  Bit Score: 170.37  E-value: 1.38e-50
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKA 322
Cdd:cd12507    1 VVRARGLPWQSSDQDIAQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVYKA 75
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
248-327 3.38e-48

RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM1 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.


Pssm-ID: 241182 [Multi-domain]  Cd Length: 80  Bit Score: 163.93  E-value: 3.38e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKATGEEF 327
Cdd:cd12738    1 VVRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKATGEDF 80
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
464-544 3.90e-46

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.


Pssm-ID: 409931 [Multi-domain]  Cd Length: 81  Bit Score: 158.41  E-value: 3.90e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 464 RDCVRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEVVPC 543
Cdd:cd12509    1 RDCIRLRGLPYSATVEDILNFLGEFAKHIAPQGVHMVINAQGRPSGDAFIQMLSAEFARLAAQKRHKHHMGERYIEVFQC 80

                 .
gi 157818053 544 S 544
Cdd:cd12509   81 S 81
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
347-426 6.21e-46

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.


Pssm-ID: 409930 [Multi-domain]  Cd Length: 80  Bit Score: 157.90  E-value: 6.21e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 347 QVILRLRGLPFSAGPADVLDFLGPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12508    1 QVIVRMRGLPFSATAADILAFFGGECPVTGGKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFRS 80
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
331-426 3.92e-33

RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM2 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.


Pssm-ID: 410137 [Multi-domain]  Cd Length: 99  Bit Score: 122.64  E-value: 3.92e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 331 AGGTSLEVARFLSREDQVILRLRGLPFSAGPADVLDFL---GPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQA 407
Cdd:cd12741    1 AGGESNEAQNFLSKGGQVIIRMRGLPYDCTPKQVVEFFctgDKIPHVLDGAEGVLFVKKPDGRATGDAFVLFETEEVAEK 80
                         90
                 ....*....|....*....
gi 157818053 408 ALRRHKGMLGKRYIELFRS 426
Cdd:cd12741   81 ALEKHRQHIGSRYIELFRS 99
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
464-544 1.42e-29

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.


Pssm-ID: 241187 [Multi-domain]  Cd Length: 85  Bit Score: 112.29  E-value: 1.42e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 464 RDCVRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVM----KERYVE 539
Cdd:cd12743    1 KDCIRLRGLPYEAQVEHILEFLGDFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASACAQQRHNRYMvfgkKQRYIE 80

                 ....*
gi 157818053 540 VVPCS 544
Cdd:cd12743   81 VFQCS 85
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
248-320 5.73e-26

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).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 101.48  E-value: 5.73e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
349-424 1.55e-24

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).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 97.25  E-value: 1.55e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 349 ILRLRGLPFSAGPADVLDFLGPECPVTGGVdglLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGI---HIVYDDDGRPTGEAYVEFASEEDAQRALRRHKGKMGGRYIEVF 73
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
248-321 7.75e-24

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.


Pssm-ID: 409926 [Multi-domain]  Cd Length: 77  Bit Score: 95.53  E-value: 7.75e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARG--GVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12503    1 VVRARGLPWSATAEDVLNFFTDCRIKGGenGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFR 76
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
466-540 2.53e-23

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).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 93.78  E-value: 2.53e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 466 CVRLRGLPYTATIEDILSFLGEAaaDIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEV 540
Cdd:cd12254    1 VVRLRGLPFSATEEDIRDFFSGL--DIPPDGIHIVYDDDGRPTGEAYVEFASEEDAQRALRR-HKGKMGGRYIEV 72
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
247-323 5.22e-21

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family; This subfamily corresponds to the RRM2 of hnRNP H protein family which 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). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing 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. 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. 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. 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.


Pssm-ID: 409927 [Multi-domain]  Cd Length: 77  Bit Score: 87.41  E-value: 5.22e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818053 247 TVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKAT 323
Cdd:cd12504    1 GVVRLRGLPYGCTKEEIAQFFSGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
349-426 7.50e-20

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.


Pssm-ID: 409926 [Multi-domain]  Cd Length: 77  Bit Score: 83.98  E-value: 7.50e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157818053 349 ILRLRGLPFSAGPADVLDFLgPECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12503    1 VVRARGLPWSATAEDVLNFF-TDCRIKGGENGIHFTYTREGRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVFRS 77
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
245-326 5.37e-19

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.


Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 82.37  E-value: 5.37e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 245 NETVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKATG 324
Cdd:cd12731    7 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSR 86

                 ..
gi 157818053 325 EE 326
Cdd:cd12731   87 AE 88
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
246-320 1.62e-18

RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM2 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.


Pssm-ID: 409928 [Multi-domain]  Cd Length: 77  Bit Score: 80.26  E-value: 1.62e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 246 ETVVRARGLPWQSSDQDVARFFKGLNIarGGVALCLNAQG-RRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12505    1 DGVVRLRGLPYSCTEADIAHFFSGLDI--VDITFVMDLRGgRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIF 74
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
234-323 3.37e-18

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.


Pssm-ID: 410131 [Multi-domain]  Cd Length: 96  Bit Score: 79.97  E-value: 3.37e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 234 TGPCSKADVVDneTVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMG 313
Cdd:cd12732    8 NGPTDTENSSD--GTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIG 85
                         90
                 ....*....|
gi 157818053 314 VRYIEVYKAT 323
Cdd:cd12732   86 HRYIEIFKSS 95
RRM1_hnRNPH_GRSF1_like cd12503
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
467-540 1.88e-17

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.


Pssm-ID: 409926 [Multi-domain]  Cd Length: 77  Bit Score: 77.43  E-value: 1.88e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818053 467 VRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMS---VERALaAAQRCHkkvMKERYVEV 540
Cdd:cd12503    2 VRARGLPWSATAEDVLNFFTDCRIKGGENGIHFTYTREGRPSGEAFIELESeedVEKAL-EKHNEH---MGHRYIEV 74
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
248-321 3.19e-17

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.


Pssm-ID: 410129 [Multi-domain]  Cd Length: 79  Bit Score: 76.76  E-value: 3.19e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARG--GVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12730    3 IVRARGLPWSCTAEDVLSFFSDCRIRNGedGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVFE 78
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
467-540 3.36e-17

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.


Pssm-ID: 409930 [Multi-domain]  Cd Length: 80  Bit Score: 76.63  E-value: 3.36e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 467 VRLRGLPYTATIEDILSFLGEAAADIR-PHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEV 540
Cdd:cd12508    4 VRMRGLPFSATAADILAFFGGECPVTGgKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGK-HKELLGKRYIEL 77
RRM3_ESRPs_Fusilli cd12509
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
249-321 1.05e-16

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.


Pssm-ID: 409931 [Multi-domain]  Cd Length: 81  Bit Score: 75.20  E-value: 1.05e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 249 VRARGLPWQSSDQDVARFFKGL--NIARGGVALCLNAQGRRNGEALIRFEDSEQ-RDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12509    4 IRLRGLPYSATVEDILNFLGEFakHIAPQGVHMVINAQGRPSGDAFIQMLSAEFaRLAAQKRHKHHMGERYIEVFQ 79
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
349-427 1.09e-16

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family; This subfamily corresponds to the RRM2 of hnRNP H protein family which 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). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing 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. 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. 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. 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.


Pssm-ID: 409927 [Multi-domain]  Cd Length: 77  Bit Score: 75.09  E-value: 1.09e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157818053 349 ILRLRGLPFSAGPADVLDFLGPECPVTGGVdglLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRST 427
Cdd:cd12504    2 VVRLRGLPYGCTKEEIAQFFSGLEIVPNGI---TLPMDRRGRSTGEAFVQFASQEIAEQALGKHKEKIGHRYIEIFRSS 77
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
248-322 1.15e-16

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.


Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 75.20  E-value: 1.15e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARG--GVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKA 322
Cdd:cd12729    3 VVKVRGLPWSCSADEVQNFFSDCKIANGasGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
349-432 1.80e-16

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.


Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 75.05  E-value: 1.80e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 349 ILRLRGLPFSAGPADVLDFL-GPE-CPvtggvDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12731   10 FVRLRGLPFGCSKEEIVQFFsGLEiVP-----NGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS 84

                 ....*.
gi 157818053 427 TAAEVQ 432
Cdd:cd12731   85 SRAEVR 90
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
466-540 2.09e-16

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.


Pssm-ID: 410129 [Multi-domain]  Cd Length: 79  Bit Score: 74.45  E-value: 2.09e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 466 CVRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEV 540
Cdd:cd12730    3 IVRARGLPWSCTAEDVLSFFSDCRIRNGEDGIHFLLNRDGKRRGDALIELESEEDVQKALEQ-HRKYMGQRYVEV 76
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
346-427 2.46e-16

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.


Pssm-ID: 410140 [Multi-domain]  Cd Length: 86  Bit Score: 74.40  E-value: 2.46e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 346 DQVILRLRGLPFSAGPADVLDFLGPECpvtggVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFR 425
Cdd:cd12746    1 DDVYLFLRGMPYSATEDDVRNFFSGLK-----VDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTR 75

                 ..
gi 157818053 426 ST 427
Cdd:cd12746   76 TT 77
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
252-333 3.88e-16

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.


Pssm-ID: 410140 [Multi-domain]  Cd Length: 86  Bit Score: 74.01  E-value: 3.88e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 252 RGLPWQSSDQDVARFFKGLNIArgGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKATGEEFVKiA 331
Cdd:cd12746    8 RGMPYSATEDDVRNFFSGLKVD--GVIFLKHPNGRNNGNGLVKFATKEDASEGLKRHRQYMGSRFIEVTRTTEEQWIE-A 84

                 ..
gi 157818053 332 GG 333
Cdd:cd12746   85 GG 86
RRM2_ESRPs_Fusilli cd12508
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
246-321 1.20e-15

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.


Pssm-ID: 409930 [Multi-domain]  Cd Length: 80  Bit Score: 72.39  E-value: 1.20e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157818053 246 ETVVRARGLPWQSSDQDVARFFKGL---NIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYK 321
Cdd:cd12508    1 QVIVRMRGLPFSATAADILAFFGGEcpvTGGKDGILFVTYPDGRPTGDAFVLFATEEDAQQALGKHKELLGKRYIELFR 79
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
349-426 1.25e-15

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.


Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 72.12  E-value: 1.25e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157818053 349 ILRLRGLPFSAGPADVLDFLGpECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12729    3 VVKVRGLPWSCSADEVQNFFS-DCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVFKS 79
RRM1_GRSF1 cd12730
RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
349-424 4.64e-15

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.


Pssm-ID: 410129 [Multi-domain]  Cd Length: 79  Bit Score: 70.60  E-value: 4.64e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 349 ILRLRGLPFSAGPADVLDFLGpECPVTGGVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12730    3 IVRARGLPWSCTAEDVLSFFS-DCRIRNGEDGIHFLLNRDGKRRGDALIELESEEDVQKALEQHRKYMGQRYVEVF 77
RRM2_hnRNPH_CRSF1_like cd12504
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H ...
466-544 1.78e-14

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family; This subfamily corresponds to the RRM2 of hnRNP H protein family which 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). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing 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. 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. 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. 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.


Pssm-ID: 409927 [Multi-domain]  Cd Length: 77  Bit Score: 68.92  E-value: 1.78e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157818053 466 CVRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVPCS 544
Cdd:cd12504    2 VVRLRGLPYGCTKEEIAQFF--SGLEIVPNGITLPMDRRGRSTGEAFVQFASQEIAEQALGK-HKEKIGHRYIEIFRSS 77
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
467-552 1.08e-13

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).


Pssm-ID: 241184 [Multi-domain]  Cd Length: 107  Bit Score: 67.70  E-value: 1.08e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLG-EAAADIRPHGVHMVLNQQGRPSGDAFIqMMSVERALAAAQRCHKKVMKERYVEVVPCST 545
Cdd:cd12740   19 IRMRGLPFTATPEDVLGFLGpECPVTGGTEGLLFVKYPDGRPTGDAFV-LFACEEYAQNALKKHKGILGKRYIELFRSTA 97

                 ....*..
gi 157818053 546 EEMSRVL 552
Cdd:cd12740   98 AEVQQVL 104
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
248-320 1.10e-13

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.


Pssm-ID: 409929 [Multi-domain]  Cd Length: 75  Bit Score: 66.63  E-value: 1.10e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARggVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12506    2 TVHMRGLPYRATENDIFEFFSPLNPVN--VRIRYNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELF 72
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
349-426 1.27e-13

RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM2 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.


Pssm-ID: 409928 [Multi-domain]  Cd Length: 77  Bit Score: 66.39  E-value: 1.27e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157818053 349 ILRLRGLPFSAGPADVLDFLGPECPVtggvdGLLFV-RHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12505    3 VVRLRGLPYSCTEADIAHFFSGLDIV-----DITFVmDLRGGRKTGEAFVQFASPEMAAQALLKHKEEIGNRYIEIFPS 76
RRM2_hnRNPH_hnRNPH2_hnRNPF cd12731
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP ...
457-548 1.78e-13

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.


Pssm-ID: 410130 [Multi-domain]  Cd Length: 90  Bit Score: 66.57  E-value: 1.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 457 PLAGGTGrdCVRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKER 536
Cdd:cd12731    3 PDTANDG--FVRLRGLPFGCSKEEIVQFF--SGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHR 77
                         90
                 ....*....|..
gi 157818053 537 YVEVVPCSTEEM 548
Cdd:cd12731   78 YIEIFKSSRAEV 89
RRM1_ESRPs_Fusilli cd12507
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, ...
466-540 1.95e-13

RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins; This subfamily corresponds to the RRM1 of ESRPs and Fusilli. 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). 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 fibroblast growth factor receptor 2 (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.


Pssm-ID: 240951 [Multi-domain]  Cd Length: 75  Bit Score: 65.98  E-value: 1.95e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 466 CVRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEV 540
Cdd:cd12507    1 VVRARGLPWQSSDQDIAQFF--RGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQR-HKHHMGTRYIEV 72
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
349-424 2.03e-13

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.


Pssm-ID: 409929 [Multi-domain]  Cd Length: 75  Bit Score: 65.86  E-value: 2.03e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157818053 349 ILRLRGLPFSAGPADVLDFLGPECPVTggvdgllfVR---HPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12506    2 TVHMRGLPYRATENDIFEFFSPLNPVN--------VRiryNKDGRATGEADVEFATHEDAVAAMSKDRENMGHRYIELF 72
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
465-540 2.71e-13

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.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 65.32  E-value: 2.71e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 465 DCVRLRGLPYTATIEDILSFLGeaAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFY--GYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVRELNNRPLGGRKVKL 74
RRM1_hnRNPH_hnRNPH2_hnRNPF cd12729
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
467-540 5.33e-13

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.


Pssm-ID: 410128 [Multi-domain]  Cd Length: 79  Bit Score: 64.80  E-value: 5.33e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 467 VRLRGLPYTATIEDILSFLGEAAADIRPHGVHMVLNQQGRPSGDAFIQMMSvERALAAAQRCHKKVMKERYVEV 540
Cdd:cd12729    4 VKVRGLPWSCSADEVQNFFSDCKIANGASGIHFIYTREGRPSGEAFVELES-EEDVKLALKKDRETMGHRYVEV 76
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
245-322 1.50e-12

RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM2 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.


Pssm-ID: 410137 [Multi-domain]  Cd Length: 99  Bit Score: 64.09  E-value: 1.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 245 NETVVRARGLPWQSSDQDVARFFKGLNI------ARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIE 318
Cdd:cd12741   16 GQVIIRMRGLPYDCTPKQVVEFFCTGDKiphvldGAEGVLFVKKPDGRATGDAFVLFETEEVAEKALEKHRQHIGSRYIE 95

                 ....
gi 157818053 319 VYKA 322
Cdd:cd12741   96 LFRS 99
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
349-427 1.68e-12

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.


Pssm-ID: 410131 [Multi-domain]  Cd Length: 96  Bit Score: 63.79  E-value: 1.68e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 349 ILRLRGLPFSAGPADVLDF-LGPE-CPvtggvDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12732   20 TVRLRGLPFGCSKEEIVQFfSGLEiVP-----NGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIFKS 94

                 .
gi 157818053 427 T 427
Cdd:cd12732   95 S 95
RRM3_ESRP1_ESRP2 cd12742
RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 ...
249-321 2.28e-12

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).


Pssm-ID: 410138 [Multi-domain]  Cd Length: 81  Bit Score: 62.90  E-value: 2.28e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 249 VRARGLPWQSSDQDVARFFK--GLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQR-HKHHMGVRYIEVYK 321
Cdd:cd12742    4 IRLRGLPYAATIEDILEFLGefAADIRPHGVHMVLNHQGRPSGDAFIQMKSADRAFLAAQKcHKKTMKDRYVEVFQ 79
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
350-424 2.50e-12

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.


Pssm-ID: 409933 [Multi-domain]  Cd Length: 73  Bit Score: 62.57  E-value: 2.50e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 350 LRLRGLPFSAGPADVLDFLGPECpvtggVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12511    2 LSLHGMPYSAMENDVRDFFHGLR-----VDGVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVS 71
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
351-424 3.10e-12

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).


Pssm-ID: 409925 [Multi-domain]  Cd Length: 72  Bit Score: 62.43  E-value: 3.10e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 351 RLRGLPFSAGPADVLDFLGPECPVTggvdgLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12502    4 KLRGAPFNVKEKQIREFFSPLKPVA-----IRIVKNAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
466-539 3.31e-12

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.


Pssm-ID: 409929 [Multi-domain]  Cd Length: 75  Bit Score: 62.39  E-value: 3.31e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 466 CVRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVE 539
Cdd:cd12506    2 TVHMRGLPYRATENDIFEFF----SPLNPVNVRIRYNKDGRATGEADVEFATHEDAVAAMSK-DRENMGHRYIE 70
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
249-322 4.20e-12

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.


Pssm-ID: 409933 [Multi-domain]  Cd Length: 73  Bit Score: 62.18  E-value: 4.20e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIArgGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKA 322
Cdd:cd12511    2 LSLHGMPYSAMENDVRDFFHGLRVD--GVHLLKDHVGRNNGNALVKFASPQDASEGLKCHRMLMGQRFVEVSPA 73
RRM2_GRSF1 cd12505
RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
467-542 1.17e-11

RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM2 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.


Pssm-ID: 409928 [Multi-domain]  Cd Length: 77  Bit Score: 61.00  E-value: 1.17e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQG-RPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVP 542
Cdd:cd12505    4 VRLRGLPYSCTEADIAHFF----SGLDIVDITFVMDLRGgRKTGEAFVQFASPEMAAQALLK-HKEEIGNRYIEIFP 75
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
350-424 1.41e-11

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.


Pssm-ID: 241179 [Multi-domain]  Cd Length: 75  Bit Score: 60.41  E-value: 1.41e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 350 LRLRGLPFSAGPADVLDFLGPECPVTGGVDgllfvRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12735    3 VHMRGLPFRATESDIANFFSPLNPIRVHID-----IGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELF 72
RRM2_hnRNPH3 cd12732
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
455-544 2.81e-11

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.


Pssm-ID: 410131 [Multi-domain]  Cd Length: 96  Bit Score: 60.32  E-value: 2.81e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 455 PFPLAGGTgrdcVRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMK 534
Cdd:cd12732   13 TENSSDGT----VRLRGLPFGCSKEEIVQFF--SGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGK-HKERIG 85
                         90
                 ....*....|
gi 157818053 535 ERYVEVVPCS 544
Cdd:cd12732   86 HRYIEIFKSS 95
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
467-552 3.17e-11

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).


Pssm-ID: 410136 [Multi-domain]  Cd Length: 111  Bit Score: 60.83  E-value: 3.17e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLGEAAADI-RPHGVHMVLNQQGRPSGDAFIqMMSVERALAAAQRCHKKVMKERYVEVVPCST 545
Cdd:cd12739   19 VRMRGLPFTATAEEVLAFFGQHCPVTgGKEGILFVTYPDSRPTGDAFV-LFACEEYAQNALKKHKDLLGKRYIELFRSTA 97

                 ....*..
gi 157818053 546 EEMSRVL 552
Cdd:cd12739   98 AEVQQVL 104
RRM2_RBM12B cd12746
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
467-547 7.32e-11

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.


Pssm-ID: 410140 [Multi-domain]  Cd Length: 86  Bit Score: 58.99  E-value: 7.32e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVPCSTE 546
Cdd:cd12746    5 LFLRGMPYSATEDDVRNFF----SGLKVDGVIFLKHPNGRNNGNGLVKFATKEDASEGLKR-HRQYMGSRFIEVTRTTEE 79

                 .
gi 157818053 547 E 547
Cdd:cd12746   80 Q 80
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
249-320 9.96e-11

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.


Pssm-ID: 241179 [Multi-domain]  Cd Length: 75  Bit Score: 58.09  E-value: 9.96e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIARggVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12735    3 VHMRGLPFRATESDIANFFSPLNPIR--VHIDIGADGRATGEADVEFATHEDAVAAMSKDKNHMQHRYIELF 72
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
249-323 1.19e-10

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.


Pssm-ID: 409934 [Multi-domain]  Cd Length: 101  Bit Score: 58.71  E-value: 1.19e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKAT 323
Cdd:cd12512   12 VYLKGLPYEAENKHVIEFFKKLDIVEDSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQVHPIT 86
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
348-432 1.72e-10

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.


Pssm-ID: 410139 [Multi-domain]  Cd Length: 79  Bit Score: 57.53  E-value: 1.72e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 348 VILRLRGLPFSAGPADVLDF-LGPECPvTGGVdgllfvrHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12744    2 VVIRLQGLPVVAGSTDIRHFfTGLTIP-DGGV-------HIIGGELGEAFIIFATDEDARRAMSRSGGFIKGSRVELFLS 73

                 ....*.
gi 157818053 427 TAAEVQ 432
Cdd:cd12744   74 SKAEMQ 79
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
249-322 3.70e-10

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.


Pssm-ID: 410141 [Multi-domain]  Cd Length: 75  Bit Score: 56.72  E-value: 3.70e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIArgGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVYKA 322
Cdd:cd12747    4 VHLHGMPFSATEADVRDFFHGLRID--AIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVSPA 75
RRM1_ESRP2 cd12737
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
467-547 3.94e-10

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).


Pssm-ID: 410135 [Multi-domain]  Cd Length: 80  Bit Score: 56.55  E-value: 3.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVPCSTE 546
Cdd:cd12737    2 IRARGLPWQSSDQDIARFF--KGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALER-HKHHMGSRYIEVYKATGE 78

                 .
gi 157818053 547 E 547
Cdd:cd12737   79 E 79
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
249-320 1.11e-09

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.


Pssm-ID: 410132 [Multi-domain]  Cd Length: 75  Bit Score: 55.16  E-value: 1.11e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIARggVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12733    3 VHMRGLPFQANGQDIINFFAPLKPVR--ITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELF 72
RRM2_Fusilli cd12741
RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar ...
467-540 1.57e-09

RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM2 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.


Pssm-ID: 410137 [Multi-domain]  Cd Length: 99  Bit Score: 55.61  E-value: 1.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPH------GVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEV 540
Cdd:cd12741   20 IRMRGLPYDCTPKQVVEFF--CTGDKIPHvldgaeGVLFVKKPDGRATGDAFVLFETEEVAEKALEK-HRQHIGSRYIEL 96
RRM3_Fusilli cd12743
RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar ...
249-323 1.65e-09

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.


Pssm-ID: 241187 [Multi-domain]  Cd Length: 85  Bit Score: 54.90  E-value: 1.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 249 VRARGLPWQSSDQDVARFFK--GLNIARGGVALCLNAQGRRNGEALIRFeDSEQ--RDLALQRHKHHMGV----RYIEVY 320
Cdd:cd12743    4 IRLRGLPYEAQVEHILEFLGdfAKMIVFQGVHMVYNAQGQPSGEAFIQM-DSEQsaSACAQQRHNRYMVFgkkqRYIEVF 82

                 ...
gi 157818053 321 KAT 323
Cdd:cd12743   83 QCS 85
RRM2_RBM12_like cd12511
RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
467-542 2.58e-09

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.


Pssm-ID: 409933 [Multi-domain]  Cd Length: 73  Bit Score: 54.10  E-value: 2.58e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSVERAlAAAQRCHKKVMKERYVEVVP 542
Cdd:cd12511    2 LSLHGMPYSAMENDVRDFF----HGLRVDGVHLLKDHVGRNNGNALVKFASPQDA-SEGLKCHRMLMGQRFVEVSP 72
RRM2_ESRP1 cd12739
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
244-330 2.90e-09

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).


Pssm-ID: 410136 [Multi-domain]  Cd Length: 111  Bit Score: 55.06  E-value: 2.90e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 244 DNETVVRARGLPWQSSDQDVARFFKG---LNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12739   14 ENQVIVRMRGLPFTATAEEVLAFFGQhcpVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELF 93
                         90
                 ....*....|
gi 157818053 321 KATGEEFVKI 330
Cdd:cd12739   94 RSTAAEVQQV 103
RRM2_ESRP2 cd12740
RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and ...
244-330 3.09e-09

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).


Pssm-ID: 241184 [Multi-domain]  Cd Length: 107  Bit Score: 54.99  E-value: 3.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 244 DNETVVRARGLPWQSSDQDVARFFKGLNIARGGVALCL---NAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12740   14 ENQVIIRMRGLPFTATPEDVLGFLGPECPVTGGTEGLLfvkYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELF 93
                         90
                 ....*....|
gi 157818053 321 KATGEEFVKI 330
Cdd:cd12740   94 RSTAAEVQQV 103
RRM1_Fusilli cd12738
RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar ...
467-547 3.50e-09

RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar proteins; This subgroup corresponds to the RRM1 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.


Pssm-ID: 241182 [Multi-domain]  Cd Length: 80  Bit Score: 53.76  E-value: 3.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVPCSTE 546
Cdd:cd12738    2 VRARGLPWQSSDQDIAKFF--RGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKR-HKHHIGQRYIEVYKATGE 78

                 .
gi 157818053 547 E 547
Cdd:cd12738   79 D 79
RRM1_ESRP1 cd12736
RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and ...
467-551 3.62e-09

RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and similar proteins; This subgroup corresponds to the RRM1 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 (p120-Catenin) and ENAH (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).


Pssm-ID: 410134 [Multi-domain]  Cd Length: 93  Bit Score: 54.25  E-value: 3.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVPCSTE 546
Cdd:cd12736   12 IRARGLPWQSSDQDIARFF--KGLNIAKGGAALCLNAQGRRNGEALVRFVNEEHRDLALQR-HKHHMGNRYIEVYKATGE 88

                 ....*
gi 157818053 547 EMSRV 551
Cdd:cd12736   89 DFLKI 93
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
352-424 4.33e-09

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.


Pssm-ID: 410132 [Multi-domain]  Cd Length: 75  Bit Score: 53.62  E-value: 4.33e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157818053 352 LRGLPFSAGPADVLDFLGPECPVTggvdgLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12733    5 MRGLPFQANGQDIINFFAPLKPVR-----ITMEYGPDGKATGEADVHFASHEDAVAAMAKDRSHMQHRYIELF 72
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
249-320 6.59e-09

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).


Pssm-ID: 409925 [Multi-domain]  Cd Length: 72  Bit Score: 52.80  E-value: 6.59e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 157818053 249 VRARGLPWQSSDQDVARFF-----KGLNIARggvalclNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12502    3 VKLRGAPFNVKEKQIREFFsplkpVAIRIVK-------NAHGNKTGYVFVDFKSEEDVEKALKRNKDYMGGRYIEVF 72
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
350-424 7.08e-09

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.


Pssm-ID: 410141 [Multi-domain]  Cd Length: 75  Bit Score: 52.87  E-value: 7.08e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 350 LRLRGLPFSAGPADVLDFLgpecpvTG-GVDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12747    4 VHLHGMPFSATEADVRDFF------HGlRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKRNRMMMGQRYIEVS 73
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
348-424 1.31e-08

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.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 52.22  E-value: 1.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 348 VILRLRGLPFSAGPADVLDFLG--PECPvtggvDGLLFVRHPDGRPTGDAFALFACEELAQAALR-RHKGMLGKRYIELF 424
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFYgyRVIP-----DSVSIRYNDDGQPTGDARVAFPSPREARRAVReLNNRPLGGRKVKLF 75
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
466-540 1.67e-08

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


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 51.64  E-value: 1.67e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 466 CVRLRGLPYTATIEDILSFLGEAAAdiRPHGVHMVLNQQGRPSGDAFIQMMSVERAlAAAQRCHKKVMKERYVEV 540
Cdd:cd12514    1 FIRITNLPYDATPVDIQRFFEDHGV--RPEDVHLLRNKKGRGNGEALVTFKSEGDA-REVLKLNGKKLGKREAVV 72
RRM2_RBM12 cd12747
RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
467-542 1.85e-08

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.


Pssm-ID: 410141 [Multi-domain]  Cd Length: 75  Bit Score: 51.72  E-value: 1.85e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVP 542
Cdd:cd12747    4 VHLHGMPFSATEADVRDFF----HGLRIDAIHMLKDHLGRNNGNALVKFYSPQDTFEALKR-NRMMMGQRYIEVSP 74
RRM2_RMB19 cd12502
RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
467-540 1.99e-08

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).


Pssm-ID: 409925 [Multi-domain]  Cd Length: 72  Bit Score: 51.65  E-value: 1.99e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSvERALAAAQRCHKKVMKERYVEV 540
Cdd:cd12502    3 VKLRGAPFNVKEKQIREFF----SPLKPVAIRIVKNAHGNKTGYVFVDFKS-EEDVEKALKRNKDYMGGRYIEV 71
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
348-427 2.48e-08

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.


Pssm-ID: 409932 [Multi-domain]  Cd Length: 74  Bit Score: 51.12  E-value: 2.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 348 VILRLRGLPFSAGPADVLDFL-GPECPvTGGVdgllfvrHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRS 426
Cdd:cd12510    2 VVIRLQGLPWEAGSLDIRRFFsGLTIP-DGGV-------HIIGGEKGEAFIIFATDEDARLAMMRDGQTIKGSKVKLFLS 73

                 .
gi 157818053 427 T 427
Cdd:cd12510   74 S 74
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
248-307 2.70e-08

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.


Pssm-ID: 409932 [Multi-domain]  Cd Length: 74  Bit Score: 51.12  E-value: 2.70e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALClnaqGRRNGEALIRFEDSEQRDLALQR 307
Cdd:cd12510    3 VIRLQGLPWEAGSLDIRRFFSGLTIPDGGVHII----GGEKGEAFIIFATDEDARLAMMR 58
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
466-545 3.80e-08

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which 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; bothe 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.


Pssm-ID: 410133 [Multi-domain]  Cd Length: 76  Bit Score: 50.81  E-value: 3.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 466 CVRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEVVPCST 545
Cdd:cd12734    2 CVHMRGLPYRATENDIYNFF----SPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSK-DKANMQHRYVELFLNST 76
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
350-424 6.44e-08

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which 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; bothe 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.


Pssm-ID: 410133 [Multi-domain]  Cd Length: 76  Bit Score: 50.43  E-value: 6.44e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 350 LRLRGLPFSAGPADVLDFLGPECPVTGGVDgllfvRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12734    3 VHMRGLPYRATENDIYNFFSPLNPVRVHIE-----IGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELF 72
RRM3_hnRNPH3 cd12735
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) ...
467-540 7.53e-08

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.


Pssm-ID: 241179 [Multi-domain]  Cd Length: 75  Bit Score: 50.00  E-value: 7.53e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 467 VRLRGLPYTATIEDILSFLGEaaadIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRcHKKVMKERYVEV 540
Cdd:cd12735    3 VHMRGLPFRATESDIANFFSP----LNPIRVHIDIGADGRATGEADVEFATHEDAVAAMSK-DKNHMQHRYIEL 71
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
247-320 1.55e-07

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.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 49.14  E-value: 1.55e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 247 TVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLAL-QRHKHHMGVRYIEVY 320
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFYGYRVIPDSVSIRYNDDGQPTGDARVAFPSPREARRAVrELNNRPLGGRKVKLF 75
RRM5_RBM12B cd12750
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
467-540 2.39e-07

RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM5 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.


Pssm-ID: 410144 [Multi-domain]  Cd Length: 77  Bit Score: 48.65  E-value: 2.39e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:cd12750    3 VKLFNLPFKATVNEILDFF--YGYRVIPDSVSIQYNEQGLPTGDAIIAMETYEEAMAAVQDLNDRPIGPRKVKL 74
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
467-540 6.12e-07

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.


Pssm-ID: 410132 [Multi-domain]  Cd Length: 75  Bit Score: 47.45  E-value: 6.12e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAA--AQRCHkkvMKERYVEV 540
Cdd:cd12733    3 VHMRGLPFQANGQDIINFF----APLKPVRITMEYGPDGKATGEADVHFASHEDAVAAmaKDRSH---MQHRYIEL 71
RRM3_hnRNPH_hnRNPH2_hnRNPF cd12734
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , ...
249-320 6.18e-07

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins; This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which 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; bothe 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.


Pssm-ID: 410133 [Multi-domain]  Cd Length: 76  Bit Score: 47.35  E-value: 6.18e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIARggVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12734    3 VHMRGLPYRATENDIYNFFSPLNPVR--VHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELF 72
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
352-423 1.90e-06

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.


Pssm-ID: 409934 [Multi-domain]  Cd Length: 101  Bit Score: 46.76  E-value: 1.90e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157818053 352 LRGLPFSAGPADVLDFLGPECPVTggvDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIEL 423
Cdd:cd12512   14 LKGLPYEAENKHVIEFFKKLDIVE---DSIYIAYGPNGRATGEGFVEFRNEIDYKAALCRHKQYMGNRFIQV 82
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
350-419 2.71e-06

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


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 45.48  E-value: 2.71e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 350 LRLRGLPFSAGPADVLDFLGPECPVTggvDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKR 419
Cdd:cd12514    2 IRITNLPYDATPVDIQRFFEDHGVRP---EDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
82-214 2.83e-06

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.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 47.99  E-value: 2.83e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  82 LSPQCREASGLSADSLARAESLDKVLQQFSQLVSGDvallggGPYVLCTDGQQLLRQVLHPEASRKNLVLPDTFFSFYDL 161
Cdd:cd06133   54 LSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKN------GKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDL 127
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 162 RREF--HVQHPstcsaRDLTVGTMAQDLGLETDATEDDfGVWEVKTMVAVILHLL 214
Cdd:cd06133  128 KKEFakFYGLK-----KRTGLSKALEYLGLEFEGRHHR-GLDDARNIARILKRLL 176
RRM3_RBM12 cd12512
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
466-548 3.34e-06

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.


Pssm-ID: 409934 [Multi-domain]  Cd Length: 101  Bit Score: 45.99  E-value: 3.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 466 CVRLRGLPYTATIEDILSFLGEaaADIRPHGVHMVLNQQGRPSGDAFIQMMSvERALAAAQRCHKKVMKERYVEVVPCST 545
Cdd:cd12512   11 CVYLKGLPYEAENKHVIEFFKK--LDIVEDSIYIAYGPNGRATGEGFVEFRN-EIDYKAALCRHKQYMGNRFIQVHPITK 87

                 ...
gi 157818053 546 EEM 548
Cdd:cd12512   88 KAM 90
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
466-548 3.70e-06

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.


Pssm-ID: 409935 [Multi-domain]  Cd Length: 81  Bit Score: 45.48  E-value: 3.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 466 CVRLRGLPYTATIEDILSFLGEAaaDIRPHGVHMVLNQQGRPSGDAFIqMMSVERALAAAQRCHKKVMKERYVEVVPCST 545
Cdd:cd12513    2 CVHLKNLSYSVDKRDIRNFFRDL--DISDDQIKFLHDKYGKRTREAFV-MFKNEKDYQTALSLHKGCLGNRTVYIYPISR 78

                 ...
gi 157818053 546 EEM 548
Cdd:cd12513   79 KAM 81
RRM1_RBM12 cd12745
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
348-435 1.05e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgrup corresponds to the RRM1 of 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.


Pssm-ID: 241189 [Multi-domain]  Cd Length: 92  Bit Score: 44.64  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 348 VILRLRGLPFSAGPADVLDFLGPECPVTGGVdgllfvrHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELFRST 427
Cdd:cd12745    3 VVIRLQGLPIVAGTMDIRHFFSGLTIPDGGV-------HIVGGELGEAFIVFATDEDARLGMMRTGGTIKGSKVSLLLSS 75

                 ....*...
gi 157818053 428 AAEVQQVL 435
Cdd:cd12745   76 KTEMQNMI 83
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
664-693 1.14e-05

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.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 43.75  E-value: 1.14e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 157818053 664 ALVRMQGVPYTAGMKDLLSVFQAYQLAPDD 693
Cdd:cd12515    1 CVVKMRNLPFKATIEDILDFFYGYRVIPDS 30
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
354-421 2.52e-05

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.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 42.70  E-value: 2.52e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157818053 354 GLPFSAGPADVLDFLGPECPVTGgVDGLLFvrhPD-GRPTGDAFALFACEELAQAALRRHKGMLGKRYI 421
Cdd:cd12271    5 GIPYYSTEAEIRSYFSSCGEVRS-VDLMRF---PDsGNFRGIAFITFKTEEAAKRALALDGEMLGNRFL 69
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
248-315 3.91e-05

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


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 42.40  E-value: 3.91e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVR 315
Cdd:cd12514    1 FIRITNLPYDATPVDIQRFFEDHGVRPEDVHLLRNKKGRGNGEALVTFKSEGDAREVLKLNGKKLGKR 68
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
467-540 6.74e-05

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).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 41.50  E-value: 6.74e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 157818053 467 VRLRGLPYTATIEDILSFLgeaaadiRPHG----VHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELF-------SKFGevvsVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM1_RBM12B cd12744
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
248-307 7.68e-05

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.


Pssm-ID: 410139 [Multi-domain]  Cd Length: 79  Bit Score: 41.73  E-value: 7.68e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALClnaqGRRNGEALIRFEDSEQRDLALQR 307
Cdd:cd12744    3 VIRLQGLPVVAGSTDIRHFFTGLTIPDGGVHII----GGELGEAFIIFATDEDARRAMSR 58
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
469-540 1.14e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 40.79  E-value: 1.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053 469 LRGLPYTATIEDILSFL---GEAAAdirphgVHMVL-NQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:cd12316    4 VRNLPFTATEDELRELFeafGKISE------VHIPLdKQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73
RRM smart00360
RNA recognition motif;
466-540 1.25e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.65  E-value: 1.25e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157818053   466 CVRLRGLPYTATIEDILSFLGEaAADIRphGVHMVLNQQ-GRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSK-FGKVE--SVRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM4_RBM12B cd12748
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
252-310 1.63e-04

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.


Pssm-ID: 410142 [Multi-domain]  Cd Length: 76  Bit Score: 40.46  E-value: 1.63e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157818053 252 RGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQ--RDLALQRHKH 310
Cdd:cd12748    6 RNLPFDVTKVEVQDFFEGFALAEDDIILLYDDKGVGLGEALVKFKSEEEamKAERLNGQRF 66
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
350-424 2.45e-04

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.


Pssm-ID: 409935 [Multi-domain]  Cd Length: 81  Bit Score: 40.09  E-value: 2.45e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 350 LRLRGLPFSAGPADVLDFLGPecPVTGGvDGLLFVRHPDGRPTGDAFALFACEELAQAALRRHKGMLGKRYIELF 424
Cdd:cd12513    3 VHLKNLSYSVDKRDIRNFFRD--LDISD-DQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIY 74
RRM4_RBM12 cd12749
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
466-551 2.51e-04

RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM4 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.


Pssm-ID: 410143 [Multi-domain]  Cd Length: 88  Bit Score: 40.57  E-value: 2.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 466 CVRLRGLPYTATIEDILSFL-GEAAADirpHGVHMVLNQQGRPSGDAFIQMMSVERALaAAQRCHKKVMKERYVEVVPCS 544
Cdd:cd12749    1 CAHISNIPYNITKKDVLQFLeGIGLDE---NSVQVLVDNNGQGLGQALVQFKSEDDAR-KAERLHRKKLNGRDAFLHLVT 76

                 ....*..
gi 157818053 545 TEEMSRV 551
Cdd:cd12749   77 LEEMKEI 83
RRM5_RBM12 cd12751
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
467-541 6.38e-04

RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM5 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RBMs), 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.


Pssm-ID: 410145 [Multi-domain]  Cd Length: 76  Bit Score: 39.10  E-value: 6.38e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVLNQQGRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEVV 541
Cdd:cd12751    4 IKVQNMPFTVSVDEILDFF--YGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAMAAVVDLNDRPIGSRKVKLV 76
PHA03247 PHA03247
large tegument protein UL36; Provisional
555-678 6.61e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.39  E-value: 6.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  555 GSLSRSGLSPPPCKLPCLSPPTYATFQASPALIPTETTALYPSSALLPAARVPAAATPLAYYPGPATQlymnyTAYYPSP 634
Cdd:PHA03247 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP-----PAASPAG 2826
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 157818053  635 PVSPTTVGYLTTPPTALASTPTSMLSQ----PGALVRMQGVPYTAGMK 678
Cdd:PHA03247 2827 PLPPPTSAQPTAPPPPPGPPPPSLPLGgsvaPGGDVRRRPPSRSPAAK 2874
RRM3_RBM12B cd12513
RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
249-320 6.78e-04

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.


Pssm-ID: 409935 [Multi-domain]  Cd Length: 81  Bit Score: 38.93  E-value: 6.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157818053 249 VRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQRDLALQRHKHHMGVRYIEVY 320
Cdd:cd12513    3 VHLKNLSYSVDKRDIRNFFRDLDISDDQIKFLHDKYGKRTREAFVMFKNEKDYQTALSLHKGCLGNRTVYIY 74
RRM5_RBM12 cd12751
RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
247-300 7.32e-04

RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM5 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RBMs), 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.


Pssm-ID: 410145 [Multi-domain]  Cd Length: 76  Bit Score: 38.72  E-value: 7.32e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 157818053 247 TVVRARGLPWQSSDQDVARFFKGLNIARGGVALCLNAQGRRNGEALIRFEDSEQ 300
Cdd:cd12751    2 TVIKVQNMPFTVSVDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 55
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
462-542 7.76e-04

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 38.94  E-value: 7.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 462 TGRdcVRLRGLPYTATiEDILSFLGEAAADIRPhgVHMVLNQQ-GRPSGDAFIQMMSVERALAAAQRCHKKVMKERYVEV 540
Cdd:cd12566    2 TGR--LFLRNLPYSTK-EDDLQKLFSKFGEVSE--VHVPIDKKtKKSKGFAYVLFLDPEDAVQAYNELDGKVFQGRLIHI 76

                 ..
gi 157818053 541 VP 542
Cdd:cd12566   77 LP 78
RRM1_RBM12 cd12745
RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
248-307 7.97e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgrup corresponds to the RRM1 of 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.


Pssm-ID: 241189 [Multi-domain]  Cd Length: 92  Bit Score: 39.24  E-value: 7.97e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053 248 VVRARGLPWQSSDQDVARFFKGLNIARGGVALClnaqGRRNGEALIRFEDSEQRDLALQR 307
Cdd:cd12745    4 VIRLQGLPIVAGTMDIRHFFSGLTIPDGGVHIV----GGELGEAFIVFATDEDARLGMMR 59
PHA03247 PHA03247
large tegument protein UL36; Provisional
555-664 1.02e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.62  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157818053  555 GSLSRSGLSPPPCKLPclSPPTYATFQASPA-LIPTETTALYPSSALLPAARVPAAATPLAYYPGPATQLYMNYTAYYPS 633
Cdd:PHA03247 2693 GSLTSLADPPPPPPTP--EPAPHALVSATPLpPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPA 2770
                          90       100       110
                  ....*....|....*....|....*....|.
gi 157818053  634 PPVSPTTVGYLTTPPTALASTPTSMLSQPGA 664
Cdd:PHA03247 2771 PPAAPAAGPPRRLTRPAVASLSESRESLPSP 2801
RRM1_RBM12_like cd12510
RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
467-527 2.82e-03

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.


Pssm-ID: 409932 [Multi-domain]  Cd Length: 74  Bit Score: 36.87  E-value: 2.82e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157818053 467 VRLRGLPYTATIEDILSFLgeAAADIRPHGVHMVlnqqGRPSGDAFIQMMSVERALAAAQR 527
Cdd:cd12510    4 IRLQGLPWEAGSLDIRRFF--SGLTIPDGGVHII----GGEKGEAFIIFATDEDARLAMMR 58
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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