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Conserved domains on  [gi|1907114522|ref|XP_036015549|]
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RNA binding protein fox-1 homolog 2 isoform X18 [Mus musculus]

Protein Classification

RNA binding protein fox-1 homolog( domain architecture ID 10350647)

RNA binding protein fox-1 homolog is an RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements

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 ...
180-219 2.19e-28

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 cd12407:

Pssm-ID: 450164 [Multi-domain]  Cd Length: 76  Bit Score: 106.33  E-value: 2.19e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1907114522 180 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK 219
Cdd:cd12407     1 KRLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIFNERGSK 40
Fox-1_C pfam12414
Calcitonin gene-related peptide regulator C terminal; This domain family is found in ...
289-337 2.40e-16

Calcitonin gene-related peptide regulator C terminal; This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with pfam00076. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion.


:

Pssm-ID: 432537  Cd Length: 96  Bit Score: 73.82  E-value: 2.40e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907114522 289 IPGFPYPTAATTAAAFRGAHLRGRGRTVYGAVR-AVPPTAIPAYPGVDMQ 337
Cdd:pfam12414   1 VPGFPYPTAATAAAAYRGAHLRGRGRTVYNTFRaAVPPPPIPAYGGVVYQ 50
 
Name Accession Description Interval E-value
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
180-219 2.19e-28

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 106.33  E-value: 2.19e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1907114522 180 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK 219
Cdd:cd12407     1 KRLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIFNERGSK 40
Fox-1_C pfam12414
Calcitonin gene-related peptide regulator C terminal; This domain family is found in ...
289-337 2.40e-16

Calcitonin gene-related peptide regulator C terminal; This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with pfam00076. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion.


Pssm-ID: 432537  Cd Length: 96  Bit Score: 73.82  E-value: 2.40e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907114522 289 IPGFPYPTAATTAAAFRGAHLRGRGRTVYGAVR-AVPPTAIPAYPGVDMQ 337
Cdd:pfam12414   1 VPGFPYPTAATAAAAYRGAHLRGRGRTVYNTFRaAVPPPPIPAYGGVVYQ 50
RRM smart00360
RNA recognition motif;
181-215 1.01e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.05  E-value: 1.01e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1907114522  181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 215
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDK 35
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
163-214 1.10e-04

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


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 43.78  E-value: 1.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907114522 163 QQSQTQSSENSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 214
Cdd:COG0724    99 FRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
184-218 7.47e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 37.60  E-value: 7.47e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907114522 184 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS 218
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGR 37
 
Name Accession Description Interval E-value
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
180-219 2.19e-28

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 106.33  E-value: 2.19e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1907114522 180 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK 219
Cdd:cd12407     1 KRLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIFNERGSK 40
Fox-1_C pfam12414
Calcitonin gene-related peptide regulator C terminal; This domain family is found in ...
289-337 2.40e-16

Calcitonin gene-related peptide regulator C terminal; This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with pfam00076. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion.


Pssm-ID: 432537  Cd Length: 96  Bit Score: 73.82  E-value: 2.40e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907114522 289 IPGFPYPTAATTAAAFRGAHLRGRGRTVYGAVR-AVPPTAIPAYPGVDMQ 337
Cdd:pfam12414   1 VPGFPYPTAATAAAAYRGAHLRGRGRTVYNTFRaAVPPPPIPAYGGVVYQ 50
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
182-223 5.76e-07

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: 46.51  E-value: 5.76e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1907114522 182 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKVNNA 223
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFA 42
RRM smart00360
RNA recognition motif;
181-215 1.01e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.05  E-value: 1.01e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1907114522  181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 215
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDK 35
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
176-233 2.25e-05

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


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 42.27  E-value: 2.25e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907114522 176 KSTpkrLHVSNIPFRFRDPDLRQMFGQFGKILDVEII---------------FNERGSKVNnaTARVMTNKKM 233
Cdd:cd12393     1 KST---VYVSNLPFSLTNNDLHQIFSKYGKVVKVTILkdketrkskgvafvlFLDRESAHN--AVRAMNNKEL 68
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
181-211 6.32e-05

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 41.00  E-value: 6.32e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 211
Cdd:cd12414     1 RLIVRNLPFKCTEDDLKKLFSKFGKVLEVTI 31
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
181-214 6.96e-05

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


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 40.62  E-value: 6.96e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 214
Cdd:cd21608     1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITD 34
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
179-212 9.06e-05

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 40.67  E-value: 9.06e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1907114522 179 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 212
Cdd:cd12412     2 PNRIFVGGIDWDTTEEELREFFSKFGKVKDVKII 35
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
181-224 9.60e-05

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 40.25  E-value: 9.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKVNNAT 224
Cdd:cd12418     2 RVRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDRSGRSTGTAY 45
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
163-214 1.10e-04

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


Pssm-ID: 223796 [Multi-domain]  Cd Length: 306  Bit Score: 43.78  E-value: 1.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907114522 163 QQSQTQSSENSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 214
Cdd:COG0724    99 FRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
181-212 3.86e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 38.71  E-value: 3.86e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 212
Cdd:cd12226     1 RLFVGGLSPSITEDDLERRFSRFGTVSDVEII 32
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
182-219 6.50e-04

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 37.88  E-value: 6.50e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1907114522 182 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFnERGSK 219
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPM-DRETK 37
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
184-218 7.47e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C-terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 37.60  E-value: 7.47e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907114522 184 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS 218
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGR 37
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
182-232 1.52e-03

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 36.83  E-value: 1.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907114522 182 LHVSNIPFRFRDPDLRQMFGQFGKILdveiifnergskvnnaTARVMTNKK 232
Cdd:cd12362     1 LFVYHLPNEFTDQDLYQLFAPFGNVV----------------SAKVFVDKN 35
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
179-217 1.61e-03

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 37.17  E-value: 1.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907114522 179 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 217
Cdd:cd12673     2 PNRIFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDRAG 40
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
182-223 1.62e-03

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 36.92  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1907114522 182 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKVNNA 223
Cdd:cd21607     5 IYCSNLPLSTAESDLYDLFETIGKVNNAELKYDETGDPTGSA 46
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
181-217 2.20e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 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. In addition, it is 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: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 36.52  E-value: 2.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 217
Cdd:cd12564     2 RLIVKNLPSSITEDRLRKLFSAFGTITDVQLKYTKDG 38
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
180-219 2.51e-03

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: 36.63  E-value: 2.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1907114522 180 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK 219
Cdd:cd12566     3 GRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDKKTKK 42
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
180-211 3.59e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 36.20  E-value: 3.59e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1907114522 180 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEI 211
Cdd:cd12312     1 TSLFVRNVADDTRPDDLRREFGRYGPIVDVYI 32
RRM2_VICKZ cd12359
RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds ...
180-224 4.24e-03

RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 409794 [Multi-domain]  Cd Length: 76  Bit Score: 35.81  E-value: 4.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1907114522 180 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKVNNAT 224
Cdd:cd12359     1 RKIQIRNIPPHARWEDLDSLLSTYGTVENCEQVNTKSETATVNVT 45
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
181-218 4.28e-03

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9); This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 241042 [Multi-domain]  Cd Length: 72  Bit Score: 35.54  E-value: 4.28e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIfNERGS 218
Cdd:cd12598     1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELK-NRRGL 37
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
181-217 5.56e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 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). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It 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: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 35.23  E-value: 5.56e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 217
Cdd:cd12565     2 RIIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKDG 38
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
181-217 6.91e-03

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 35.28  E-value: 6.91e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 217
Cdd:cd12680     2 KLLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSG 38
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
181-214 7.47e-03

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 35.09  E-value: 7.47e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1907114522 181 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 214
Cdd:cd21609     1 RLYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYD 34
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
182-211 8.79e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 34.94  E-value: 8.79e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1907114522 182 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI 211
Cdd:cd12311     1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYI 30
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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