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Conserved domains on  [gi|528515624|ref|XP_005174031|]
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nucleolar protein 8 isoform X1 [Danio rerio]

Protein Classification

NOL8 family RNA-binding protein( domain architecture ID 10187814)

NOL8 family RNA-binding protein recognizes RNA via an RNA recognition motif (RRM); similar to nucleolar protein 8, a RNA-binding protein that up-regulated in some cancer cells, and that its decreased expression results in induction of apoptosis in cancer cells

Gene Ontology:  GO:0003723
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
3-82 5.66e-31

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: 116.52  E-value: 5.66e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDdqgAPLKTFGYININITDAEFKRCVGILNKSTWKGGTLLIQLAK 82
Cdd:cd12226     1 RLFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKD---APDRGFAYIDLRTSEAALQKCLSTLNGVKWKGSRLKIQLAK 77
 
Name Accession Description Interval E-value
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
3-82 5.66e-31

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: 116.52  E-value: 5.66e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDdqgAPLKTFGYININITDAEFKRCVGILNKSTWKGGTLLIQLAK 82
Cdd:cd12226     1 RLFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKD---APDRGFAYIDLRTSEAALQKCLSTLNGVKWKGSRLKIQLAK 77
RRM smart00360
RNA recognition motif;
3-78 4.21e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.14  E-value: 4.21e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528515624      3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIItrKDDQGAPLKTFGYIN-INITDAEfkRCVGILNKSTWKGGTLLI 78
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLV--RDKETGKSKGFAFVEfESEEDAE--KALEALNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-83 6.43e-09

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 53.95  E-value: 6.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    1 MKRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYININiTDAEFKRCVGILNKSTWKGGTLLIQL 80
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETGRS--RGFGFVEMP-DDEEAQAAIEALNGAELMGRTLKVNE 77

                  ...
gi 528515624   81 AKE 83
Cdd:COG0724    78 ARP 80
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
4-77 3.44e-07

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 48.77  E-value: 3.44e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528515624     4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkdDQGAPLKTFGYIN-INITDAEfkRCVGILNKSTWKGGTLL 77
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVR---DETGRSKGFAFVEfEDEEDAE--KAIEALNGKELGGRELK 70
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
3-50 3.52e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 44.52  E-value: 3.52e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 528515624     3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDDQGAPLKTFGYI 50
Cdd:TIGR01622  216 RLYVGNLHFNITEQDLRQIFEPFGEIEFVQL--QKDPETGRSKGYGFI 261
PLN03213 PLN03213
repressor of silencing 3; Provisional
3-94 6.39e-04

repressor of silencing 3; Provisional


Pssm-ID: 178752 [Multi-domain]  Cd Length: 759  Bit Score: 44.07  E-value: 6.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDdqgaplKTFGYININITDA-EFKRCVGILNKSTWKGGTLLIQLA 81
Cdd:PLN03213   12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG------RSFAYIDFSPSSTnSLTKLFSTYNGCVWKGGRLRLEKA 85
                          90
                  ....*....|...
gi 528515624   82 KESFLHRLAEERE 94
Cdd:PLN03213   86 KEHYLARLKREWE 98
 
Name Accession Description Interval E-value
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
3-82 5.66e-31

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: 116.52  E-value: 5.66e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDdqgAPLKTFGYININITDAEFKRCVGILNKSTWKGGTLLIQLAK 82
Cdd:cd12226     1 RLFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKD---APDRGFAYIDLRTSEAALQKCLSTLNGVKWKGSRLKIQLAK 77
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
4-79 1.96e-09

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: 54.98  E-value: 1.96e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGaplKTFGYIN-INITDAEfkRCVGILNKSTWKGGTLLIQ 79
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKS---KGFAFVEfESPEDAE--KALEALNGTELGGRPLKVS 72
RRM smart00360
RNA recognition motif;
3-78 4.21e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.14  E-value: 4.21e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528515624      3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIItrKDDQGAPLKTFGYIN-INITDAEfkRCVGILNKSTWKGGTLLI 78
Cdd:smart00360    1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLV--RDKETGKSKGFAFVEfESEEDAE--KALEALNGKELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-83 6.43e-09

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 53.95  E-value: 6.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    1 MKRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYININiTDAEFKRCVGILNKSTWKGGTLLIQL 80
Cdd:COG0724     1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETGRS--RGFGFVEMP-DDEEAQAAIEALNGAELMGRTLKVNE 77

                  ...
gi 528515624   81 AKE 83
Cdd:COG0724    78 ARP 80
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
4-37 9.57e-08

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 50.36  E-value: 9.57e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRK 37
Cdd:cd12224     4 LYVGGLGDKITEKDLRDHFYQFGEIRSITVVARQ 37
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
4-77 3.44e-07

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 48.77  E-value: 3.44e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 528515624     4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkdDQGAPLKTFGYIN-INITDAEfkRCVGILNKSTWKGGTLL 77
Cdd:pfam00076    1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVR---DETGRSKGFAFVEfEDEEDAE--KAIEALNGKELGGRELK 70
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
4-73 3.59e-06

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


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 45.71  E-value: 3.59e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYINI-NITDAEfkRCVGILNKSTWKG 73
Cdd:cd12417     2 LWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSARTPGS--RCYGYVTMaSVEEAD--LCIKSLNKTELHG 68
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
3-81 4.34e-06

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: 45.62  E-value: 4.34e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkDDQGAPLKTFGYININiTDAEFKRCVGILNKSTWKGGTLLIQLA 81
Cdd:cd21608     1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVIT--DRETGRSRGFGFVTFS-TAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
3-50 3.23e-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: 43.37  E-value: 3.23e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIItrKDDQGAPlKTFGYI 50
Cdd:cd12412     4 RIFVGGIDWDTTEEELREFFSKFGKVKDVKII--KDRAGVS-KGYGFV 48
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
2-61 3.26e-05

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: 43.16  E-value: 3.26e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528515624    2 KRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkDDQGAplKTFGYIN-INITDAEFKR 61
Cdd:cd12407     1 KRLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIF--NERGS--KGFGFVTfANSADADRAR 57
RRM_SLTM cd12678
RNA recognition motif (RRM) found in Scaffold attachment factor (SAF)-like transcription ...
4-73 4.59e-05

RNA recognition motif (RRM) found in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins; This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines.


Pssm-ID: 410079 [Multi-domain]  Cd Length: 74  Bit Score: 42.76  E-value: 4.59e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYININiTDAEFKRCVGILNKSTWKG 73
Cdd:cd12678     2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGA--KCYGIVTMS-SSTEVARCISHLHRTELHG 68
RRM_G3BP cd12229
RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, ...
3-50 4.72e-05

RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins; This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif).


Pssm-ID: 409676 [Multi-domain]  Cd Length: 81  Bit Score: 42.79  E-value: 4.72e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAPLktFGYI 50
Cdd:cd12229     5 QLFVGNLPHDITEDELKEFFSRFGNVLELRINSKGGGGRLPN--FGFV 50
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
4-50 4.90e-05

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 42.60  E-value: 4.90e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDDQGAPLKTFGYI 50
Cdd:cd12347     1 LYVGGLAEEVDEKVLHAAFIPFGDIVDIQI--PLDYETEKHRGFAFV 45
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
3-82 1.30e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 41.52  E-value: 1.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKddqGAPLK--TFGYININ-ITDAEFKRCVGILNKSTWKGGTLLIQ 79
Cdd:cd12355     1 RLWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFHK---TGPLKgqPRGYCFVTfETKEEAEKAIECLNGKLALGKKLVVR 77

                  ...
gi 528515624   80 LAK 82
Cdd:cd12355    78 WAH 80
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
3-38 1.49e-04

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 41.10  E-value: 1.49e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKD 38
Cdd:cd12328     1 KLFVGGLKEDVEEEDLREYFSQFGKVESVEIVTDKE 36
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
4-40 1.55e-04

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 41.51  E-value: 1.55e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEII-TRKDDQ 40
Cdd:cd12223     4 LYVGNLPPSVTEEVLLREFGRFGPLASVKIMwPRTEEE 41
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
3-31 2.71e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 40.69  E-value: 2.71e-04
                          10        20
                  ....*....|....*....|....*....
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDV 31
Cdd:cd12373     1 KVYVGNLGPRVTKRELEDAFEKYGPLRNV 29
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
4-35 3.39e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 40.20  E-value: 3.39e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIIT 35
Cdd:cd12325     1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMK 32
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
3-50 3.52e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 44.52  E-value: 3.52e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 528515624     3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDDQGAPLKTFGYI 50
Cdd:TIGR01622  216 RLYVGNLHFNITEQDLRQIFEPFGEIEFVQL--QKDPETGRSKGYGFI 261
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
4-33 4.19e-04

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 40.08  E-value: 4.19e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEI 33
Cdd:cd12309     5 LFVGNLEITITEEELRRAFERYGVVEDVDI 34
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
2-50 5.25e-04

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 40.01  E-value: 5.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528515624    2 KRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDdqGAPlKTFGYI 50
Cdd:cd12392     3 NKLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRN--GKP-KGLAYV 48
PLN03213 PLN03213
repressor of silencing 3; Provisional
3-94 6.39e-04

repressor of silencing 3; Provisional


Pssm-ID: 178752 [Multi-domain]  Cd Length: 759  Bit Score: 44.07  E-value: 6.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDdqgaplKTFGYININITDA-EFKRCVGILNKSTWKGGTLLIQLA 81
Cdd:PLN03213   12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG------RSFAYIDFSPSSTnSLTKLFSTYNGCVWKGGRLRLEKA 85
                          90
                  ....*....|...
gi 528515624   82 KESFLHRLAEERE 94
Cdd:PLN03213   86 KEHYLARLKREWE 98
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
3-50 7.11e-04

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 39.61  E-value: 7.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYI 50
Cdd:cd12330     1 KIFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDHDTGRS--RGFGFV 46
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
4-50 7.79e-04

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. 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: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 39.38  E-value: 7.79e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkdDQGAPLKTFGYI 50
Cdd:cd12672     8 VFVGGIDIRMDENEIRSFFARYGSVKEVKIIT---DRTGVSKGYGFV 51
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
3-57 9.41e-04

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 40.79  E-value: 9.41e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkDDQGAPLKTFGYININITDA 57
Cdd:PLN03134   36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIV--DRETGRSRGFGFVNFNDEGA 88
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
3-63 1.16e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 39.05  E-value: 1.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDqgAPLKTFGYININITDAEFKRCV 63
Cdd:cd12579     1 KLFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKDT--GKKRGFGFVYFEDHDSADKAAV 59
RRM1_SRSF9 cd12598
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 ...
3-37 1.19e-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: 38.63  E-value: 1.19e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRK 37
Cdd:cd12598     1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRR 35
RRM2_hnRNPD_like cd12329
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, ...
3-37 1.30e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins; This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus.


Pssm-ID: 240775 [Multi-domain]  Cd Length: 75  Bit Score: 38.50  E-value: 1.30e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRK 37
Cdd:cd12329     1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDK 35
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
3-33 2.02e-03

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: 37.94  E-value: 2.02e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEI 33
Cdd:cd12418     2 RVRVSNLHPDVTEEDLRELFGRVGPVKSVKI 32
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
2-58 2.08e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. 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 first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 38.28  E-value: 2.08e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528515624    2 KRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDDQGAPLKTFGYININITDAE 58
Cdd:cd21619     2 NTIYVGNIDMTINEDALEKIFSRYGQVESVRR--PPIHTDKADRTTGFGFIKYTDAE 56
RRM1_hnRNPAB cd12757
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) ...
3-50 2.59e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins; This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop.


Pssm-ID: 410151 [Multi-domain]  Cd Length: 80  Bit Score: 38.03  E-value: 2.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDDQGAPLKTFGYI 50
Cdd:cd12757     6 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI--KMDPNTGRSRGFGFI 51
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
4-50 2.80e-03

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 37.86  E-value: 2.80e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIItrKDDQGAPLKTFGYI 50
Cdd:cd12577     1 MFIGGLNWDTTEEGLRDYFSQFGTVVDCTIM--KDSATGRSRGFGFL 45
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
5-50 3.70e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 37.26  E-value: 3.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 528515624    5 YIGGLGHTVTEKDLKDRFGKFGDVKDVEIItrkddqgaPLKTFGYI 50
Cdd:cd12354     4 YVGNITKGLTEALLQQTFSPFGQILEVRVF--------PDKGYAFI 41
RRM2_DAZAP1 cd12327
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
2-50 4.05e-03

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409765 [Multi-domain]  Cd Length: 80  Bit Score: 37.48  E-value: 4.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 528515624    2 KRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYI 50
Cdd:cd12327     3 KKVFVGGIPHNCGETELRDYFKRYGVVTEVVMMYDAEKQRS--RGFGFI 49
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
3-50 4.08e-03

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 37.28  E-value: 4.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDdqgaplKTFGYI 50
Cdd:cd12332     3 RLFVGNLPNDITEEEFKELFQKYGEVSEVFL--NKG------KGFGFI 42
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
3-38 4.13e-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: 37.16  E-value: 4.13e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 528515624    3 RLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKD 38
Cdd:cd12565     2 RIIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKD 37
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
4-50 4.37e-03

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 37.00  E-value: 4.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIitRKDDQGAPLKTFGYI 50
Cdd:cd12321     2 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQV--KKDPKTGRSKGFGFV 46
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
4-33 5.58e-03

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 36.92  E-value: 5.58e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEI 33
Cdd:cd12346     4 VFVGGLDPNVTEEDLRVLFGPFGEIVYVKI 33
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
4-81 6.63e-03

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: 36.73  E-value: 6.63e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKdDQGAPlKTFGYININiTDAEFKRCVGILNKSTWKGGTLLIQLA 81
Cdd:cd12399     1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDR-ETKRP-RGFGFVELQ-EEESAEKAIAKLDGTDFMGRTIRVNEA 75
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
4-82 6.68e-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: 6.68e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 528515624    4 LYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkDDQGAPLKTFGYININITDAEFkrCVGILNKSTWKGGTLLIQLAK 82
Cdd:cd21607     5 IYCSNLPLSTAESDLYDLFETIGKVNNAELKY--DETGDPTGSAVVEYENLDDADV--CISKLNNYNYGGCDLKISYAK 79
RRM_SAFB1_SAFB2 cd12679
RNA recognition motif (RRM) found in scaffold attachment factor B1 (SAFB1), scaffold ...
2-73 7.63e-03

RNA recognition motif (RRM) found in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins; This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1.


Pssm-ID: 410080 [Multi-domain]  Cd Length: 76  Bit Score: 36.40  E-value: 7.63e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 528515624    2 KRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITRKDDQGAplKTFGYININITDaEFKRCVGILNKSTWKG 73
Cdd:cd12679     2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGA--RCYGFVTMSTSE-EATKCISHLHRTELHG 70
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
8-73 8.81e-03

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 36.44  E-value: 8.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 528515624    8 GLGHTVTEKDLKDRFGKFGDVKDVEIItrKDDQGAPLKTFGYINI-NITDAefKRCVGILNKSTWKG 73
Cdd:cd12363     8 GLSLYTTERDLREVFSRYGPIEKVQVV--YDQQTGRSRGFGFVYFeSVEDA--KEAKERLNGQEIDG 70
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
9-81 8.87e-03

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 36.62  E-value: 8.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 528515624    9 LGHTVTEKDLKDRFGKFGDVKDVEIITrkDDQGAPLKTFGYININITDAEFKRCvgILNKSTWKGGTLLIQLA 81
Cdd:cd12451    11 LGEDTIRDELREHFGECGEVTNVRIPT--DRETGELKGFAYIEFSTKEAKEKAL--ELNGSDIAGGNLVVDEA 79
RRM2_hnRNPA2B1 cd12581
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP ...
2-56 9.48e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409995 [Multi-domain]  Cd Length: 80  Bit Score: 36.50  E-value: 9.48e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 528515624    2 KRLYIGGLGHTVTEKDLKDRFGKFGDVKDVEIITrkDDQGAPLKTFGYININITD 56
Cdd:cd12581     1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIIT--DRQSGKKRGFGFVTFDDHD 53
 
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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