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Conserved domains on  [gi|17862472|gb|AAL39713|]
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LD29830p [Drosophila melanogaster]

Protein Classification

RNA-binding protein( domain architecture ID 10188075)

RNA-binding protein containing an RNA recognition motif (RRM) similar to Homo sapiens splicing regulatory glutamine/lysine-rich protein 1 (SREK1) that participates in the regulation of alternative splicing by modulating the activity of other splice facors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
 160-242 1.33e-40

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


:

Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 140.91  E-value: 1.33e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472 160 EEIRRTIIVCDVKNEWRLDDLMECFQRAGEVKYARWAEKD--NKTYCMIEFCEQTSIIHALRMQGQEFKGGHLSVYHSTY 237
Cdd:cd12260   1 EEIRRTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDEtqPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSNN 80


                ....*
gi 17862472 238 SITKP 242
Cdd:cd12260  81 AIVKP 85
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
 9-85 8.47e-40

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


:

Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 138.60  E-value: 8.47e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17862472   9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPTIRDVsCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIP 85
Cdd:cd12259   1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPSEDDL-APVLSKVCFVKYEDPEDVAVALHLTNTVFIDRALIVIP 76
 
Name Accession Description Interval E-value
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
 160-242 1.33e-40

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 140.91  E-value: 1.33e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472 160 EEIRRTIIVCDVKNEWRLDDLMECFQRAGEVKYARWAEKD--NKTYCMIEFCEQTSIIHALRMQGQEFKGGHLSVYHSTY 237
Cdd:cd12260   1 EEIRRTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDEtqPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSNN 80


                ....*
gi 17862472 238 SITKP 242
Cdd:cd12260  81 AIVKP 85
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
 9-85 8.47e-40

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 138.60  E-value: 8.47e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17862472   9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPTIRDVsCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIP 85
Cdd:cd12259   1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPSEDDL-APVLSKVCFVKYEDPEDVAVALHLTNTVFIDRALIVIP 76
RRM smart00360
RNA recognition motif;
9-83 1.32e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.97  E-value: 1.32e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17862472      9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptIRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFID-RALIV 83
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRL---VRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDgRPLKV 73
RRM smart00360
RNA recognition motif;
165-232 2.67e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 39.50  E-value: 2.67e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17862472    165 TIIVCDVKNEWRLDDLMECFQRAGEVKYARWAeKDNKT-----YCMIEFCEQTSIIHALR-MQGQEFKGGHLSV 232
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLV-RDKETgkskgFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 12-81 7.11e-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 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: 37.98  E-value: 7.11e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17862472    12 VTNIAPQATKDQMQTLFGNIGKIEEIRLYPTIRDVScpvqSRICYVKYTDTTSVPVA-QHLTNTVFIDRAL 81
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRS----KGFAFVEFEDEEDAEKAiEALNGKELGGREL 69
PLN03120 PLN03120
nucleic acid binding protein; Provisional
 8-94 1.26e-03

nucleic acid binding protein; Provisional


Pssm-ID: 215588  Cd Length: 260  Bit Score: 40.80  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472    8 RVIQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptirdVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIPVl 87
Cdd:PLN03120   5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEM------QSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPA- 77


                 ....*..
gi 17862472   88 aipEEYR 94
Cdd:PLN03120  78 ---EDYQ 81
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 8-115 3.94e-03

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: 39.90  E-value: 3.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472     8 RVIQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptIRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIPVL 87
Cdd:TIGR01622 115 RTVFVQQLAARARERDLYEFFSKVGKVRDVQI---IKDRNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQLSE 191

                          90       100
                  ....*....|....*....|....*...
gi 17862472    88 AipEEYRALEMLKNGTIVPGLQKPDSKL 115
Cdd:TIGR01622 192 A--EKNRAARAATETSGHHPNSIPFHRL 217
 
Name Accession Description Interval E-value
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
 160-242 1.33e-40

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 140.91  E-value: 1.33e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472 160 EEIRRTIIVCDVKNEWRLDDLMECFQRAGEVKYARWAEKD--NKTYCMIEFCEQTSIIHALRMQGQEFKGGHLSVYHSTY 237
Cdd:cd12260   1 EEIRRTVYVGNLDPSTTADQLLEFFSQAGEVKYVRMAGDEtqPTRYAFVEFAEQTSVINALKLNGKMFGGRPLKVNHSNN 80


                ....*
gi 17862472 238 SITKP 242
Cdd:cd12260  81 AIVKP 85
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
 9-85 8.47e-40

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 138.60  E-value: 8.47e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17862472   9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPTIRDVsCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIP 85
Cdd:cd12259   1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPSEDDL-APVLSKVCFVKYEDPEDVAVALHLTNTVFIDRALIVIP 76
RRM_SRSF11 cd12518
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and ...
 9-85 5.91e-32

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and similar proteins; This subgroup corresponds to the RRM of SRSF11, also termed arginine-rich 54 kDa nuclear protein (SRp54 or p54), which belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family). It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion. SRSF11 is a unique SR family member and may regulate the alternative splicing in a tissue- and substrate-dependent manner. It can directly interact with the U2 auxiliary factor 65-kDa subunit (U2AF65), a protein associated with the 3' splice site. In addition, unlike the typical SR proteins, SRSF11 associates with other SR proteins but not with the U1 small nuclear ribonucleoprotein U1-70K or the U2 auxiliary factor 35-kDa subunit (U2AF35). SREK1 has unique properties in regulating alternative splicing of different pre-mRNAs; it promotes the use of the distal 5' splice site in E1A pre-mRNA alternative splicing. It also inhibits cryptic splice site selection on the beta-globin pre-mRNA containing competing 5' splice sites. SREK1 contains an RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and one serine-arginine (SR)-rich domains (SR domains).


Pssm-ID: 409940 [Multi-domain]  Cd Length: 80  Bit Score: 117.45  E-value: 5.91e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17862472   9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPTiRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIP 85
Cdd:cd12518   1 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFPP-DDSPLPVTSRVCFVKFHEPDSAVVAQHLTNTVFVDRALIVVP 76
RRM1_SREK1 cd12519
RNA recognition motif 1 (RRM1) found in splicing regulatory glutamine/lysine-rich protein 1 ...
 9-85 1.12e-26

RNA recognition motif 1 (RRM1) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subgroup corresponds to the RRM1 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), and is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 generally contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1; plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409941 [Multi-domain]  Cd Length: 80  Bit Score: 103.17  E-value: 1.12e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17862472   9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPTiRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIP 85
Cdd:cd12519   1 VIQVTNLSAAVTSDQMRTLFSFLGDIEELRLYPP-DNAPLAFSSKVCYVKYREPSSVGVAQHLTNTVFIDRALIVVP 76
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 10-83 6.24e-06

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: 44.20  E-value: 6.24e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17862472  10 IQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPTIRDVScpvqSRICYVKYTDTTSVPVA-QHLTNTVFIDRALIV 83
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKS----KGFAFVEFESPEDAEKAlEALNGTELGGRPLKV 71
RRM smart00360
RNA recognition motif;
9-83 1.32e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 42.97  E-value: 1.32e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17862472      9 VIQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptIRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFID-RALIV 83
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRL---VRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDgRPLKV 73
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
 8-83 7.23e-05

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: 41.36  E-value: 7.23e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17862472   8 RVIQVTNIAPQATKDQMQTLFGNIGKIEEIRLYPtiRDVSCPVQSR-ICYVKYTDTTSVPVA-QHLTNTVFIDRALIV 83
Cdd:cd21619   2 NTIYVGNIDMTINEDALEKIFSRYGQVESVRRPP--IHTDKADRTTgFGFIKYTDAESAERAmQQADGILLGRRRLVV 77
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 12-41 2.46e-04

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: 39.57  E-value: 2.46e-04
                        10        20        30
                ....*....|....*....|....*....|
gi 17862472  12 VTNIAPQATKDQMQTLFGNIGKIEEIRLYP 41
Cdd:cd12354   5 VGNITKGLTEALLQQTFSPFGQILEVRVFP 34
RRM smart00360
RNA recognition motif;
165-232 2.67e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 39.50  E-value: 2.67e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17862472    165 TIIVCDVKNEWRLDDLMECFQRAGEVKYARWAeKDNKT-----YCMIEFCEQTSIIHALR-MQGQEFKGGHLSV 232
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLV-RDKETgkskgFAFVEFESEEDAEKALEaLNGKELDGRPLKV 73
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 12-83 3.59e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 39.14  E-value: 3.59e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17862472  12 VTNIAPQATKDQMQTLFGNIGKIEEIRLyptIRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIV 83
Cdd:cd12283   4 VMQLSLKARERDLYEFFSKAGKVRDVRL---IMDRNSRRSKGVAYVEFYDVESVPLALALTGQRLLGQPIMV 72
RRM_Vip1_like cd12269
RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to ...
 10-83 4.27e-04

RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to fission yeast Vip1; This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409712 [Multi-domain]  Cd Length: 69  Bit Score: 38.67  E-value: 4.27e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17862472  10 IQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptirdVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIV 83
Cdd:cd12269   1 VEVTNVSPLATERDLHEFFSFSGDIEHIEI------QREGEQSRIAFVTFKDPYALETAVLLSGATIVDQRVTI 68
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 166-232 5.16e-04

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: 38.42  E-value: 5.16e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17862472 166 IIVCDVKNEWRLDDLMECFQRAGEVKYARW---AEKDNKTYCMIEFCEQTSIIHALR-MQGQEFKGGHLSV 232
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIvrdRDGKSKGFAFVEFESPEDAEKALEaLNGTELGGRPLKV 71
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 12-81 7.11e-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 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: 37.98  E-value: 7.11e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17862472    12 VTNIAPQATKDQMQTLFGNIGKIEEIRLYPTIRDVScpvqSRICYVKYTDTTSVPVA-QHLTNTVFIDRAL 81
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRS----KGFAFVEFEDEEDAEKAiEALNGKELGGREL 69
PLN03120 PLN03120
nucleic acid binding protein; Provisional
 8-94 1.26e-03

nucleic acid binding protein; Provisional


Pssm-ID: 215588  Cd Length: 260  Bit Score: 40.80  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472    8 RVIQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptirdVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIPVl 87
Cdd:PLN03120   5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEM------QSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPA- 77


                 ....*..
gi 17862472   88 aipEEYR 94
Cdd:PLN03120  78 ---EDYQ 81
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 12-84 1.63e-03

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 37.36  E-value: 1.63e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17862472  12 VTNIAPQATKDQMQTLFGNIGKIEEIRLyPTIRDVScpvQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVI 84
Cdd:cd12297   5 VTNFPPSYDERSIRDLFGDYGVILSVRL-PSLRYNT---SRRFCYIDFTSPESARAAVELLNGLLEEGYTLVV 73
RRM1_2_CID8_like cd12225
RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting ...
 164-235 2.91e-03

RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins; This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear.


Pssm-ID: 409672 [Multi-domain]  Cd Length: 76  Bit Score: 36.67  E-value: 2.91e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17862472 164 RTIIVCDVKNEWRLDDLMECFQRAGEVKYARWAEKDNKT-YCMIEFCEQTSIIHALRMQGQEFKGGHLSVYHS 235
Cdd:cd12225   1 RTIHVGGIDGSLSEDELADYFSNCGEVTQVRLCGDRVHTrFAWVEFATDASALSALNLDGTTLGGHPLRVSPS 73
RRM3_PUB1 cd12622
RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated ...
 12-81 2.97e-03

RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which 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 RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410033 [Multi-domain]  Cd Length: 74  Bit Score: 36.66  E-value: 2.97e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17862472  12 VTNIAPQATKDQMQTLFGNIGKIEEIRLYptiRDVSCpvqsriCYVKYTDTTSVPVA-QHLTNTVFIDRAL 81
Cdd:cd12622   5 VGNLPPEVTQADLIPLFQNFGVIEEVRVQ---RDKGF------GFVKYDTHEEAALAiQQLNGQPFLGRPI 66
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 8-115 3.94e-03

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: 39.90  E-value: 3.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17862472     8 RVIQVTNIAPQATKDQMQTLFGNIGKIEEIRLyptIRDVSCPVQSRICYVKYTDTTSVPVAQHLTNTVFIDRALIVIPVL 87
Cdd:TIGR01622 115 RTVFVQQLAARARERDLYEFFSKVGKVRDVQI---IKDRNSRRSKGVGYVEFYDVDSVQAALALTGQKLLGIPVIVQLSE 191

                          90       100
                  ....*....|....*....|....*...
gi 17862472    88 AipEEYRALEMLKNGTIVPGLQKPDSKL 115
Cdd:TIGR01622 192 A--EKNRAARAATETSGHHPNSIPFHRL 217
 
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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