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Conserved domains on  [gi|17556566|ref|NP_499569|]
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RRM domain-containing protein [Caenorhabditis elegans]

Protein Classification

RNA recognition motif domain-containing protein( domain architecture ID 11266229)

RNA recognition motif (RRM) domain-containing protein similar to Arabidopsis thaliana serine/arginine-rich splicing factor RS31A, which is probably involved in intron recognition and spliceosome assembly

Gene Ontology:  GO:0003723
PubMed:  15853797|22278943|18515081
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM smart00360
RNA recognition motif;
123-192 1.87e-03

RNA recognition motif;


:

Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 35.65  E-value: 1.87e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17556566    123 CILVGNIPSALTSSEMMGHFGGLKGFTGI-LFKGEDTSLSK-TVRILFDESSSAEAAAKDIDGSNWNGKELD 192
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVrLVRDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLK 72
 
Name Accession Description Interval E-value
RRM smart00360
RNA recognition motif;
123-192 1.87e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 35.65  E-value: 1.87e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17556566    123 CILVGNIPSALTSSEMMGHFGGLKGFTGI-LFKGEDTSLSK-TVRILFDESSSAEAAAKDIDGSNWNGKELD 192
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVrLVRDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLK 72
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 124-191 2.39e-03

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: 35.34  E-value: 2.39e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17556566 124 ILVGNIPSALTSSEMMGHFGGLKGFTGILFKGEDTSLSK-TVRILFDESSSAEAAAKDIDGSNWNGKEL 191
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPL 69
 
Name Accession Description Interval E-value
RRM smart00360
RNA recognition motif;
123-192 1.87e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 35.65  E-value: 1.87e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17556566    123 CILVGNIPSALTSSEMMGHFGGLKGFTGI-LFKGEDTSLSK-TVRILFDESSSAEAAAKDIDGSNWNGKELD 192
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVrLVRDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLK 72
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 124-191 2.39e-03

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: 35.34  E-value: 2.39e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17556566 124 ILVGNIPSALTSSEMMGHFGGLKGFTGILFKGEDTSLSK-TVRILFDESSSAEAAAKDIDGSNWNGKEL 191
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPL 69
 
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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