NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1370511788|ref|XP_024302822|]
View 

RNA-binding protein with multiple splicing isoform X6 [Homo sapiens]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 14-40 3.43e-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).


The actual alignment was detected with superfamily member cd12684:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 83  Bit Score: 43.75  E-value: 3.43e-06
                          10        20
                  ....*....|....*....|....*..
gi 1370511788  14 SEANLQEEEGIRFDPEIPQTLRLEFAK 40
Cdd:cd12684    57 AEAAKQDLQGVRFDPDLPQTLRLEFAK 83
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 52-141 7.64e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 36.84  E-value: 7.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370511788   52 GTPNPSTP-LPNTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPAELAPALPPPAFTYPASLHAQVSSPPPAMGALCPR 130
Cdd:PHA03247  2765 GPPAPAPPaAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG 2844

                           90
                   ....*....|.
gi 1370511788  131 PVLSHLSQEGS 141
Cdd:PHA03247  2845 PPPPSLPLGGS 2855
 
Name Accession Description Interval E-value
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
 14-40 3.43e-06

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 43.75  E-value: 3.43e-06
                          10        20
                  ....*....|....*....|....*..
gi 1370511788  14 SEANLQEEEGIRFDPEIPQTLRLEFAK 40
Cdd:cd12684    57 AEAAKQDLQGVRFDPDLPQTLRLEFAK 83
PHA03247 PHA03247
large tegument protein UL36; Provisional
 52-141 7.64e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 36.84  E-value: 7.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370511788   52 GTPNPSTP-LPNTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPAELAPALPPPAFTYPASLHAQVSSPPPAMGALCPR 130
Cdd:PHA03247  2765 GPPAPAPPaAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG 2844

                           90
                   ....*....|.
gi 1370511788  131 PVLSHLSQEGS 141
Cdd:PHA03247  2845 PPPPSLPLGGS 2855
 
Name Accession Description Interval E-value
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
 14-40 3.43e-06

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 43.75  E-value: 3.43e-06
                          10        20
                  ....*....|....*....|....*..
gi 1370511788  14 SEANLQEEEGIRFDPEIPQTLRLEFAK 40
Cdd:cd12684    57 AEAAKQDLQGVRFDPDLPQTLRLEFAK 83
RRM_RBPMS cd12682
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing ...
 12-38 3.65e-04

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS); This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development.


Pssm-ID: 410083 [Multi-domain]  Cd Length: 76  Bit Score: 37.72  E-value: 3.65e-04
                          10        20
                  ....*....|....*....|....*..
gi 1370511788  12 TPSEANLQEEEGIRFDPEIPQTLRLEF 38
Cdd:cd12682    50 SEAEAAKNALNGIRFDPEIPQTLRLEF 76
RRM_RBPMS2 cd12683
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 ...
 14-38 4.62e-03

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2); This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410084 [Multi-domain]  Cd Length: 76  Bit Score: 34.63  E-value: 4.62e-03
                          10        20
                  ....*....|....*....|....*
gi 1370511788  14 SEANLQEEEGIRFDPEIPQTLRLEF 38
Cdd:cd12683    52 AEAAKNALNGIRFDPENPQTLRLEF 76
PHA03247 PHA03247
large tegument protein UL36; Provisional
 52-141 7.64e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 36.84  E-value: 7.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370511788   52 GTPNPSTP-LPNTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPAELAPALPPPAFTYPASLHAQVSSPPPAMGALCPR 130
Cdd:PHA03247  2765 GPPAPAPPaAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPG 2844

                           90
                   ....*....|.
gi 1370511788  131 PVLSHLSQEGS 141
Cdd:PHA03247  2845 PPPPSLPLGGS 2855
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH