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Dcaf1 DDB1 and CUL4 associated factor 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 315987, updated on 9-Dec-2024

Summary

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Official Symbol
Dcaf1provided by RGD
Official Full Name
DDB1 and CUL4 associated factor 1provided by RGD
Primary source
RGD:1305176
See related
EnsemblRapid:ENSRNOG00000013841 AllianceGenome:RGD:1305176
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Vprbp; RGD1305176
Summary
Predicted to enable histone H2AT120 kinase activity; nuclear estrogen receptor binding activity; and ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in several processes, including V(D)J recombination; cell competition in a multicellular organism; and negative regulation of transcription by RNA polymerase II. Predicted to be located in fibrillar center and nucleoplasm. Predicted to be part of COP9 signalosome and Cul4-RING E3 ubiquitin ligase complex. Predicted to be active in centrosome and nucleus. Orthologous to human DCAF1 (DDB1 and CUL4 associated factor 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression
Biased expression in Testes (RPKM 165.7), Thymus (RPKM 125.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Dcaf1 in Genome Data Viewer
Location:
8q32
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (116344927..116419329)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (107466229..107540633)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (115538365..115615282)

Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene RAD54 like 2 Neighboring gene translocase of inner mitochondrial membrane 8A1, pseudogene 1 Neighboring gene RNA binding motif protein 15B Neighboring gene mesencephalic astrocyte-derived neurotrophic factor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. VprBP has intrinsic kinase activity targeting histone H2A and represses gene transcription. Kim K, et al. Mol Cell, 2013 Nov 7. PMID 24140421, Free PMC Article
  2. Merlin/NF2 suppresses tumorigenesis by inhibiting the E3 ubiquitin ligase CRL4(DCAF1) in the nucleus. Li W, et al. Cell, 2010 Feb 19. PMID 20178741, Free PMC Article
  3. The Hippo kinases LATS1 and 2 control human breast cell fate via crosstalk with ERα. Britschgi A, et al. Nature, 2017 Jan 26. PMID 28068668, Free PMC Article
  4. VprBP binds full-length RAG1 and is required for B-cell development and V(D)J recombination fidelity. Kassmeier MD, et al. EMBO J, 2012 Feb 15. PMID 22157821, Free PMC Article
  5. Involvement of Lgl and Mahjong/VprBP in cell competition. Tamori Y, et al. PLoS Biol, 2010 Jul 13. PMID 20644714, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables histone H2AT120 kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H2AT120 kinase activity ISO
Inferred from Sequence Orthology
more info
  
enables nuclear estrogen receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear estrogen receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables ubiquitin-like ligase-substrate adaptor activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in B cell differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in V(D)J recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in cell competition in a multicellular organism ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in post-translational protein modification ISO
Inferred from Sequence Orthology
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of COP9 signalosome ISO
Inferred from Sequence Orthology
more info
  
part_of Cul4-RING E3 ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Cul4-RING E3 ubiquitin ligase complex ISO
Inferred from Sequence Orthology
more info
  
is_active_in centrosome ISO
Inferred from Sequence Orthology
more info
  
located_in fibrillar center IEA
Inferred from Electronic Annotation
more info
  
located_in fibrillar center ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
DDB1- and CUL4-associated factor 1
Names
Vpr (HIV-1) binding protein
protein VPRBP
NP_001341133.1
XP_038937498.1
XP_038937499.1
XP_038937500.1
XP_038937501.1
XP_038937502.1
XP_038937503.1
XP_063121688.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001354204.3 → NP_001341133.1  DDB1- and CUL4-associated factor 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000008
    UniProtKB/TrEMBL
    D3ZKB7
    Related
    ENSRNOP00000018932.8, ENSRNOT00000018932.8
    Conserved Domains (2) summary
    sd00039
    Location:1096 → 1132
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:1092 → 1310
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086026.1 Reference GRCr8

    Range
    116344927..116419329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039081571.2 → XP_038937499.1  DDB1- and CUL4-associated factor 1 isoform X2

    UniProtKB/TrEMBL
    D3ZKB7
    Related
    ENSRNOP00000075456.3, ENSRNOT00000079801.3
    Conserved Domains (2) summary
    sd00039
    Location:1106 → 1142
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:1102 → 1320
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. XM_039081573.2 → XP_038937501.1  DDB1- and CUL4-associated factor 1 isoform X4

    UniProtKB/TrEMBL
    D3ZKB7
    Conserved Domains (2) summary
    sd00039
    Location:1123 → 1159
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:1119 → 1337
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  3. XM_063265618.1 → XP_063121688.1  DDB1- and CUL4-associated factor 1 isoform X6

    UniProtKB/TrEMBL
    D3ZKB7

  4. XM_039081570.2 → XP_038937498.1  DDB1- and CUL4-associated factor 1 isoform X1

    UniProtKB/TrEMBL
    D3ZKB7
    Conserved Domains (2) summary
    sd00039
    Location:1123 → 1159
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:1119 → 1337
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  5. XM_039081572.2 → XP_038937500.1  DDB1- and CUL4-associated factor 1 isoform X3

    UniProtKB/TrEMBL
    D3ZKB7
    Conserved Domains (2) summary
    sd00039
    Location:1123 → 1159
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:1119 → 1337
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  6. XM_039081574.2 → XP_038937502.1  DDB1- and CUL4-associated factor 1 isoform X5

    UniProtKB/TrEMBL
    D3ZKB7
    Related
    ENSRNOP00000105563.1, ENSRNOT00000156185.1
    Conserved Domains (2) summary
    sd00039
    Location:1096 → 1132
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:1092 → 1310
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  7. XM_039081575.2 → XP_038937503.1  DDB1- and CUL4-associated factor 1 isoform X5

    UniProtKB/TrEMBL
    D3ZKB7
    Conserved Domains (2) summary
    sd00039
    Location:1096 → 1132
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:1092 → 1310
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

  1. XR_005487844.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001191798.1: Suppressed sequence

    Description
    NM_001191798.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

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