U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 315987, updated on 6-Jun-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Dcaf1provided by RGD
    Official Full Name
    DDB1 and CUL4 associated factor 1provided by RGD
    Primary source
    RGD:1305176
    See related
    Ensembl: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 estrogen receptor binding activity and histone kinase activity (H2A-T120 specific). Predicted to be involved in several processes, including cell competition in a multicellular organism; histone H2A-T120 phosphorylation; and immune system development. Predicted to be located in fibrillar center and nucleoplasm. Predicted to be part of Cul4-RING E3 ubiquitin ligase complex. Predicted to be active in nucleus. Orthologous to human DCAF1 (DDB1 and CUL4 associated factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Testes (RPKM 165.7), Thymus (RPKM 125.5) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    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 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
    		  
    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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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
      ENSRNOP00000018932.7, ENSRNOT00000018932.7
      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
      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
      ENSRNOP00000075456.2
      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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools