Human Gene DCAF1 (ENST00000423656.5_9) from GENCODE V47lift37
  Description: DDB1 and CUL4 associated factor 1, transcript variant 1 (from RefSeq NM_014703.3)
Gencode Transcript: ENST00000423656.5_9
Gencode Gene: ENSG00000145041.17_16
Transcript (Including UTRs)
   Position: hg19 chr3:51,433,298-51,534,010 Size: 100,713 Total Exon Count: 24 Strand: -
Coding Region
   Position: hg19 chr3:51,436,200-51,517,844 Size: 81,645 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:51,433,298-51,534,010)mRNA (may differ from genome)Protein (1454 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VPRBP_HUMAN
DESCRIPTION: RecName: Full=Protein VPRBP; AltName: Full=DDB1- and CUL4-associated factor 1; AltName: Full=HIV-1 Vpr-binding protein; Short=VprBP; AltName: Full=Vpr-interacting protein;
FUNCTION: Component of the CUL4A-RBX1-DDB1-VprBP/DCAF1 E3 ubiquitin-protein ligase complex, VprBP/DCAF1 may function as the substrate recognition module within this complex. For example, VprBP/DCAF1 targets NF2 to the E3 ubiquitin-ligase complex for ubiquitination and subsequent proteasome-dependent degradation. In case of infection by HIV-1 virus, it is recruited by HIV-1 Vpr in order to hijack the CUL4A-RBX1-DDB1 function leading to arrest the cell cycle in G2 phase, and also to protect the viral protein from proteasomal degradation by another E3 ubiquitin ligase. In case of infection by HIV-2 virus, it is recruited by HIV-2 Vpx in order to hijack the CUL4A-RBX1-DDB1 function leading to enhanced efficiency of macrophage infection and promotion of the replication of cognate primate lentiviruses in cells of monocyte/macrophage lineage. Associated with chromatin in a DDB1-independent and cell cycle-dependent manner, VprBP/DCAF1 is recruited to chromatin as DNA is being replicated and is released from chromatin before mitosis.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Component of the CUL4A-RBX1-DDB1-VprBP/DCAF1 E3 ubiquitin-protein ligase complex that could interact with HIV-1 virus Vpr protein and HIV-2 virus Vpx protein. Interacts directly with DDB1. Also forms a ternary complex with DDA1 and DDB1. Interacts with NF2 (via FERM domain). Component of EDD/UBR5-DDB1- VprBP/DCAF1 E3 ubiquitin-protein ligase complex. Associates with the E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and VPRBP proteins (EDVP complex). Interacts directly with DYRK2.
INTERACTION: P12520:vpr (xeno); NbExp=5; IntAct=EBI-1996353, EBI-6164519;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Ubiquitously expressed.
DOMAIN: The DWD boxes are required for interaction with DDB1.
SIMILARITY: Belongs to the VPRBP/DCAF1 family.
SIMILARITY: Contains 1 LisH domain.
SIMILARITY: Contains 5 WD repeats.
SEQUENCE CAUTION: Sequence=BAA34520.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DCAF1
Diseases sorted by gene-association score: hiv-1 (6), aicardi-goutieres syndrome (1)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 63.67 RPKM in Testis
Total median expression: 370.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -47.80130-0.368 Picture PostScript Text
3' UTR -429.801292-0.333 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR006594 - LisH_dimerisation
IPR015943 - WD40/YVTN_repeat-like_dom
IPR017986 - WD40_repeat_dom

SCOP Domains:
48371 - ARM repeat
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q9Y4B6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0030331 estrogen receptor binding
GO:1990244 histone kinase activity (H2A-T120 specific)

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016032 viral process
GO:0016310 phosphorylation
GO:0016567 protein ubiquitination
GO:0030183 B cell differentiation
GO:0033151 V(D)J recombination
GO:0035212 cell competition in a multicellular organism
GO:1990245 histone H2A-T120 phosphorylation

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0080008 Cul4-RING E3 ubiquitin ligase complex
GO:0008180 COP9 signalosome


-  Descriptions from all associated GenBank mRNAs
  AB018343 - Homo sapiens KIAA0800 mRNA for KIAA0800 protein.
BC110371 - Homo sapiens Vpr (HIV-1) binding protein, mRNA (cDNA clone MGC:102804 IMAGE:5547856), complete cds.
BC022792 - Homo sapiens Vpr (HIV-1) binding protein, mRNA (cDNA clone MGC:23092 IMAGE:4853730), complete cds.
AB384527 - Synthetic construct DNA, clone: pF1KA0800, Homo sapiens VPRBP gene for vpr (HIV-1) binding protein, complete cds, without stop codon, in Flexi system.
CU692716 - Synthetic construct Homo sapiens gateway clone IMAGE:100021998 5' read VPRBP mRNA.
AL080145 - Homo sapiens mRNA; cDNA DKFZp434P113 (from clone DKFZp434P113).
JD106595 - Sequence 87619 from Patent EP1572962.
JD136655 - Sequence 117679 from Patent EP1572962.
JD219649 - Sequence 200673 from Patent EP1572962.
JD409156 - Sequence 390180 from Patent EP1572962.
JD290349 - Sequence 271373 from Patent EP1572962.
JD038815 - Sequence 19839 from Patent EP1572962.
JD146352 - Sequence 127376 from Patent EP1572962.
JD400001 - Sequence 381025 from Patent EP1572962.
JD044979 - Sequence 26003 from Patent EP1572962.
JD135338 - Sequence 116362 from Patent EP1572962.
JD363874 - Sequence 344898 from Patent EP1572962.
JD473426 - Sequence 454450 from Patent EP1572962.
JD375904 - Sequence 356928 from Patent EP1572962.
JD061713 - Sequence 42737 from Patent EP1572962.
JD370859 - Sequence 351883 from Patent EP1572962.
JD434136 - Sequence 415160 from Patent EP1572962.
JD430709 - Sequence 411733 from Patent EP1572962.
JD082532 - Sequence 63556 from Patent EP1572962.
JD064035 - Sequence 45059 from Patent EP1572962.
JD259758 - Sequence 240782 from Patent EP1572962.
JD344486 - Sequence 325510 from Patent EP1572962.
JD368717 - Sequence 349741 from Patent EP1572962.
JD059141 - Sequence 40165 from Patent EP1572962.
JD434246 - Sequence 415270 from Patent EP1572962.
AK023239 - Homo sapiens cDNA FLJ13177 fis, clone NT2RP3003870, highly similar to Homo sapiens Vpr-binding protein (VprBP), mRNA.
JD455914 - Sequence 436938 from Patent EP1572962.
AF061935 - Homo sapiens HIV-1 Vpr-binding protein (VprBP) mRNA, partial cds.
DQ573450 - Homo sapiens piRNA piR-41562, complete sequence.
JD181087 - Sequence 162111 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y4B6 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: DCAF1 , DCAF1_HUMAN, ENST00000423656.1, ENST00000423656.2, ENST00000423656.3, ENST00000423656.4, KIAA0800, NM_014703, Q2YD74, Q8TBD9, Q9HCA1, Q9UG37, Q9Y4B6, RIP, uc319syl.1, uc319syl.2, VPRBP
UCSC ID: ENST00000423656.5_9
RefSeq Accession: NM_014703.3
Protein: Q9Y4B6 (aka VPRBP_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.