Human Gene DCAF4 (uc010ttr.2)
  Description: Homo sapiens DDB1 and CUL4 associated factor 4 (DCAF4), transcript variant 5, mRNA.
RefSeq Summary (NM_001163509): This gene encodes a WD repeat-containing protein that interacts with the Cul4-Ddb1 E3 ligase macromolecular complex. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2009].
Transcript (Including UTRs)
   Position: hg19 chr14:73,393,040-73,426,357 Size: 33,318 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr14:73,404,721-73,425,513 Size: 20,793 Coding Exon Count: 13 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:73,393,040-73,426,357)mRNA (may differ from genome)Protein (474 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 5.93 RPKM in Thyroid
Total median expression: 144.99 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 -76.70254-0.302 Picture PostScript Text
3' UTR -257.20844-0.305 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
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
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
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on B4DN30
FrontTopSide
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK315499 - Homo sapiens cDNA, FLJ96563, highly similar to Homo sapiens WD repeat domain 21 (WDR21), mRNA.
LF384867 - JP 2014500723-A/192370: Polycomb-Associated Non-Coding RNAs.
BX161489 - human full-length cDNA clone CS0DJ006YD20 of T cells (Jurkat cell line) of Homo sapiens (human).
AK297571 - Homo sapiens cDNA FLJ53137 complete cds, highly similar to WD repeat protein 21A.
BC035901 - Homo sapiens WD repeat domain 21A, mRNA (cDNA clone MGC:46524 IMAGE:5241663), complete cds.
AK300786 - Homo sapiens cDNA FLJ52764 complete cds, highly similar to WD repeat protein 21A.
AK027745 - Homo sapiens cDNA FLJ14839 fis, clone OVARC1001791.
AK297742 - Homo sapiens cDNA FLJ52699 complete cds, highly similar to WD repeat protein 21A.
BX247962 - human full-length cDNA clone CS0DA010YD24 of Neuroblastoma of Homo sapiens (human).
BC018979 - Homo sapiens WD repeat domain 21A, mRNA (cDNA clone MGC:20547 IMAGE:3604168), complete cds.
MA620444 - JP 2018138019-A/192370: Polycomb-Associated Non-Coding RNAs.
JD479407 - Sequence 460431 from Patent EP1572962.
JD199145 - Sequence 180169 from Patent EP1572962.
JD421142 - Sequence 402166 from Patent EP1572962.
CU676348 - Synthetic construct Homo sapiens gateway clone IMAGE:100019671 5' read WDR21A mRNA.
HQ448372 - Synthetic construct Homo sapiens clone IMAGE:100071796; CCSB006992_01 WD repeat domain 21A (WDR21A) gene, encodes complete protein.
KJ898594 - Synthetic construct Homo sapiens clone ccsbBroadEn_07988 DCAF4 gene, encodes complete protein.
AL080157 - Homo sapiens mRNA; cDNA DKFZp434K114 (from clone DKFZp434K114).
JD191934 - Sequence 172958 from Patent EP1572962.
LF329914 - JP 2014500723-A/137417: Polycomb-Associated Non-Coding RNAs.
LF329915 - JP 2014500723-A/137418: Polycomb-Associated Non-Coding RNAs.
JD102743 - Sequence 83767 from Patent EP1572962.
HQ257934 - Synthetic construct Homo sapiens clone IMAGE:100072243 DDB1 and CUL4 associated factor 4 (DCAF4), transcript variant 2 (DCAF4) gene, encodes complete protein.
KJ898595 - Synthetic construct Homo sapiens clone ccsbBroadEn_07989 DCAF4 gene, encodes complete protein.
LF329918 - JP 2014500723-A/137421: Polycomb-Associated Non-Coding RNAs.
LF329919 - JP 2014500723-A/137422: Polycomb-Associated Non-Coding RNAs.
LF329920 - JP 2014500723-A/137423: Polycomb-Associated Non-Coding RNAs.
LF329921 - JP 2014500723-A/137424: Polycomb-Associated Non-Coding RNAs.
LF329922 - JP 2014500723-A/137425: Polycomb-Associated Non-Coding RNAs.
JD147907 - Sequence 128931 from Patent EP1572962.
JD552516 - Sequence 533540 from Patent EP1572962.
JD302306 - Sequence 283330 from Patent EP1572962.
JD301830 - Sequence 282854 from Patent EP1572962.
JD201203 - Sequence 182227 from Patent EP1572962.
JD163945 - Sequence 144969 from Patent EP1572962.
JD333413 - Sequence 314437 from Patent EP1572962.
JD187805 - Sequence 168829 from Patent EP1572962.
JD068231 - Sequence 49255 from Patent EP1572962.
JD417187 - Sequence 398211 from Patent EP1572962.
MA565491 - JP 2018138019-A/137417: Polycomb-Associated Non-Coding RNAs.
MA565492 - JP 2018138019-A/137418: Polycomb-Associated Non-Coding RNAs.
MA565495 - JP 2018138019-A/137421: Polycomb-Associated Non-Coding RNAs.
MA565496 - JP 2018138019-A/137422: Polycomb-Associated Non-Coding RNAs.
MA565497 - JP 2018138019-A/137423: Polycomb-Associated Non-Coding RNAs.
MA565498 - JP 2018138019-A/137424: Polycomb-Associated Non-Coding RNAs.
MA565499 - JP 2018138019-A/137425: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DN30, B4DN30_HUMAN, NM_001163509, NP_001156981
UCSC ID: uc010ttr.2
RefSeq Accession: NM_001163509
Protein: B4DN30 CCDS: CCDS9809.1, CCDS55926.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001163509.1
exon count: 14CDS single in 3' UTR: no RNA size: 2539
ORF size: 1425CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2992.00frame shift in genome: no % Coverage: 99.37
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.