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DCAF4 DDB1 and CUL4 associated factor 4 [ Homo sapiens (human) ]

Gene ID: 26094, updated on 2-Nov-2024

Summary

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Official Symbol
DCAF4provided by HGNC
Official Full Name
DDB1 and CUL4 associated factor 4provided by HGNC
Primary source
HGNC:HGNC:20229
See related
Ensembl:ENSG00000119599 MIM:616372; AllianceGenome:HGNC:20229
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
WDR21; WDR21A
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 4.7), testis (RPKM 3.5) and 25 other tissues See more
Orthologs
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Genomic context

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See DCAF4 in Genome Data Viewer
Location:
14q24.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (72926464..72962098)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (67132127..67167702)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (73393172..73428806)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984711 Neighboring gene uncharacterized LOC124903429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73391284-73392150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:73393882-73394746 Neighboring gene ribosomal protein L36 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73406131-73406632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73406633-73407132 Neighboring gene sperm microtubule associated protein 1 pseudogene Neighboring gene tRNA-Cys (anticodon GCA) 8-1 Neighboring gene ribosomal protein S12 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Association between WDR21A polymorphisms and airway responsiveness to inhaled corticosteroids in asthmatic patients. Cho SH, et al. Pharmacogenet Genomics, 2012 May. PMID 22366774
  2. DCAF4, a novel gene associated with leucocyte telomere length. Mangino M, et al. J Med Genet, 2015 Mar. PMID 25624462, Free PMC Article
  3. Functional variants in DCAF4 associated with lung cancer risk in European populations. Liu H, et al. Carcinogenesis, 2017 May 1. PMID 28383684, Free PMC Article
  4. Genome-wide siRNA screening reveals that DCAF4-mediated ubiquitination of optineurin stimulates autophagic degradation of Cu,Zn-superoxide dismutase. Homma K, et al. J Biol Chem, 2020 Mar 6. PMID 32014991, Free PMC Article
  5. Small molecule NSC1892 targets the CUL4A/4B-DDB1 interactions and causes impairment of CRL4(DCAF4) E3 ligases to inhibit colorectal cancer cell growth. Yang C, et al. Int J Biol Sci, 2020. PMID 32140073, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. our results suggest that rs12587742 is associated with an increased lung cancer risk, possibly by up-regulating mRNA expression and decreasing methylation status of DCAF4.
    Title: Functional variants in DCAF4 associated with lung cancer risk in European populations.
  2. Genome-wide association (GWA) meta-analysis and de novo genotyping of 20 022 individuals revealed a novel association (p=6.4x10(-10)) between LTL and rs2535913, which lies within DCAF4
    Title: DCAF4, a novel gene associated with leucocyte telomere length.
  3. The minor allele of WDR21A may induce a good response to inhaled corticosteroids possibly through competition with the Gbeta(1) proteins for binding to GRs
    Title: Association between WDR21A polymorphisms and airway responsiveness to inhaled corticosteroids in asthmatic patients.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC20547, MGC46524, DKFZp434K114

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
DDB1- and CUL4-associated factor 4
Names
WD repeat domain 21A
WD repeat-containing protein 21A

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.

Genomic

  1. NG_047140.1 RefSeqGene

    Range
    5133..38372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001163508.2 → NP_001156980.1  DDB1- and CUL4-associated factor 4 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses two alternate in-frame splice sites in the coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
    Source sequence(s)
    AK027745, AK315499, AL442663, BC018979, DC314513
    Consensus CDS
    CCDS55926.1
    UniProtKB/TrEMBL
    B2RDD6
    Related
    ENSP00000452131.1, ENST00000555042.5
    Conserved Domains (3) summary
    COG2319
    Location:310 → 475
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:286 → 316
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:363 → 463
    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. NM_001163509.2 → NP_001156981.1  DDB1- and CUL4-associated factor 4 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses two alternate splice sites in the coding region and uses an alternate translational start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK027745, AK297742, AL442663, BC018979, DC314513
    UniProtKB/TrEMBL
    B4DN30
    Conserved Domains (3) summary
    COG2319
    Location:265 → 460
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 301
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:265 → 448
    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. NM_001352447.2 → NP_001339376.1  DDB1- and CUL4-associated factor 4 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC007160, AL442663
    UniProtKB/TrEMBL
    B4DMQ0
    Conserved Domains (2) summary
    sd00039
    Location:71 → 108
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:124 → 255
    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 ...

  4. NM_001352448.3 → NP_001339377.1  DDB1- and CUL4-associated factor 4 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC007160, AL442663
    UniProtKB/TrEMBL
    B2RDD6
    Conserved Domains (2) summary
    sd00039
    Location:285 → 322
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:315 → 434
    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. NM_001352449.2 → NP_001339378.1  DDB1- and CUL4-associated factor 4 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) encodes the longest isoform (8).
    Source sequence(s)
    AC007160, AL442663
    UniProtKB/TrEMBL
    B2RDD6
    Conserved Domains (2) summary
    sd00039
    Location:286 → 323
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:287 → 470
    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. NM_015604.4 → NP_056419.2  DDB1- and CUL4-associated factor 4 isoform 1

    See identical proteins and their annotated locations for NP_056419.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AK027745, AK315499, AL442663, BC018979, DC314513
    Consensus CDS
    CCDS9809.1
    UniProtKB/Swiss-Prot
    B4DUT6, G3V522, Q86U31, Q8IV10, Q8WV16, Q96K22, Q9Y4P5
    UniProtKB/TrEMBL
    B2RDD6
    Related
    ENSP00000351147.2, ENST00000358377.7
    Conserved Domains (3) summary
    COG2319
    Location:301 → 481
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:285 → 322
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:286 → 469
    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. NM_181340.3 → NP_851937.1  DDB1- and CUL4-associated factor 4 isoform 2

    See identical proteins and their annotated locations for NP_851937.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream translational start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK027745, AL442663, BC018979, BC035901, DC314513
    Consensus CDS
    CCDS9810.1
    UniProtKB/TrEMBL
    G3V3D6
    Related
    ENSP00000377781.2, ENST00000394234.6
    Conserved Domains (2) summary
    sd00039
    Location:185 → 222
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:186 → 369
    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 ...

  8. NM_181341.3 → NP_851938.2  DDB1- and CUL4-associated factor 4 isoform 3

    See identical proteins and their annotated locations for NP_851938.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks two alternate exons in the coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AK027745, AK300786, AL442663, BC018979, DC314513
    Consensus CDS
    CCDS41968.2
    UniProtKB/TrEMBL
    B2RDD6
    Related
    ENSP00000426178.1, ENST00000509153.5
    Conserved Domains (3) summary
    COG2319
    Location:241 → 421
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:225 → 262
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:278 → 409
    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. NR_147990.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC007160, AL442663

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    72926464..72962098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021205.2 → XP_016876694.1  DDB1- and CUL4-associated factor 4 isoform X5

    UniProtKB/TrEMBL
    B2RDD6
    Conserved Domains (2) summary
    sd00039
    Location:286 → 323
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:287 → 470
    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_017021206.2 → XP_016876695.1  DDB1- and CUL4-associated factor 4 isoform X5

    UniProtKB/TrEMBL
    B2RDD6
    Conserved Domains (2) summary
    sd00039
    Location:286 → 323
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:287 → 470
    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_017021213.3 → XP_016876702.1  DDB1- and CUL4-associated factor 4 isoform X6

    UniProtKB/TrEMBL
    B4DN30
    Conserved Domains (3) summary
    COG2319
    Location:265 → 460
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 301
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:265 → 448
    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 ...

  4. XM_047431256.1 → XP_047287212.1  DDB1- and CUL4-associated factor 4 isoform X3

  5. XM_047431257.1 → XP_047287213.1  DDB1- and CUL4-associated factor 4 isoform X4

  6. XM_047431254.1 → XP_047287210.1  DDB1- and CUL4-associated factor 4 isoform X1

  7. XM_047431255.1 → XP_047287211.1  DDB1- and CUL4-associated factor 4 isoform X2

  8. XM_047431259.1 → XP_047287215.1  DDB1- and CUL4-associated factor 4 isoform X6

  9. XM_047431258.1 → XP_047287214.1  DDB1- and CUL4-associated factor 4 isoform X6

  10. XM_047431260.1 → XP_047287216.1  DDB1- and CUL4-associated factor 4 isoform X7

RNA

  1. XR_007064003.1 RNA Sequence

  2. XR_007064002.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    67132127..67167702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375843.1 → XP_054231818.1  DDB1- and CUL4-associated factor 4 isoform X6

  2. XM_054375841.1 → XP_054231816.1  DDB1- and CUL4-associated factor 4 isoform X5

  3. XM_054375839.1 → XP_054231814.1  DDB1- and CUL4-associated factor 4 isoform X10

  4. XM_054375840.1 → XP_054231815.1  DDB1- and CUL4-associated factor 4 isoform X11

  5. XM_054375837.1 → XP_054231812.1  DDB1- and CUL4-associated factor 4 isoform X8

  6. XM_054375838.1 → XP_054231813.1  DDB1- and CUL4-associated factor 4 isoform X9

  7. XM_054375844.1 → XP_054231819.1  DDB1- and CUL4-associated factor 4 isoform X6

  8. XM_054375842.1 → XP_054231817.1  DDB1- and CUL4-associated factor 4 isoform X6

  9. XM_054375845.1 → XP_054231820.1  DDB1- and CUL4-associated factor 4 isoform X7

RNA

  1. XR_008488853.1 RNA Sequence

  2. XR_008488852.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WV16.3 GenPept UniProtKB/Swiss-Prot:Q8WV16

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