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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
    mouse all
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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 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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    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)

    Genotypes

    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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    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.

    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

    Gene LinkOut

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