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DCAF16 DDB1 and CUL4 associated factor 16 [ Homo sapiens (human) ]

Gene ID: 54876, updated on 27-Nov-2024

Summary

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Official Symbol
DCAF16provided by HGNC
Official Full Name
DDB1 and CUL4 associated factor 16provided by HGNC
Primary source
HGNC:HGNC:25987
See related
Ensembl:ENSG00000163257 MIM:620524; AllianceGenome:HGNC:25987
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C4orf30
Summary
Predicted to be involved in protein ubiquitination. Part of Cul4-RING E3 ubiquitin ligase complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 5.2), endometrium (RPKM 5.1) and 25 other tissues See more
Orthologs
all
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Genomic context

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See DCAF16 in Genome Data Viewer
Location:
4p15.31
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (17793446..17810757, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (17775792..17793109, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (17795069..17812380, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene MED28 divergent transcript Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:17615609-17616808 Neighboring gene leucine aminopeptidase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15312 Neighboring gene mediator complex subunit 28 Neighboring gene family with sequence similarity 184 member B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17812049-17812560 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17812561-17813073 Neighboring gene non-SMC condensin I complex subunit G Neighboring gene ligand dependent nuclear receptor corepressor like Neighboring gene keratin 18 pseudogene 63

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. Selective degradation of PARP2 by PROTACs via recruiting DCAF16 for triple-negative breast cancer. Pu C, et al. Eur J Med Chem, 2022 Jun 5. PMID 35430559
  2. Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16. Zhang X, et al. Nat Chem Biol, 2019 Jul. PMID 31209349, Free PMC Article
  3. SPIN4 Is a Principal Endogenous Substrate of the E3 Ubiquitin Ligase DCAF16. Zhang X, et al. Biochemistry, 2021 Mar 9. PMID 33636084, Free PMC Article
  4. PIKES Analysis Reveals Response to Degraders and Key Regulatory Mechanisms of the CRL4 Network. Reichermeier KM, et al. Mol Cell, 2020 Mar 5. PMID 31973889
  5. An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases. Olma MH, et al. J Cell Sci, 2009 Apr 1. PMID 19295130, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Selective degradation of PARP2 by PROTACs via recruiting DCAF16 for triple-negative breast cancer.
    Title: Selective degradation of PARP2 by PROTACs via recruiting DCAF16 for triple-negative breast cancer.
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

EBI GWAS Catalog

Description
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat is identified to have a physical interaction with DDB1 and CUL4 associated factor 16 (DCAF16) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20280, MGC126765, MGC126767

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 16

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.

mRNA and Protein(s)

  1. NM_001345880.2 → NP_001332809.1  DDB1- and CUL4-associated factor 16

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1-6 all encode the same protein.
    Source sequence(s)
    AC005768
    Consensus CDS
    CCDS3423.1
    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7
    Conserved Domains (1) summary
    pfam15349
    Location:1 → 216
    DCA16; DDB1- and CUL4-associated factor 16

  2. NM_001345881.2 → NP_001332810.1  DDB1- and CUL4-associated factor 16

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) plus variants 1-2 and 4-6 all encode the same protein.
    Source sequence(s)
    AC005768
    Consensus CDS
    CCDS3423.1
    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7
    Conserved Domains (1) summary
    pfam15349
    Location:1 → 216
    DCA16; DDB1- and CUL4-associated factor 16

  3. NM_001345882.2 → NP_001332811.1  DDB1- and CUL4-associated factor 16

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) plus variants 1-3 and 5-6 all encode the same protein.
    Source sequence(s)
    AC005768
    Consensus CDS
    CCDS3423.1
    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7
    Conserved Domains (1) summary
    pfam15349
    Location:1 → 216
    DCA16; DDB1- and CUL4-associated factor 16

  4. NM_001345884.2 → NP_001332813.1  DDB1- and CUL4-associated factor 16

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) plus variants 1-4 and 6 all encode the same protein.
    Source sequence(s)
    AC005768
    Consensus CDS
    CCDS3423.1
    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7
    Conserved Domains (1) summary
    pfam15349
    Location:1 → 216
    DCA16; DDB1- and CUL4-associated factor 16

  5. NM_001345885.2 → NP_001332814.1  DDB1- and CUL4-associated factor 16

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) plus variants 1-5 all encode the same protein.
    Source sequence(s)
    AC005768
    Consensus CDS
    CCDS3423.1
    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7
    Conserved Domains (1) summary
    pfam15349
    Location:1 → 216
    DCA16; DDB1- and CUL4-associated factor 16

  6. NM_017741.4 → NP_060211.3  DDB1- and CUL4-associated factor 16

    See identical proteins and their annotated locations for NP_060211.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) plus variants 1 and 3-6 all encode the same protein.
    Source sequence(s)
    AC005768
    Consensus CDS
    CCDS3423.1
    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7
    Related
    ENSP00000371682.1, ENST00000382247.6
    Conserved Domains (1) summary
    pfam15349
    Location:1 → 216
    DCA16; DDB1- and CUL4-associated factor 16

RNA

  1. NR_144301.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC005768

  2. NR_144303.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC005768

  3. NR_144305.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC005768

  4. NR_144310.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC005768

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    17793446..17810757 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047415860.1 → XP_047271816.1  DDB1- and CUL4-associated factor 16 isoform X1

    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7

  2. XM_047415861.1 → XP_047271817.1  DDB1- and CUL4-associated factor 16 isoform X1

    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7

  3. XM_047415859.1 → XP_047271815.1  DDB1- and CUL4-associated factor 16 isoform X1

    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    17775792..17793109 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350303.1 → XP_054206278.1  DDB1- and CUL4-associated factor 16 isoform X1

    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7

  2. XM_054350301.1 → XP_054206276.1  DDB1- and CUL4-associated factor 16 isoform X1

    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7

  3. XM_054350302.1 → XP_054206277.1  DDB1- and CUL4-associated factor 16 isoform X1

    UniProtKB/Swiss-Prot
    B3KPB7, Q9NXF7

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_144299.1: Suppressed sequence

    Description
    NR_144299.1: This RefSeq was removed because there is insufficient support for the transcript.

  2. NR_144300.1: Suppressed sequence

    Description
    NR_144300.1: This RefSeq was removed because there is insufficient support for the transcript.

  3. NR_144302.1: Suppressed sequence

    Description
    NR_144302.1: This RefSeq was removed because there is insufficient support for the transcript.

  4. NR_144304.1: Suppressed sequence

    Description
    NR_144304.1: This RefSeq was removed because there is insufficient support for the transcript.

  5. NR_144306.1: Suppressed sequence

    Description
    NR_144306.1: This RefSeq was removed because there is insufficient support for the transcript.

  6. NR_144307.1: Suppressed sequence

    Description
    NR_144307.1: This RefSeq was removed because there is insufficient support for the transcript.

  7. NR_144308.1: Suppressed sequence

    Description
    NR_144308.1: This RefSeq was removed because there is insufficient support for the transcript.

  8. NR_144309.1: Suppressed sequence

    Description
    NR_144309.1: This RefSeq was removed because there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXF7.1 GenPept UniProtKB/Swiss-Prot:Q9NXF7

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