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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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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