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WDTC1 WD and tetratricopeptide repeats 1 [ Homo sapiens (human) ]

Gene ID: 23038, updated on 3-Nov-2024

Summary

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Official Symbol
WDTC1provided by HGNC
Official Full Name
WD and tetratricopeptide repeats 1provided by HGNC
Primary source
HGNC:HGNC:29175
See related
Ensembl:ENSG00000142784 MIM:619763; AllianceGenome:HGNC:29175
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
ADP; DCAF9
Summary
Predicted to enable enzyme inhibitor activity; histone binding activity; and histone deacetylase binding activity. Predicted to be involved in negative regulation of fatty acid biosynthetic process. Predicted to act upstream of or within several processes, including cellular response to insulin stimulus; glucose metabolic process; and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of Cul4-RING E3 ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 28.2), heart (RPKM 14.1) and 25 other tissues See more
Orthologs
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Genomic context

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See WDTC1 in Genome Data Viewer
Location:
1p36.11
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27234441..27308636)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27075661..27149870)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27560952..27635127)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SNRPE pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 506 Neighboring gene WDTC1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27613415-27614057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27615731-27616716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27625813-27626326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 541 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27627354-27627866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27627867-27628380 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27633747-27634272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27634273-27634798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27634799-27635323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27648068-27648614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27648615-27649162 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27649163-27649709 Neighboring gene actin gamma 1 pseudogene 20 Neighboring gene transmembrane protein 222 Neighboring gene RNA, U6 small nuclear 48, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27669148-27669765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27673548-27674088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27674089-27674627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 509 Neighboring gene synaptotagmin like 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. Adipose tissue expression of adipose (WDTC1) gene is associated with lower fat mass and enhanced insulin sensitivity in humans. Galgani JE, et al. Obesity (Silver Spring), 2013 Nov. PMID 23512946, Free PMC Article
  2. WDTC1, the ortholog of Drosophila adipose gene, associates with human obesity, modulated by MUFA intake. Lai CQ, et al. Obesity (Silver Spring), 2009 Mar. PMID 19238144, Free PMC Article
  3. The putative oncogenic role of WDTC1 in colorectal cancer. Wang X, et al. Carcinogenesis, 2022 Jun 27. PMID 35238908, Free PMC Article
  4. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Song N, et al. Mol Carcinog, 2023 Oct. PMID 37314216
  5. Control of triglyceride storage by a WD40/TPR-domain protein. Häder T, et al. EMBO Rep, 2003 May. PMID 12717455, Free PMC Article

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The putative oncogenic role of WDTC1 in colorectal cancer.
    Title: The putative oncogenic role of WDTC1 in colorectal cancer.
  2. Our results identify a biochemical role for WDTC1 and extend the functional range of the CRL4 complex to the suppression of fat accumulation.
    Title: The antiobesity factor WDTC1 suppresses adipogenesis via the CRL4WDTC1 E3 ligase.
  3. High adp expression in human adipose tissue is associated with lower adiposity and enhanced glucose utilization.
    Title: Adipose tissue expression of adipose (WDTC1) gene is associated with lower fat mass and enhanced insulin sensitivity in humans.
  4. WDTC1 variation may be an important risk factor contributing to obesity in both Puerto Rican and white populations.
    Title: WDTC1, the ortholog of Drosophila adipose gene, associates with human obesity, modulated by MUFA intake.
  5. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: WDTC1, the ortholog of Drosophila adipose gene, associates with human obesity, modulated by MUFA intake.
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)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of WD and tetratricopeptide repeats 1 (WDTC1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells 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

  • KIAA1037

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables enzyme inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
enables histone binding IEA
Inferred from Electronic Annotation
more info
  
enables histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to insulin stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in glucose metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular chemical homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of fatty acid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell size 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
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
WD and tetratricopeptide repeats protein 1
Names
DDB1 and CUL4 associated factor 9
adipose homolog

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_001276252.2 → NP_001263181.1  WD and tetratricopeptide repeats protein 1 isoform a

    See identical proteins and their annotated locations for NP_001263181.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK315564, BC032523, DB072151, FO393419, HY218382
    Consensus CDS
    CCDS60044.1
    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4
    Related
    ENSP00000317971.3, ENST00000319394.8
    Conserved Domains (4) summary
    PLN03088
    Location:368 → 438
    PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional
    sd00006
    Location:366 → 390
    TPR; TPR repeat [structural motif]
    sd00039
    Location:51 → 88
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:34 → 163
    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_001410767.1 → NP_001397696.1  WD and tetratricopeptide repeats protein 1 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL590640, FO393419
    Consensus CDS
    CCDS90895.1
    Related
    ENSP00000434578.1, ENST00000447062.2

  3. NM_015023.5 → NP_055838.2  WD and tetratricopeptide repeats protein 1 isoform b

    See identical proteins and their annotated locations for NP_055838.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (b) that is 1 aa shorter than isoform a.
    Source sequence(s)
    BC032523, DB072151, FO393419, HY218382
    Consensus CDS
    CCDS296.1
    UniProtKB/Swiss-Prot
    Q8N5D0
    Related
    ENSP00000355317.3, ENST00000361771.7
    Conserved Domains (4) summary
    PLN03088
    Location:367 → 437
    PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional
    sd00006
    Location:365 → 389
    TPR; TPR repeat [structural motif]
    sd00039
    Location:51 → 88
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:34 → 163
    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 ...

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    27234441..27308636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449749.1 → XP_047305705.1  WD and tetratricopeptide repeats protein 1 isoform X1

    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4

  2. XM_047449760.1 → XP_047305716.1  WD and tetratricopeptide repeats protein 1 isoform X2

  3. XM_047449761.1 → XP_047305717.1  WD and tetratricopeptide repeats protein 1 isoform X3

  4. XM_011541058.4 → XP_011539360.1  WD and tetratricopeptide repeats protein 1 isoform X5

    Conserved Domains (7) summary
    COG2319
    Location:41 → 329
    WD40; WD40 repeat [General function prediction only]
    sd00006
    Location:366 → 390
    TPR; TPR repeat [structural motif]
    pfam00515
    Location:396 → 430
    TPR_1; Tetratricopeptide repeat
    pfam13414
    Location:366 → 430
    TPR_11; TPR repeat
    pfam13432
    Location:402 → 467
    TPR_16; Tetratricopeptide repeat
    sd00039
    Location:51 → 88
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:34 → 163
    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. XM_011541057.2 → XP_011539359.1  WD and tetratricopeptide repeats protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011539359.1

    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4
    Conserved Domains (4) summary
    PLN03088
    Location:368 → 438
    PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional
    sd00006
    Location:366 → 390
    TPR; TPR repeat [structural motif]
    sd00039
    Location:51 → 88
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:34 → 163
    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. XM_047449750.1 → XP_047305706.1  WD and tetratricopeptide repeats protein 1 isoform X1

    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4

  7. XM_047449768.1 → XP_047305724.1  WD and tetratricopeptide repeats protein 1 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    27075661..27149870
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335262.1 → XP_054191237.1  WD and tetratricopeptide repeats protein 1 isoform X1

    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4

  2. XM_054335265.1 → XP_054191240.1  WD and tetratricopeptide repeats protein 1 isoform X2

  3. XM_054335266.1 → XP_054191241.1  WD and tetratricopeptide repeats protein 1 isoform X3

  4. XM_054335268.1 → XP_054191243.1  WD and tetratricopeptide repeats protein 1 isoform X5

  5. XM_054335264.1 → XP_054191239.1  WD and tetratricopeptide repeats protein 1 isoform X1

    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4

  6. XM_054335263.1 → XP_054191238.1  WD and tetratricopeptide repeats protein 1 isoform X1

    UniProtKB/Swiss-Prot
    D3DPL5, Q5SSC5, Q8N5D0, Q9NV87, Q9UPW4

  7. XM_054335267.1 → XP_054191242.1  WD and tetratricopeptide repeats protein 1 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N5D0.2 GenPept UniProtKB/Swiss-Prot:Q8N5D0

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