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CCDC3 coiled-coil domain containing 3 [ Homo sapiens (human) ]

Gene ID: 83643, updated on 2-Nov-2024

Summary

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Official Symbol
CCDC3provided by HGNC
Official Full Name
coiled-coil domain containing 3provided by HGNC
Primary source
HGNC:HGNC:23813
See related
Ensembl:ENSG00000151468 MIM:620579; AllianceGenome:HGNC:23813
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
Summary
Involved in negative regulation of lipid metabolic process; negative regulation of tumor necrosis factor-mediated signaling pathway; and signal transduction. Located in endoplasmic reticulum and extracellular region. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in skin (RPKM 47.2), fat (RPKM 42.7) and 21 other tissues See more
Orthologs
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Genomic context

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See CCDC3 in Genome Data Viewer
Location:
10p13
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (12896625..13099989, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (12911015..13114320, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (12938625..13141989, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene calcium/calmodulin dependent protein kinase ID Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3048 Neighboring gene Sharpr-MPRA regulatory region 13393 Neighboring gene microRNA 4481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2148 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:12781907-12782408 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:12782409-12782908 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:12808306-12808806 Neighboring gene microRNA 548q Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:12830027-12830528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:12830529-12831028 Neighboring gene NANOG hESC enhancer GRCh37_chr10:12838401-12838902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:12845476-12845976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:12845977-12846477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:12849244-12849744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:12860895-12861500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:12861501-12862105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:12862106-12862710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:12891157-12891656 Neighboring gene uncharacterized LOC105376418 Neighboring gene 10p13 CCDC3 distal Alu-mediated recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:12958041-12958581 Neighboring gene RNA, 5S ribosomal pseudogene 300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13042842-13043342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13043343-13043843 Neighboring gene 10p13 CCDC3 medial Alu-mediated recombination region Neighboring gene NANOG hESC enhancer GRCh37_chr10:13091983-13092484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13108727-13109240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13108212-13108726 Neighboring gene 10p13 CCDC3 proximal Alu-mediated recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3049 Neighboring gene 10p13 OPTN distal Alu-mediated recombination region Neighboring gene 10p13 OPTN proximal Alu-mediated recombination region Neighboring gene ribosomal protein L5 pseudogene 25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3050 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 5 Neighboring gene optineurin Neighboring gene BTB domain containing 7 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. CCDC3 Gene Regulates the Proliferation of Breast Cancer Cells. Mao J, et al. Bull Exp Biol Med, 2023 Mar. PMID 37052857
  2. Extracellular and intracellular functions of coiled-coil domain containing 3. Omari S, et al. J Mol Cell Biol, 2023 Nov 27. PMID 37263799, Free PMC Article
  3. Identification of a new secretory factor, CCDC3/Favine, in adipocytes and endothelial cells. Kobayashi S, et al. Biochem Biophys Res Commun, 2010 Jan 29. PMID 20043878
  4. Coiled-coil domain containing 3 suppresses breast cancer growth by protecting p53 from proteasome-mediated degradation. Li C, et al. Oncogene, 2023 Jan. PMID 36396725
  5. Coiled-coil domain containing 3 (CCDC3) represses tumor necrosis factor-α/nuclear factor κB-induced endothelial inflammation. Azad AK, et al. Cell Signal, 2014 Dec. PMID 25193116

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Extracellular and intracellular functions of coiled-coil domain containing 3.
    Title: Extracellular and intracellular functions of coiled-coil domain containing 3.
  2. CCDC3 Gene Regulates the Proliferation of Breast Cancer Cells.
    Title: CCDC3 Gene Regulates the Proliferation of Breast Cancer Cells.
  3. Coiled-coil domain containing 3 suppresses breast cancer growth by protecting p53 from proteasome-mediated degradation.
    Title: Coiled-coil domain containing 3 suppresses breast cancer growth by protecting p53 from proteasome-mediated degradation.
  4. CCDC3 represses TNF-alpha/NF-kappaB-induced pro-inflammatory response in endothelial cells.
    Title: Coiled-coil domain containing 3 (CCDC3) represses tumor necrosis factor-α/nuclear factor κB-induced endothelial inflammation.
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
Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
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)

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

  • FLJ20925, DKFZp761F241

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in lipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of lipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of lipid metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of fat cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of lipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
is_active_in extracellular region IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
coiled-coil domain-containing protein 3
Names
fat/vessel-derived secretory protein
favine

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_001282658.2 → NP_001269587.1  coiled-coil domain-containing protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001269587.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL353586, AL355355
    Consensus CDS
    CCDS60484.1
    UniProtKB/Swiss-Prot
    Q9BQI4
    Related
    ENSP00000368116.1, ENST00000378839.1
    Conserved Domains (1) summary
    cl23748
    Location:53 → 94
    DUF3585; Protein of unknown function (DUF3585)

  2. NM_031455.4 → NP_113643.1  coiled-coil domain-containing protein 3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_113643.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL353586, AL355355
    Consensus CDS
    CCDS7093.1
    UniProtKB/Swiss-Prot
    Q5VYV8, Q5VYV9, Q9BQI4
    Related
    ENSP00000368102.3, ENST00000378825.5
    Conserved Domains (1) summary
    cl23748
    Location:178 → 219
    DUF3585; Protein of unknown function (DUF3585)

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    12896625..13099989 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    12911015..13114320 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQI4.1 GenPept UniProtKB/Swiss-Prot:Q9BQI4

Gene LinkOut

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

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Chemical Information
Molecular Biology Databases
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