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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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    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.

    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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