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

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

    Summary

    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 gene expression; negative regulation of lipid metabolic process; and negative regulation of tumor necrosis factor-mediated signaling pathway. Located in endoplasmic reticulum and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in skin (RPKM 47.2), fat (RPKM 42.7) and 21 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CCDC3 in Genome Data Viewer
    Location:
    10p13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (12896625..13099989, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (12911015..13114320, complement)
    105.20220307 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20925, DKFZp761F241

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    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_001282658.2NP_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:5394
      DUF3585; Protein of unknown function (DUF3585)
    2. NM_031455.4NP_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:178219
      DUF3585; Protein of unknown function (DUF3585)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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)