U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    CCDC80 coiled-coil domain containing 80 [ Homo sapiens (human) ]

    Gene ID: 151887, updated on 28-Oct-2024

    Summary

    Official Symbol
    CCDC80provided by HGNC
    Official Full Name
    coiled-coil domain containing 80provided by HGNC
    Primary source
    HGNC:HGNC:30649
    See related
    Ensembl:ENSG00000091986 MIM:608298; AllianceGenome:HGNC:30649
    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
    CL2; URB; DRO1; SSG1; okuribin; LINC01279
    Summary
    Predicted to enable fibronectin binding activity and heparin binding activity. Predicted to be involved in extracellular matrix organization and positive regulation of cell-substrate adhesion. Predicted to act upstream of or within response to bacterium. Predicted to be located in extracellular region; interstitial matrix; and membrane. Predicted to be active in basement membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in gall bladder (RPKM 132.5), endometrium (RPKM 126.0) and 17 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CCDC80 in Genome Data Viewer
    Location:
    3q13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (112596797..112641143, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (115317839..115362183, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (112315644..112359990, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 7 subfamily E member 100 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20245 Neighboring gene autophagy related 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112279571-112280380 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:112280381-112281190 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112282811-112283620 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:112283621-112284430 Neighboring gene solute carrier family 35 member A5 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:112383725-112384298 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:112405169-112405758 Neighboring gene MAT2A pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 2042 Neighboring gene microRNA 9900

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ44429, MGC131805, MGC134851

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables fibronectin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables heparin binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of cell-substrate adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in interstitial matrix IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    coiled-coil domain-containing protein 80
    Names
    TCONS_00006930
    down-regulated by oncogenes protein 1
    long intergenic non-protein coding RNA 1279
    nuclear envelope protein okuribin
    steroid sensitive gene 1
    up-regulated in BRS-3 deficient mouse homolog

    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_199511.3NP_955805.1  coiled-coil domain-containing protein 80 precursor

      See identical proteins and their annotated locations for NP_955805.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC048334
      Consensus CDS
      CCDS2968.1
      UniProtKB/Swiss-Prot
      D3DN67, Q5PR20, Q6GPG9, Q76M96, Q8IVT6, Q8NBV1, Q8NHY8
      UniProtKB/TrEMBL
      A3KC71, A8KA16
      Related
      ENSP00000206423.3, ENST00000206423.8
      Conserved Domains (2) summary
      pfam13778
      Location:771900
      DUF4174; Domain of unknown function (DUF4174)
      pfam15961
      Location:28150
      DUF4764; Domain of unknown function (DUF4764)
    2. NM_199512.3NP_955806.1  coiled-coil domain-containing protein 80 precursor

      See identical proteins and their annotated locations for NP_955806.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC048334
      Consensus CDS
      CCDS2968.1
      UniProtKB/Swiss-Prot
      D3DN67, Q5PR20, Q6GPG9, Q76M96, Q8IVT6, Q8NBV1, Q8NHY8
      UniProtKB/TrEMBL
      A3KC71, A8KA16
      Related
      ENSP00000411814.2, ENST00000439685.6
      Conserved Domains (2) summary
      pfam13778
      Location:771900
      DUF4174; Domain of unknown function (DUF4174)
      pfam15961
      Location:28150
      DUF4764; Domain of unknown function (DUF4764)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      112596797..112641143 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447495.1XP_047303451.1  coiled-coil domain-containing protein 80 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      115317839..115362183 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_178274.2: Suppressed sequence

      Description
      NM_178274.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.