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    COL17A1 collagen type XVII alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1308, updated on 5-May-2024

    Summary

    Official Symbol
    COL17A1provided by HGNC
    Official Full Name
    collagen type XVII alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2194
    See related
    Ensembl:ENSG00000065618 MIM:113811; AllianceGenome:HGNC:2194
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ERED; JEB4; BP180; BPA-2; BPAG2; LAD-1; BA16H23.2
    Summary
    This gene encodes the alpha chain of type XVII collagen. Unlike most collagens, collagen XVII is a transmembrane protein. Collagen XVII is a structural component of hemidesmosomes, multiprotein complexes at the dermal-epidermal basement membrane zone that mediate adhesion of keratinocytes to the underlying membrane. Mutations in this gene are associated with both generalized atrophic benign and junctional epidermolysis bullosa. Two homotrimeric forms of type XVII collagen exist. The full length form is the transmembrane protein. A soluble form, referred to as either ectodomain or LAD-1, is generated by proteolytic processing of the full length form. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in skin (RPKM 286.9), colon (RPKM 25.5) and 2 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See COL17A1 in Genome Data Viewer
    Location:
    10q25.1
    Exon count:
    56
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (104031286..104085880, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (104918673..104973997, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (105791044..105845638, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2794 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105730769-105731270 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105731271-105731770 Neighboring gene RNA, 7SL, cytoplasmic 524, pseudogene Neighboring gene STE20 like kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105812840-105813426 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:105813739-105814938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105826696-105827351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105827352-105828006 Neighboring gene microRNA 936 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:105879992-105881191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105881347-105882010 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:105906549-105907080 Neighboring gene SWI5 dependent homologous recombination repair protein 1 Neighboring gene cilia and flagella associated protein 43 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:105915186-105915853 Neighboring gene tropomyosin 3 pseudogene

    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

    Associated conditions

    Description Tests
    Epidermolysis bullosa, junctional 4, intermediate
    MedGen: C2608084 OMIM: 619787 GeneReviews: Not available
    Compare labs
    Epithelial recurrent erosion dystrophy
    MedGen: C1852551 OMIM: 122400 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ60881, KIAA0204

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell-matrix adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in epidermis development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in hemidesmosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell-cell junction TAS
    Traceable Author Statement
    more info
    PubMed 
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in hemidesmosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in hemidesmosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XVII) chain
    Names
    180 kDa bullous pemphigoid antigen 2
    alpha 1 type XVII collagen
    bA16H23.2 (collagen, type XVII, alpha 1 (BP180))
    bullous pemphigoid antigen 2 (180kD)
    collagen XVII, alpha-1 polypeptide
    collagen, type XVII, alpha 1
    type XVII collagen alpha-1

    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.

    Genomic

    1. NG_007069.1 RefSeqGene

      Range
      5001..59595
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1249

    mRNA and Protein(s)

    1. NM_000494.4NP_000485.3  collagen alpha-1(XVII) chain

      See identical proteins and their annotated locations for NP_000485.3

      Status: REVIEWED

      Source sequence(s)
      AF136185, AI572644, AL138761, DA646288, M91669
      Consensus CDS
      CCDS7554.1
      UniProtKB/Swiss-Prot
      Q02802, Q5JV36, Q99018, Q9NQK9, Q9UC14, Q9UMD9
      UniProtKB/TrEMBL
      D3DRA2
      Related
      ENSP00000497653.1, ENST00000648076.2
      Conserved Domains (1) summary
      pfam01391
      Location:576635
      Collagen; Collagen triple helix repeat (20 copies)

    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
      104031286..104085880 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      104918673..104973997 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_130778.1: Suppressed sequence

      Description
      NM_130778.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.