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    COL15A1 collagen type XV alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1306, updated on 5-Mar-2024

    Summary

    Official Symbol
    COL15A1provided by HGNC
    Official Full Name
    collagen type XV alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2192
    See related
    Ensembl:ENSG00000204291 MIM:120325; AllianceGenome:HGNC:2192
    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
    Summary
    This gene encodes the alpha chain of type XV collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Type XV collagen has a wide tissue distribution but the strongest expression is localized to basement membrane zones so it may function to adhere basement membranes to underlying connective tissue stroma. The proteolytically produced C-terminal fragment of type XV collagen is restin, a potentially antiangiogenic protein that is closely related to endostatin. Mouse studies have shown that collagen XV deficiency is associated with muscle and microvessel deterioration. [provided by RefSeq, May 2013]
    Expression
    Broad expression in placenta (RPKM 113.8), fat (RPKM 52.0) and 17 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    9q22.33
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98943907..99070787)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (111115608..111242488)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (101706189..101833069)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101668137-101668343 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101670754-101670994 Neighboring gene NME2 pseudogene 3 Neighboring gene adipocyte associated pyruvate carboxylase interacting lncRNA Neighboring gene CRISPRi-validated cis-regulatory element chr9.1708 Neighboring gene Sharpr-MPRA regulatory region 4619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101724037-101724537 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:101725038-101725622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101733335-101733912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101733913-101734490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101760575-101761331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101761332-101762087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101834521-101835021 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101834020-101834520 Neighboring gene CRISPRi-validated cis-regulatory element chr9.1735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20125 Neighboring gene transforming growth factor beta receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28699 Neighboring gene RNA, 5S ribosomal pseudogene 290 Neighboring gene Sharpr-MPRA regulatory region 12902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101932965-101933747 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101941126-101941626 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101941627-101942127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28700 Neighboring gene uncharacterized LOC105376174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28701

    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 association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ38566

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in signal transduction NAS
    Non-traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XV) chain
    Names
    collagen XV, alpha-1 polypeptide
    collagen type XV proteoglycan
    collagen, type XV, alpha 1
    endostatin-XV
    restin

    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_001855.5NP_001846.3  collagen alpha-1(XV) chain precursor

      See identical proteins and their annotated locations for NP_001846.3

      Status: REVIEWED

      Source sequence(s)
      AK095885, AL354923, BX337171, HY016428, L25286
      Consensus CDS
      CCDS35081.1
      UniProtKB/Swiss-Prot
      P39059, Q5T6J4, Q9UDC5, Q9Y4W4
      UniProtKB/TrEMBL
      A0A087X0K0
      Related
      ENSP00000364140.3, ENST00000375001.8
      Conserved Domains (3) summary
      pfam01391
      Location:670716
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:40228
      TSPN; Thrombospondin N-terminal -like domains
      cd00247
      Location:12151381
      Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      98943907..99070787
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      111115608..111242488
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)