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

Gene ID: 1306, updated on 2-Nov-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
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Genomic context

See COL15A1 in Genome Data Viewer
Location:
9q22.33
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98943907..99070787)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (111115608..111242488)
RS_2024_09 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 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)

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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
    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_2024_08

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)