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

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: mouse all
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Genomic context

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.
Title: Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.
TGF-beta2 and collagen play pivotal roles in the spheroid formation and anti-aging of human dermal papilla cells.
Title: TGF-β2 and collagen play pivotal roles in the spheroid formation and anti-aging of human dermal papilla cells.
This study identified collagen XV as a new low O2 tension sensitive gene, and provided a novel mechanistic evidence that directly HIF-1alpha (hypoxia-inducible factor-1 alpha) mediates collagen XV expression in response to hypoxia, since it was found specifically in vivo recruited at collagen XV promoter, in hypoxia-preconditioned mesenchymal stromal cells.
Title: Hypoxia Preconditioning of Human MSCs: a Direct Evidence of HIF-1α and Collagen Type XV Correlation.
COL15A1 mRNA was up-regulated in hepatocellular cancer (HCC) and collagen XV was expressed along the sinusoid-like endothelium of HCC but not in non-tumoral regions, which implies that collagen XV contributes to the capillarization of HCC.
Title: Human collagen XV is a prominent histopathological component of sinusoidal capillarization in hepatocellular carcinogenesis.
This study demonstrated that novel role for collagen XV in motor axon pathfinding and neuromuscular development.
Title: Slow Muscle Precursors Lay Down a Collagen XV Matrix Fingerprint to Guide Motor Axon Navigation.
we identified an epithelial ovarian cancer susceptibility loci at 9q22.33 (rs1413299 in COL15A1, P(meta) = 1.88 x 10(-8))
Title: Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women.
The obtained results indicate that the changes in gene expression in bone marrow progenitor cells can be involved into space flight-induced osteopenia.
Title: [The effects of simulated microgravity on the pattern of gene expression in human bone marrow mesenchymal stem cells under osteogenic differentiation].
COL15A1, provide evidence for concomitant epigenetic regulation and genetic susceptibility, and define a class of causal targets that sit at the intersection of genetic and epigenetic predisposition in the etiology of complex disease.
Title: Epigenetic regulation of COL15A1 in smooth muscle cell replicative aging and atherosclerosis.
These results suggest genetic variation in COL15A1 and COL18A1 can modify the age of onset of both early and late onset POAG.
Title: Variations in COL15A1 and COL18A1 influence age of onset of primary open angle glaucoma.
Collagen type XV and osteocalcin expression are highly sensitive markers to extracellular calcium
Title: Extracellular calcium chronically induced human osteoblasts effects: specific modulation of osteocalcin and collagen type XV.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies new susceptibility loci for epithelial ovarian cancer in Han Chinese women. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-148925 (e-PCR)
- UniSTS:176686

A003P31 (e-PCR)
- UniSTS:21559

SHGC-108127 (e-PCR)
- UniSTS:170562

D9S272 (e-PCR)
- UniSTS:10326

D9S2019 (e-PCR)
- UniSTS:27821

RH118965 (e-PCR)
- UniSTS:138933

RH79095 (e-PCR)
- UniSTS:11462

RH121036 (e-PCR)
- UniSTS:134088

D9S1092 (e-PCR)
- UniSTS:31463

D9S272 (e-PCR)
- UniSTS:1789

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	ISS Inferred from Sequence or Structural Similarity more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed

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

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type XV trimer	TAS Traceable Author Statement more info	PubMed
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	NAS Non-traceable Author Statement more info

General protein information

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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)

NM_001855.5 → NP_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:670 → 716

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:40 → 228

TSPN; Thrombospondin N-terminal -like domains

cd00247
Location:1215 → 1381

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; ...