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COL5A1 collagen type V alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 1289, updated on 13-Feb-2019

Summary

Official Symbol
COL5A1provided by HGNC
Official Full Name
collagen type V alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:2209
See related
Ensembl:ENSG00000130635 MIM:120215
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
EDSC; EDSCL1
Summary
This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
Expression
Broad expression in placenta (RPKM 45.0), endometrium (RPKM 38.1) and 16 other tissues See more
Orthologs

Genomic context

See COL5A1 in Genome Data Viewer
Location:
9q34.3
Exon count:
68
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (134641789..134844843)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (137533651..137736689)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376311 Neighboring gene uncharacterized LOC100506532 Neighboring gene COL5A1 antisense RNA 1 Neighboring gene uncharacterized LOC101448202 Neighboring gene microRNA 3689c Neighboring gene microRNA 3689a

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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Ehlers-Danlos syndrome, classic type
MedGen: C4552122 OMIM: 130000 GeneReviews: Classic Ehlers-Danlos Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2017-12-14)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2017-12-14)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study of central corneal thickness in Latinos.
NHGRI GWA Catalog
Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia.
NHGRI GWA Catalog
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus.
NHGRI GWA Catalog
Joint influence of small-effect genetic variants on human longevity.
NHGRI GWA Catalog
Multidimensional prognostic risk assessment identifies association between IL12B variation and surgery in Crohn's disease.
NHGRI GWA Catalog
New loci associated with central cornea thickness include COL5A1, AKAP13 and AVGR8.
NHGRI GWA Catalog
Population-based meta-analysis in Caucasians confirms association with COL5A1 and ZNF469 but not COL8A2 with central corneal thickness.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of collagen, type V, alpha 1 (COL5A1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Allograft Rejection, organism-specific biosystem (from WikiPathways)
    Allograft Rejection, organism-specific biosystemThis pathway illustrates molecular interactions involved in the fundamental adaptive immune response for allograft destruction. This pathway was adapted in large part from the KEGG pathway http://www...
  • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
    Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
    miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ45760

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength IEA
Inferred from Electronic Annotation
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heparin binding IDA
Inferred from Direct Assay
more info
PubMed 
integrin binding NAS
Non-traceable Author Statement
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
platelet-derived growth factor binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proteoglycan binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
blood vessel development IEA
Inferred from Electronic Annotation
more info
 
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization NAS
Non-traceable Author Statement
more info
PubMed 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
eye morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
integrin biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of endodermal cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cellular component organization IEA
Inferred from Electronic Annotation
more info
 
skin development IMP
Inferred from Mutant Phenotype
more info
PubMed 
supramolecular fiber organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
tendon development IEA
Inferred from Electronic Annotation
more info
 
wound healing, spreading of epidermal cells IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
basement membrane IEA
Inferred from Electronic Annotation
more info
 
collagen type V trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen type V trimer IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
colocalizes_with collagen-containing extracellular matrix HDA PubMed 
collagen-containing extracellular matrix IMP
Inferred from Mutant Phenotype
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(V) chain
Names
collagen, type V, alpha 1

NCBI Reference Sequences (RefSeq)

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_008030.1 RefSeqGene

    Range
    5000..208038
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_737

mRNA and Protein(s)

  1. NM_000093.4NP_000084.3  collagen alpha-1(V) chain isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_000084.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399221, CN399265, CN484933, ES314363
    Consensus CDS
    CCDS6982.1
    UniProtKB/Swiss-Prot
    P20908
    UniProtKB/TrEMBL
    A0A024R8E5, B2ZZ86, Q59EE7
    Related
    ENSP00000360882.3, ENST00000371817.7
    Conserved Domains (3) summary
    pfam01391
    Location:871930
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:39230
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:16101836
    COLFI; Fibrillar collagen C-terminal domain
  2. NM_001278074.1NP_001265003.1  collagen alpha-1(V) chain isoform 2 preproprotein

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2 which is of the same length but contains an alternate segment, compared to isoform 1. This variant is based on experimental data in PMID 22149965 and is supported by partial transcripts and RNA-seq data.
    Source sequence(s)
    AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399198, CN399221, CN399265, CN484933, ES314363
    Consensus CDS
    CCDS75932.1
    UniProtKB/TrEMBL
    A0A087WXW9, B2ZZ86, Q59EE7
    Related
    ENSP00000481360.1, ENST00000618395.4
    Conserved Domains (3) summary
    pfam01391
    Location:871930
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:39230
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:16101836
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    134641789..134844843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014266.2XP_016869755.1  collagen alpha-1(V) chain isoform X1

RNA

  1. XR_001746183.1 RNA Sequence

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