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COL5A3 collagen type V alpha 3 chain [ Homo sapiens (human) ]

Gene ID: 50509, updated on 3-Apr-2024

Summary

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Official Symbol
COL5A3provided by HGNC
Official Full Name
collagen type V alpha 3 chainprovided by HGNC
Primary source
HGNC:HGNC:14864
See related
Ensembl:ENSG00000080573 MIM:120216; AllianceGenome:HGNC:14864
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 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. Mutations in this gene are thought to be responsible for the symptoms of a subset of patients with Ehlers-Danlos syndrome type III. Messages of several sizes can be detected in northern blots but sequence information cannot confirm the identity of the shorter messages. [provided by RefSeq, Jul 2008]
Expression
Broad expression in placenta (RPKM 20.1), fat (RPKM 19.6) and 20 other tissues See more
Orthologs
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Genomic context

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See COL5A3 in Genome Data Viewer
Location:
19p13.2
Exon count:
67
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (9959561..10010504, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10085749..10136694, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10070237..10121180, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9958151-9958702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:9958703-9959252 Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 1 Neighboring gene olfactomedin 2 Neighboring gene uncharacterized LOC124904636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10046447-10047041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10047708-10048210 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:10062835-10063428 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10063429-10064021 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:10109314-10109542 Neighboring gene Sharpr-MPRA regulatory region 3549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10112173-10112674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10112675-10113174 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50731 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:10128438-10129637 Neighboring gene CRISPRi-validated cis-regulatory element chr19.1735 Neighboring gene retinol dehydrogenase 8 Neighboring gene microRNA 5589

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Absence of apparent disease causing mutations in COL5A3 in 13 patients with hypermobility Ehlers-Danlos syndrome. Hoffman GG, et al. Am J Med Genet A, 2008 Dec 15. PMID 19012342
  2. The transcription factor CCAAT-binding factor CBF/NF-Y and two repressors regulate the core promoter of the human pro-alpha3(V) collagen gene (COL5A3). Nagato H, et al. J Biol Chem, 2004 Nov 5. PMID 15316020
  3. Control of heterotypic fibril formation by collagen V is determined by chain stoichiometry. Chanut-Delalande H, et al. J Biol Chem, 2001 Jun 29. PMID 11423559
  4. Basic fibroblast growth factor decreases type V/XI collagen expression in cultured bovine aortic smooth muscle cells. Kypreos KE, et al. J Cell Biochem, 1998 Feb 1. PMID 9443080
  5. Another look at collagen V and XI molecules. Fichard A, et al. Matrix Biol, 1995 Jul. PMID 8535602

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This study identified significant interaction between two new genes, COL5A3 and MMP9, which may be accounted for by a degradation of COL5A3 by MMP9 influencing eczema susceptibility
    Title: The COL5A3 and MMP9 genes interact in eczema susceptibility.
  2. Absence of obvious disease-causing mutations and null alleles in a cohort of 13 patients with h-EDS is consistent with exclusion of COL5A3 as a candidate gene for this disease.
    Title: Absence of apparent disease causing mutations in COL5A3 in 13 patients with hypermobility Ehlers-Danlos syndrome.
  3. analysis of processing of the Pro-alpha1(V)Pro-alpha2(V)Pro-alpha3(V) procollagen heterotrimer
    Title: Biosynthetic processing of the Pro-alpha1(V)Pro-alpha2(V)Pro-alpha3(V) procollagen heterotrimer.
  4. CBF/NF-Y and two repressors regulate the core promoter of the human pro-alpha3(V) collagen gene
    Title: The transcription factor CCAAT-binding factor CBF/NF-Y and two repressors regulate the core promoter of the human pro-alpha3(V) collagen gene (COL5A3).
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables collagen binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables extracellular matrix structural constituent NAS
Non-traceable Author Statement
more info
 PubMed 
enables extracellular matrix structural constituent conferring tensile strength HDA PubMed 
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 RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables proteoglycan binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in collagen fibril organization NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skin development NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of collagen type V trimer NAS
Non-traceable Author Statement
more info
 PubMed 
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
  

General protein information

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Preferred Names
collagen alpha-3(V) chain
Names
collagen, type V, alpha 3
pro-(alpha)3(V) collagen

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.

Genomic

  1. NG_046943.1 RefSeqGene

    Range
    5035..55978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_015719.4 → NP_056534.2  collagen alpha-3(V) chain preproprotein

    See identical proteins and their annotated locations for NP_056534.2

    Status: REVIEWED

    Source sequence(s)
    AC008742, AF177941, BQ006883
    Consensus CDS
    CCDS12222.1
    UniProtKB/Swiss-Prot
    P25940, Q9NZQ6
    UniProtKB/TrEMBL
    Q59GD4
    Related
    ENSP00000264828.3, ENST00000264828.4
    Conserved Domains (3) summary
    pfam01391
    Location:572 → 631
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:1515 → 1743
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:31 → 210
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    9959561..10010504 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528042.3 → XP_011526344.1  collagen alpha-3(V) chain isoform X1

    UniProtKB/TrEMBL
    Q59GD4
    Conserved Domains (3) summary
    pfam01391
    Location:571 → 630
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:1514 → 1742
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:31 → 209
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  2. XM_017026849.2 → XP_016882338.1  collagen alpha-3(V) chain isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    10085749..10136694 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321132.1 → XP_054177107.1  collagen alpha-3(V) chain isoform X1

  2. XM_054321133.1 → XP_054177108.1  collagen alpha-3(V) chain isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P25940.3 GenPept UniProtKB/Swiss-Prot:P25940

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