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

Summary

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: mouse all
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Genomic context

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_000019.10 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
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?

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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G66875 (e-PCR)
- UniSTS:166682

SHGC-145596 (e-PCR)
- UniSTS:174670

COL5A3_310 (e-PCR)
- UniSTS:277120

STS-W80440 (e-PCR)
- UniSTS:60299

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 more info	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 more info	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

NG_046943.1 RefSeqGene

Range

5035..55978

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

9959561..10010504 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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