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COL6A5 collagen type VI alpha 5 chain [ Homo sapiens (human) ]

Gene ID: 256076, updated on 31-Oct-2022

Summary

Official Symbol
COL6A5provided by HGNC
Official Full Name
collagen type VI alpha 5 chainprovided by HGNC
Primary source
HGNC:HGNC:26674
See related
Ensembl:ENSG00000172752 MIM:611916; AllianceGenome:HGNC:26674
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
VWA4; COL29A1
Summary
This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
Expression
Biased expression in skin (RPKM 1.9), lung (RPKM 1.6) and 8 other tissues See more
Orthologs
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Genomic context

See COL6A5 in Genome Data Viewer
Location:
3q22.1
Exon count:
44
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (130345672..130484846)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (133089679..133228818)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (130064515..130203690)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374106 Neighboring gene ATP5MC2 pseudogene 5 Neighboring gene collagen type VI alpha 6 chain Neighboring gene phosphoinositide-3-kinase regulatory subunit 4

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 Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-02-02)

ClinGen Genome Curation Page
Haploinsufficency

Dosage sensitivity unlikely (Last evaluated 2021-02-02)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • FLJ35880

General protein information

Preferred Names
collagen alpha-5(VI) chain
Names
collagen, type VI, alpha 5
collagen, type XXIX, alpha 1
von Willebrand factor A domain-containing protein 4

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_021424.2 RefSeqGene

    Range
    5002..144176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278298.2NP_001265227.1  collagen alpha-5(VI) chain isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the allele encoded by the GRCh38 reference genome and encodes isoform (1).
    Source sequence(s)
    AC093004, AC117398, KF573676
    Consensus CDS
    CCDS93384.1
    UniProtKB/Swiss-Prot
    A8TX70
    Related
    ENSP00000362250.5, ENST00000373157.9
    Conserved Domains (6) summary
    pfam01391
    Location:15641623
    Collagen; Collagen triple helix repeat (20 copies)
    COG2304
    Location:445593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01450
    Location:22902467
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    cd01472
    Location:627787
    vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
    pfam00092
    Location:814985
    VWA; von Willebrand factor type A domain
    cl00057
    Location:29195
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  2. NM_001412157.1NP_001399086.1  collagen alpha-5(VI) chain isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses the same exon combination as variant 1 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. The encoded isoform (3) has a frameshifted C-terminus compared to isoform 1.
    Source sequence(s)
    CP068275
  3. NM_153264.7NP_694996.5  collagen alpha-5(VI) chain isoform 2 precursor

    Status: REVIEWED

    Source sequence(s)
    AC093004, AC117398, KF573676
    Consensus CDS
    CCDS93385.1
    UniProtKB/Swiss-Prot
    A8TX70
    Related
    ENSP00000422898.2, ENST00000512836.6
    Conserved Domains (6) summary
    cd01450
    Location:22902467
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    cd01472
    Location:627787
    vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
    pfam01391
    Location:13941447
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00092
    Location:814985
    VWA; von Willebrand factor type A domain
    NF038329
    Location:14781730
    gly_rich_SclB; LPXTG-anchored collagen-like adhesin Scl2/SclB
    cl00057
    Location:29195
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

RNA

  1. NR_022012.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC093004, AC117398, KF573676
    Related
    ENST00000312481.11

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    130345672..130484846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011512623.3XP_011510925.1  collagen alpha-5(VI) chain isoform X2

    Conserved Domains (5) summary
    pfam01391
    Location:15641623
    Collagen; Collagen triple helix repeat (20 copies)
    COG2304
    Location:445593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01472
    Location:627787
    vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
    pfam00092
    Location:814985
    VWA; von Willebrand factor type A domain
    cl00057
    Location:29195
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  2. XM_011512622.3XP_011510924.1  collagen alpha-5(VI) chain isoform X1

    Conserved Domains (5) summary
    pfam01391
    Location:15641623
    Collagen; Collagen triple helix repeat (20 copies)
    COG2304
    Location:445593
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cd01472
    Location:627787
    vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
    pfam00092
    Location:814985
    VWA; von Willebrand factor type A domain
    cl00057
    Location:29195
    vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    133089679..133228818
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)