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Col6a5 collagen, type VI, alpha 5 [ Mus musculus (house mouse) ]

Gene ID: 665033, updated on 27-Nov-2024

Summary

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Official Symbol
Col6a5provided by MGI
Official Full Name
collagen, type VI, alpha 5provided by MGI
Primary source
MGI:MGI:3648134
See related
Ensembl:ENSMUSG00000091345 AllianceGenome:MGI:3648134
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gm7455; Col29a1; EG665033
Summary
Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in cell adhesion. Located in extracellular matrix. Is expressed in several structures, including diaphragm; genitourinary system; gut; musculoskeletal system; and spleen. Orthologous to human COL6A5 (collagen type VI alpha 5 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in genital fat pad adult (RPKM 10.5), testis adult (RPKM 1.4) and 4 other tissues See more
Orthologs
human all
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Genomic context

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See Col6a5 in Genome Data Viewer
Location:
9 F1; 9 57.34 cM
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (105733269..105839743, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (105856070..105962463, complement)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_25131 Neighboring gene phosphoinositide-3-kinase regulatory subunit 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:105591833-105592016 Neighboring gene predicted gene, 22720 Neighboring gene collagen, type VI, alpha 6 Neighboring gene STARR-seq mESC enhancer starr_25132 Neighboring gene STARR-seq mESC enhancer starr_25133 Neighboring gene STARR-seq mESC enhancer starr_25134 Neighboring gene collagen, type VI, alpha 4 Neighboring gene predicted gene, 24631 Neighboring gene STARR-seq mESC enhancer starr_25137 Neighboring gene STARR-positive B cell enhancer mm9_chr9:106014267-106014568 Neighboring gene ribosomal protein L6 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The COL6A5-p.Glu2272* mutation induces chronic itch in mice. Rasheed AAB, et al. Mamm Genome, 2024 Jun. PMID 38523187
  2. Differential and restricted expression of novel collagen VI chains in mouse. Gara SK, et al. Matrix Biol, 2011 May. PMID 21477648
  3. Three novel collagen VI chains with high homology to the alpha3 chain. Gara SK, et al. J Biol Chem, 2008 Apr 18. PMID 18276594
  4. A mouse model for dominant collagen VI disorders: heterozygous deletion of Col6a3 Exon 16. Pan TC, et al. J Biol Chem, 2014 Apr 11. PMID 24563484, Free PMC Article
  5. Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI). Fitzgerald J, et al. J Biol Chem, 2008 Jul 18. PMID 18400749

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The COL6A5-p.Glu2272* mutation induces chronic itch in mice.
    Title: The COL6A5-p.Glu2272* mutation induces chronic itch in mice.
  2. The collagen VI alpha 5 chain is present in perimysium and at the neuromuscular junctions in skeletal muscle, skin, kidney glomerulus, interfollicular stroma in ovary and in the tunica albuginea of testis
    Title: Differential and restricted expression of novel collagen VI chains in mouse.
  3. discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix
    Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).
  4. analysis of collagen VI chains alpha4, alpha5, and alpha6with high homology to the alpha3 chain
    Title: Three novel collagen VI chains with high homology to the alpha3 chain.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
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 extracellular matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region ISO
Inferred from Sequence Orthology
more info
 PubMed 

General protein information

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Preferred Names
collagen alpha-5(VI) chain
Names
collagen alpha-1(XXIX) chain

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)

  1. NM_001167923.1 → NP_001161395.1  collagen alpha-5(VI) chain precursor

    Status: VALIDATED

    Source sequence(s)
    AC120386, AK134435, AM748256, AM748257, AM748258
    Consensus CDS
    CCDS85720.1
    UniProtKB/Swiss-Prot
    A6H584, A6H585, A6H586, E9Q1B5
    UniProtKB/TrEMBL
    A0A140T8W1
    Related
    ENSMUSP00000139398.3, ENSMUST00000190193.8
    Conserved Domains (5) summary
    cd01450
    Location:1995 → 2169
    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:659 → 820
    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:846 → 1016
    VWA; von Willebrand factor type A domain
    pfam03157
    Location:1435 → 1771
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:29 → 183
    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 ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    105733269..105839743 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030244492.2 → XP_030100352.2  collagen alpha-5(VI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6H584, A6H585, A6H586, E9Q1B5
    Conserved Domains (6) summary
    PHA03169
    Location:1467 → 1700
    PHA03169; hypothetical protein; Provisional
    cd01450
    Location:2046 → 2220
    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:710 → 871
    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:897 → 1067
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:1644 → 1707
    Collagen; Collagen triple helix repeat (20 copies)
    cl00057
    Location:80 → 234
    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_036155177.1 → XP_036011070.1  collagen alpha-5(VI) chain isoform X2

    UniProtKB/Swiss-Prot
    A6H584, A6H585, A6H586, E9Q1B5
    Conserved Domains (6) summary
    PHA03169
    Location:1416 → 1649
    PHA03169; hypothetical protein; Provisional
    cd01450
    Location:1995 → 2169
    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:659 → 820
    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:846 → 1016
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:1593 → 1656
    Collagen; Collagen triple helix repeat (20 copies)
    cl00057
    Location:29 → 183
    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 ...
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6H584.4 GenPept UniProtKB/Swiss-Prot:A6H584

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