U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

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

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Alleles

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

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    collagen alpha-5(VI) chain
    Names
    collagen alpha-1(XXIX) chain

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous