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    Col6a6 collagen, type VI, alpha 6 [ Mus musculus (house mouse) ]

    Gene ID: 245026, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Col6a6provided by MGI
    Official Full Name
    collagen, type VI, alpha 6provided by MGI
    Primary source
    MGI:MGI:2444259
    See related
    Ensembl:ENSMUSG00000043719 AllianceGenome:MGI:2444259
    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
    E330019B14; E330026B02Rik
    Summary
    Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell adhesion. Located in extracellular region. Is expressed in several structures, including genitourinary system; intraembryonic coelom; liver; lung; and musculoskeletal system. Orthologous to human COL6A6 (collagen type VI alpha 6 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in subcutaneous fat pad adult (RPKM 3.9), limb E14.5 (RPKM 3.2) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Col6a6 in Genome Data Viewer
    Location:
    9 F1; 9 56.99 cM
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (105566616..105705413, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (105689417..105828246, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_25127 Neighboring gene predicted gene 5621 Neighboring gene STARR-seq mESC enhancer starr_25130 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 STARR-seq mESC enhancer starr_25132 Neighboring gene STARR-seq mESC enhancer starr_25133 Neighboring gene collagen, type VI, alpha 5 Neighboring gene STARR-seq mESC enhancer starr_25134 Neighboring gene collagen, type VI, alpha 4 Neighboring gene predicted gene, 24631

    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. Differential and restricted expression of novel collagen VI chains in mouse. Gara SK, et al. Matrix Biol, 2011 May. PMID 21477648
    2. Three novel collagen VI chains with high homology to the alpha3 chain. Gara SK, et al. J Biol Chem, 2008 Apr 18. PMID 18276594
    3. 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
    4. Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI). Fitzgerald J, et al. J Biol Chem, 2008 Jul 18. PMID 18400749
    5. Histone Lysine Methyltransferase SETD2 Regulates Coronary Vascular Development in Embryonic Mouse Hearts. Chen F, et al. Front Cell Dev Biol, 2021. PMID 33898448, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 

    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
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    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 
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in extracellular region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    collagen alpha-6(VI) 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_001102607.1 → NP_001096077.1  collagen alpha-6(VI) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001096077.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK087828, AM748261, AM748262
      Consensus CDS
      CCDS52906.1
      UniProtKB/Swiss-Prot
      A6H587, A6H588, A6H589, A6H590, Q8C6K9
      UniProtKB/TrEMBL
      E9Q6A6
      Related
      ENSMUSP00000096040.4, ENSMUST00000098441.10
      Conserved Domains (6) summary
      pfam01391
      Location:1539 → 1643
      Collagen; Collagen triple helix repeat (20 copies)
      smart00327
      Location:1186 → 1344
      VWA; von Willebrand factor (vWF) type A domain
      COG2304
      Location:434 → 633
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      cd01450
      Location:1963 → 2141
      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 ...
      pfam00092
      Location:621 → 789
      VWA; von Willebrand factor type A domain
      cl00057
      Location:25 → 179
      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_172927.3 → NP_766515.2  collagen alpha-6(VI) chain isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site, compared to variant 1, that results in an isoform (2) with a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC119951, AK054356
      Consensus CDS
      CCDS23468.1
      UniProtKB/TrEMBL
      B9EK79
      Related
      ENSMUSP00000060840.5, ENSMUST00000060896.5
      Conserved Domains (3) summary
      COG2304
      Location:434 → 633
      YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
      pfam00092
      Location:621 → 789
      VWA; von Willebrand factor type A domain
      cl00057
      Location:25 → 179
      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
      105566616..105705413 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_004935438.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8C6K9.2 GenPept UniProtKB/Swiss-Prot:Q8C6K9

    Gene LinkOut

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

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