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    Col6a1 collagen, type VI, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 12833, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col6a1provided by MGI
    Official Full Name
    collagen, type VI, alpha 1provided by MGI
    Primary source
    MGI:MGI:88459
    See related
    Ensembl:ENSMUSG00000001119 AllianceGenome:MGI:88459
    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
    Col6a-1
    Summary
    Predicted to enable collagen binding activity and platelet-derived growth factor binding activity. Acts upstream of or within several processes, including extracellular matrix organization; lung development; and skeletal muscle tissue development. Located in sarcolemma. Is active in several cellular components, including lysosome; myofibril; and sarcoplasmic reticulum. Is expressed in several structures, including alimentary system; brain; genitourinary system; heart and pericardium; and sensory organ. Used to study Bethlem myopathy and Ullrich congenital muscular dystrophy. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy 1A. Orthologous to human COL6A1 (collagen type VI alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in subcutaneous fat pad adult (RPKM 393.3), ovary adult (RPKM 227.8) and 16 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Col6a1 in Genome Data Viewer
    Location:
    10 C1; 10 39.71 cM
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (76544626..76561869, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (76708792..76726044, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 51774 Neighboring gene predicted gene, 35608 Neighboring gene STARR-seq mESC enhancer starr_27183 Neighboring gene poly(rC) binding protein 3 Neighboring gene STARR-seq mESC enhancer starr_27185 Neighboring gene STARR-seq mESC enhancer starr_27186 Neighboring gene STARR-positive B cell enhancer mm9_chr10:76424592-76424893 Neighboring gene predicted gene, 35664

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Targeted (4)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables collagen binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables platelet-derived growth factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within 2-oxoglutarate metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within adipose tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within apoptotic nuclear changes IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within autophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within basement membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within bone development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within bone mineralization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within canonical Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within caveola assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cell death IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cellular response to amino acid stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within collagen fibril organization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within collagen metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endodermal cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within energy homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within energy reserve metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within extracellular matrix assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within fat cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within glycolytic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within hair follicle development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within hair follicle development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within homeostasis of number of cells IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within insulin receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within insulin-like growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within limb joint morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung alveolus development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung epithelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mitochondrial depolarization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within mitochondrial depolarization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mitochondrial transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mitochondrion organization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within mitochondrion organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organismal locomotion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within muscle cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within muscle cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within muscle organ development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within muscle structure development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within muscle system process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within myelination in peripheral nervous system IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within nervous system process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within organelle organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within ossification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within peripheral nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein lipidation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein tetramerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within reactive oxygen species metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within reduction of food intake in response to dietary excess IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of cell size IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within regulation of collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within respiratory system process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to UV IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within response to activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to bleomycin IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to decreased oxygen levels IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to lipid IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to lipopolysaccharide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to mechanical stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to muscle activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to pain IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to peptide IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to polyamine macromolecule IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to reactive oxygen species IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to toxic substance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to wounding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within response to wounding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within response to xenobiotic stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within sensory perception of mechanical stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within single fertilization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle fiber development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle fiber differentiation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle organ development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle tissue development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle tissue growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skeletal muscle tissue regeneration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within skin development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within tissue remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within transmission of nerve impulse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within tricarboxylic acid cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within uterus development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    is_active_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in extracellular matrix IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in extracellular region ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in extracellular space HDA PubMed 
    is_active_in intracellular vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in myofibril IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in sarcolemma IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in sarcoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    collagen alpha-1(VI) chain
    Names
    procollagen, type VI, alpha 1

    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.

    mRNA and Protein(s)

    1. NM_009933.5NP_034063.1  collagen alpha-1(VI) chain precursor

      See identical proteins and their annotated locations for NP_034063.1

      Status: VALIDATED

      Source sequence(s)
      AC168276
      Consensus CDS
      CCDS23952.1
      UniProtKB/Swiss-Prot
      Q04857
      Related
      ENSMUSP00000001147.5, ENSMUST00000001147.5
      Conserved Domains (2) summary
      pfam01391
      Location:271328
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:8231008
      vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than ...

    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_000076.7 Reference GRCm39 C57BL/6J

      Range
      76544626..76561869 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)