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    Col6a2 collagen type VI alpha 2 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361821, updated on 14-Nov-2024

    Summary

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    Official Symbol
    Col6a2provided by RGD
    Official Full Name
    collagen type VI alpha 2 chainprovided by RGD
    Primary source
    RGD:1305585
    See related
    EnsemblRapid:ENSRNOG00000001254 AllianceGenome:RGD:1305585
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable collagen binding activity. Involved in response to glucose. Predicted to be located in extracellular matrix; extracellular region; and sarcolemma. Predicted to be part of protein-containing complex. Predicted to be active in collagen-containing extracellular matrix. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy 1B. Orthologous to human COL6A2 (collagen type VI alpha 2 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Uterus (RPKM 1535.1), Lung (RPKM 479.2) and 7 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col6a2 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (12021182..12048932)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (12021676..12049425)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (12773472..12801179)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120098922 Neighboring gene uncharacterized LOC134483784 Neighboring gene formimidoyltransferase cyclodeaminase Neighboring gene uncharacterized LOC134483885 Neighboring gene spermatogenesis and centriole associated 1-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Type VI collagen gene expression in experimental liver fibrosis: quantitation and spatial distribution of mRNAs, and immunodetection of the protein. Takahara T, et al. Liver, 1995 Apr. PMID 7791542
    2. Hyperglycemic glucose concentrations up-regulate the expression of type VI collagen in vitro. Relevance to alterations of peripheral nerves in diabetes mellitus. Muona P, et al. Am J Pathol, 1993 May. PMID 8494053, Free PMC Article
    3. Type VI collagen mutations in Bethlem myopathy, an autosomal dominant myopathy with contractures. Jöbsis GJ, et al. Nat Genet, 1996 Sep. PMID 8782832
    4. Deposition of collagen VI in the extracellular matrix during mouse embryogenesis correlates with expression of the alpha 3(VI) subunit gene. Dziadek M, et al. Exp Cell Res, 1996 Aug 1. PMID 8806434
    5. Developmental regulation of biglycan expression in muscle and tendon. Lechner BE, et al. Muscle Nerve, 2006 Sep. PMID 16810681

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables collagen binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within response to UV ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to glucose IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in sarcolemma ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-2(VI) chain
    Names
    collagen, type VI, alpha 2
    procollagen, type VI, alpha 2

    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_001100741.1 → NP_001094211.1  collagen alpha-2(VI) chain precursor

      See identical proteins and their annotated locations for NP_001094211.1

      Status: VALIDATED

      Source sequence(s)
      BC089923, CB616438, CK365920, DN935075, FM036514, FM048712, FM093132
      UniProtKB/TrEMBL
      A6JKC0, F1LNH3
      Related
      ENSRNOP00000001695.6, ENSRNOT00000001695.8
      Conserved Domains (3) summary
      pfam01391
      Location:447 → 506
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:620 → 811
      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 ...
      pfam00092
      Location:841 → 1015
      VWA; von Willebrand factor type A domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086038.1 Reference GRCr8

      Range
      12021182..12048932
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006256300.4 → XP_006256362.1  collagen alpha-2(VI) chain isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y5R7, A0A8I5ZTZ9
      Related
      ENSRNOP00000077392.1, ENSRNOT00000109457.2
      Conserved Domains (3) summary
      pfam01391
      Location:447 → 506
      Collagen; Collagen triple helix repeat (20 copies)
      cd01480
      Location:620 → 811
      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 ...
      pfam15173
      Location:852 → 915
      FAM180; FAM180 family
    Nucleotide Protein Strain
    Heading Accession and Version

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