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    Col6a6 collagen type VI alpha 6 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315979, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Col6a6provided by RGD
    Official Full Name
    collagen type VI alpha 6 chainprovided by RGD
    Primary source
    RGD:1309172
    See related
    EnsemblRapid:ENSRNOG00000023007 AllianceGenome:RGD:1309172
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1309172
    Summary
    Predicted to be located in extracellular matrix and extracellular region. Orthologous to human COL6A6 (collagen type VI alpha 6 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 128.6), Heart (RPKM 107.0) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col6a6 in Genome Data Viewer
    Location:
    8q32
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (115196833..115352161, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (106318010..106473419, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (114352130..114449993, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene 5S ribosomal RNA Neighboring gene ribosomal protein L29 Neighboring gene phosphoinositide-3-kinase, regulatory subunit 4 Neighboring gene uncharacterized LOC103693167 Neighboring gene transfer RNA leucine (anticodon AAG) 7 Neighboring gene collagen type VI alpha 5 chain

    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
    • 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. 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
    2. Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI). Fitzgerald J, et al. J Biol Chem, 2008 Jul 18. PMID 18400749
    3. Glycoproteomics Reveals Decorin Peptides With Anti-Myostatin Activity in Human Atrial Fibrillation. Barallobre-Barreiro J, et al. Circulation, 2016 Sep 13. PMID 27559042, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    collagen alpha-6(VI) chain; collagen type VI alpha 6 chain
    Names
    collagen, type VI, alpha 6

    NCBI Reference Sequences (RefSeq)

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    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_086026.1 Reference GRCr8

      Range
      115196833..115352161 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039082609.2 → XP_038938537.1  collagen alpha-6(VI) chain isoform X3

      UniProtKB/TrEMBL
      A0A8I6GLS2, D3ZL10
      Related
      ENSRNOP00000053252.5, ENSRNOT00000056414.6
      Conserved Domains (5) summary
      smart00327
      Location:1186 → 1344
      VWA; von Willebrand factor (vWF) type A domain
      cd01450
      Location:1962 → 2140
      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
      pfam01391
      Location:1481 → 1547
      Collagen; Collagen triple helix repeat (20 copies)
      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. XM_039082610.2 → XP_038938538.2  collagen alpha-6(VI) chain isoform X2

    3. XM_063266454.1 → XP_063122524.1  collagen alpha-6(VI) chain isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

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