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    Col6a5 collagen type VI alpha 5 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 501047, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Col6a5provided by RGD
    Official Full Name
    collagen type VI alpha 5 chainprovided by RGD
    Primary source
    RGD:1565804
    See related
    EnsemblRapid:ENSRNOG00000010663 AllianceGenome:RGD:1565804
    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
    RGD1307220; RGD1565804
    Summary
    Predicted to be involved in extracellular matrix organization. Predicted to be located in extracellular matrix and extracellular region. Predicted to be active in collagen-containing extracellular matrix. Orthologous to human COL6A5 (collagen type VI alpha 5 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 165.6), Spleen (RPKM 134.2) and 5 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col6a5 in Genome Data Viewer
    Location:
    8q32
    Exon count:
    42
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (115362532..115462844, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (106483806..106584114, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (114527807..114632152, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein L29 Neighboring gene phosphoinositide-3-kinase, regulatory subunit 4 Neighboring gene collagen type VI alpha 6 chain Neighboring gene uncharacterized LOC103693167 Neighboring gene transfer RNA leucine (anticodon AAG) 7 Neighboring gene collagen, type VI, alpha 4 Neighboring gene ribosomal protein L6, pseudogene 10

    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. 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-5(VI) chain; collagen type VI alpha 5 chain
    Names
    collagen, type VI, alpha 5

    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
      115362532..115462844 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008766594.4 → XP_008764816.2  collagen alpha-5(VI) chain isoform X3

      UniProtKB/TrEMBL
      A0A0G2JTX7, A0A8I5ZRM4
      Related
      ENSRNOP00000081276.1, ENSRNOT00000112307.2
      Conserved Domains (5) summary
      cd01450
      Location:1989 → 2163
      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:653 → 814
      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:840 → 1010
      VWA; von Willebrand factor type A domain
      pfam01391
      Location:1584 → 1650
      Collagen; Collagen triple helix repeat (20 copies)
      cl00057
      Location:29 → 191
      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_039082614.2 → XP_038938542.2  collagen alpha-5(VI) chain isoform X1

    3. XM_039082612.2 → XP_038938540.2  collagen alpha-5(VI) chain isoform X1

    4. XM_063266347.1 → XP_063122417.1  collagen alpha-5(VI) chain isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version

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