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

Gene ID: 315979, updated on 2-Nov-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, Nov 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 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

Component Evidence Code Pubs
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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