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

Gene ID: 361821, updated on 5-Mar-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
Ensembl: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 and extracellular space. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL6A2 (collagen type VI alpha 2 chain). [provided by Alliance of Genome Resources, Apr 2022]
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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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
  • 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
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
    ENSRNOP00000001695.5, ENSRNOT00000001695.7
    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, ENSRNOT00000109457.1
    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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