U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 501047, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
Col6a5provided by RGD
Official Full Name
collagen type VI alpha 5 chainprovided by RGD
Primary source
RGD:1565804
See related
Ensembl: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. Orthologous to human COL6A5 (collagen type VI alpha 5 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Lung (RPKM 165.6), Spleen (RPKM 134.2) and 5 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
collagen alpha-5(VI) chain; collagen type VI alpha 5 chain
Names
collagen, type VI, alpha 5

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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
    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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.