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Col4a6 collagen type IV alpha 6 chain [ Rattus norvegicus (Norway rat) ]

Gene ID: 363458, updated on 13-Apr-2024

Summary

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Official Symbol
Col4a6provided by RGD
Official Full Name
collagen type IV alpha 6 chainprovided by RGD
Primary source
RGD:1589724
See related
Ensembl:ENSRNOG00000056772 AllianceGenome:RGD:1589724
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 be an extracellular matrix structural constituent. Predicted to act upstream of or within cellular response to amino acid stimulus; collagen-activated tyrosine kinase receptor signaling pathway; and extracellular matrix organization. Predicted to be located in basement membrane. Predicted to be part of collagen type IV trimer. Human ortholog(s) of this gene implicated in AMME complex and X-linked deafness 6. Orthologous to human COL4A6 (collagen type IV alpha 6 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Lung (RPKM 65.0), Uterus (RPKM 36.4) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Col4a6 in Genome Data Viewer
Location:
Xq33
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (109554945..109905987, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (104766463..105117499, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (112405647..112768337, complement)

Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene autophagy related 4A, cysteine peptidase Neighboring gene 60S ribosomal protein L10a-like Neighboring gene collagen type IV alpha 5 chain Neighboring gene insulin receptor substrate 4

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. Differential expression of mouse alpha5(IV) and alpha6(IV) collagen genes in epithelial basement membranes. Saito K, et al. J Biochem, 2000 Sep. PMID 10965041
  2. Developmental distribution of collagen IV isoforms and relevance to ocular diseases. Bai X, et al. Matrix Biol, 2009 May. PMID 19275937, Free PMC Article
  3. Insertional mutation of the collagen genes Col4a3 and Col4a4 in a mouse model of Alport syndrome. Lu W, et al. Genomics, 1999 Oct 15. PMID 10534397
  4. Localization of type IV collagen a 1 to a 6 chains in basement membrane during mouse molar germ development. Nagai N, et al. Int J Dev Biol, 2001 Oct. PMID 11732842
  5. Discoidin domain receptor 1 functions in axon extension of cerebellar granule neurons. Bhatt RS, et al. Genes Dev, 2000 Sep 1. PMID 10970885, Free PMC Article

See all (9) 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 extracellular matrix structural constituent ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within cellular response to amino acid stimulus ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within extracellular matrix organization ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in basement membrane ISO
Inferred from Sequence Orthology
more info
  
part_of collagen type IV trimer ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
collagen alpha-6(IV) chain
Names
collagen, type IV, alpha 6

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_001427260.1 → NP_001414189.1  collagen alpha-6(IV) chain precursor

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000021
    UniProtKB/TrEMBL
    A0A0G2K601

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_086039.1 Reference GRCr8

    Range
    109554945..109905987 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_010061203.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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