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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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    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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