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    Col17a1 collagen type XVII alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 294027, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Col17a1provided by RGD
    Official Full Name
    collagen type XVII alpha 1 chainprovided by RGD
    Primary source
    RGD:1311130
    See related
    EnsemblRapid:ENSRNOG00000012110 AllianceGenome:RGD:1311130
    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 heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization and hemidesmosome assembly. Predicted to be located in membrane. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix; extracellular space; and hemidesmosome. Human ortholog(s) of this gene implicated in epithelial recurrent erosion dystrophy and junctional epidermolysis bullosa. Orthologous to human COL17A1 (collagen type XVII alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 71.6), Kidney (RPKM 42.5) and 5 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col17a1 in Genome Data Viewer
    Location:
    1q54
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (256472648..256518857, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (246530589..246577559, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (267416681..267465049, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene 40S ribosomal protein S8 pseudogene Neighboring gene STE20-like kinase Neighboring gene small nucleolar RNA SNORA17 Neighboring gene RNA, U6 small nuclear 982

    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. Junctional Epidermolysis Bullosa in Sprague Dawley Rats Caused by a Frameshift Mutation of Col17a1 Gene. Katoh Y, et al. Lab Invest, 2024 Oct. PMID 39265891
    2. Mutations in the 180-kD bullous pemphigoid antigen (BPAG2), a hemidesmosomal transmembrane collagen (COL17A1), in generalized atrophic benign epidermolysis bullosa. McGrath JA, et al. Nat Genet, 1995 Sep. PMID 7550320
    3. Analysis of the interactions between BP180, BP230, plectin and the integrin alpha6beta4 important for hemidesmosome assembly. Koster J, et al. J Cell Sci, 2003 Jan 15. PMID 12482924
    4. Beta4 integrin is required for hemidesmosome formation, cell adhesion and cell survival. Dowling J, et al. J Cell Biol, 1996 Jul. PMID 8707838, Free PMC Article
    5. 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

    What's a GeneRIF?
    1. Junctional Epidermolysis Bullosa in Sprague Dawley Rats Caused by a Frameshift Mutation of Col17a1 Gene.
      Title: Junctional Epidermolysis Bullosa in Sprague Dawley Rats Caused by a Frameshift Mutation of Col17a1 Gene.
    Submit: New GeneRIF Correction

    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 conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in hemidesmosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in hemidesmosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in hemidesmosome 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-1(XVII) chain
    Names
    collagen, type XVII, alpha 1
    procollagen, type XVII, alpha 1

    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_001415840.1 → NP_001402769.1  collagen alpha-1(XVII) chain isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A0G2K449
      Related
      ENSRNOP00000072907.1, ENSRNOT00000084851.3

    2. NM_001415841.1 → NP_001402770.1  collagen alpha-1(XVII) chain isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      D3ZSH7
      Related
      ENSRNOP00000016645.6, ENSRNOT00000016645.8

    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_086019.1 Reference GRCr8

      Range
      256472648..256518857 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001106366.1: Suppressed sequence

      Description
      NM_001106366.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    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.

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