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

Gene ID: 294027, updated on 17-Aug-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 be an extracellular matrix structural constituent. Predicted to be involved in extracellular matrix organization and hemidesmosome assembly. Predicted to be integral component of membrane. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix; extracellular space; and hemidesmosome. Human ortholog(s) of this gene implicated in epithelial recurrent erosion dystrophy; junctional epidermolysis bullosa; and junctional epidermolysis bullosa non-Herlitz type. Orthologous to human COL17A1 (collagen type XVII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
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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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 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. 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
  2. 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
  3. 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
  4. 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

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
  
enables heparin binding 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, A0A8I6GBI7
    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
    A6JHR0, 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

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