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    Col8a1 collagen type VIII alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304021, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Col8a1provided by RGD
    Official Full Name
    collagen type VIII alpha 1 chainprovided by RGD
    Primary source
    RGD:1309361
    See related
    Ensembl:ENSRNOG00000039668 AllianceGenome:RGD:1309361
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    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 endodermal cell differentiation and extracellular matrix organization. Predicted to act upstream of or within camera-type eye morphogenesis; epithelial cell proliferation; and positive regulation of cell-substrate adhesion. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human COL8A1 (collagen type VIII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Heart (RPKM 74.5), Muscle (RPKM 36.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col8a1 in Genome Data Viewer
    Location:
    11q12
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (56245998..56378586)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (42776851..42906432)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (44877690..45006203)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120095648 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene filamin A interacting protein 1-like Neighboring gene cms1 ribosomal small subunit homolog Neighboring gene uncharacterized LOC134481062

    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. Oxidized phospholipids induce type VIII collagen expression and vascular smooth muscle cell migration. Cherepanova OA, et al. Circ Res, 2009 Mar 13. PMID 19168440, Free PMC Article
    2. Targeted disruption of Col8a1 and Col8a2 genes in mice leads to anterior segment abnormalities in the eye. Hopfer U, et al. FASEB J, 2005 Aug. PMID 16051690
    3. Regulation of endodermal differentiation of human embryonic stem cells through integrin-ECM interactions. Brafman DA, et al. Cell Death Differ, 2013 Mar. PMID 23154389, Free PMC Article
    4. FMRP recruitment of β-catenin to the translation pre-initiation complex represses translation. Ehyai S, et al. EMBO Rep, 2018 Dec. PMID 30361391, Free PMC Article
    5. Transcriptome-based systematic identification of extracellular matrix proteins. Manabe R, et al. Proc Natl Acad Sci U S A, 2008 Sep 2. PMID 18757743, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Oxidized phospholipids induce type VIII collagen expression and vascular smooth muscle cell migration.
      Title: Oxidized phospholipids induce type VIII collagen expression and vascular smooth muscle cell migration.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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
    acts_upstream_of_or_within camera-type eye morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within endothelial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of cell-substrate adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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
    		  

    General protein information

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    Preferred Names
    collagen alpha-1(VIII) chain
    Names
    collagen, type VIII, alpha 1
    procollagen, type VIII, 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_001107100.1 → NP_001100570.1  collagen alpha-1(VIII) chain precursor

      See identical proteins and their annotated locations for NP_001100570.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473967
      UniProtKB/TrEMBL
      A0A8I6AA24, A6IQM2
      Related
      ENSRNOP00000089355.1, ENSRNOT00000113782.1
      Conserved Domains (2) summary
      smart00110
      Location:612 → 743
      C1Q; Complement component C1q domain
      pfam01391
      Location:447 → 501
      Collagen; Collagen triple helix repeat (20 copies)

    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_086029.1 Reference GRCr8

      Range
      56245998..56378586
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006248208.5 → XP_006248270.1  collagen alpha-1(VIII) chain isoform X1

      See identical proteins and their annotated locations for XP_006248270.1

      UniProtKB/TrEMBL
      D4AC70
      Conserved Domains (2) summary
      smart00110
      Location:613 → 744
      C1Q; Complement component C1q domain
      pfam01391
      Location:448 → 502
      Collagen; Collagen triple helix repeat (20 copies)

    2. XM_039088381.2 → XP_038944309.1  collagen alpha-1(VIII) chain isoform X1

      UniProtKB/TrEMBL
      D4AC70
      Conserved Domains (2) summary
      smart00110
      Location:613 → 744
      C1Q; Complement component C1q domain
      pfam01391
      Location:448 → 502
      Collagen; Collagen triple helix repeat (20 copies)

    3. XM_039088382.2 → XP_038944310.1  collagen alpha-1(VIII) chain isoform X1

      UniProtKB/TrEMBL
      D4AC70
      Related
      ENSRNOP00000057564.4
      Conserved Domains (2) summary
      smart00110
      Location:613 → 744
      C1Q; Complement component C1q domain
      pfam01391
      Location:448 → 502
      Collagen; Collagen triple helix repeat (20 copies)

    4. XM_017598011.3 → XP_017453500.1  collagen alpha-1(VIII) chain isoform X1

      UniProtKB/TrEMBL
      D4AC70
      Conserved Domains (2) summary
      smart00110
      Location:613 → 744
      C1Q; Complement component C1q domain
      pfam01391
      Location:448 → 502
      Collagen; Collagen triple helix repeat (20 copies)
    Nucleotide Protein Strain
    Heading Accession and Version

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