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    Col27a1 collagen type XXVII alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 298101, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Col27a1provided by RGD
    Official Full Name
    collagen type XXVII alpha 1 chainprovided by RGD
    Primary source
    RGD:735115
    See related
    EnsemblRapid:ENSRNOG00000007657 AllianceGenome:RGD:735115
    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 conferring tensile strength. Predicted to be involved in several processes, including collagen fibril organization; endothelial cell morphogenesis; and notochord development. Predicted to act upstream of or within extracellular matrix organization and growth plate cartilage chondrocyte development. Predicted to be part of fibrillar collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Orthologous to human COL27A1 (collagen type XXVII alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 57.5), Uterus (RPKM 24.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col27a1 in Genome Data Viewer
    Location:
    5q24
    Exon count:
    61
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (81662822..81781502)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (76647302..76765989)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (79054004..79172442)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene alpha-1-microglobulin/bikunin precursor Neighboring gene kinesin family member 12 Neighboring gene microRNA 455 Neighboring gene orosomucoid 1 Neighboring gene AT-hook transcription factor Neighboring gene uncharacterized LOC102547858

    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. Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1. Pace JM, et al. Matrix Biol, 2003 Mar. PMID 12714037
    2. Collagen XXVII is developmentally regulated and forms thin fibrillar structures distinct from those of classical vertebrate fibrillar collagens. Plumb DA, et al. J Biol Chem, 2007 Apr 27. PMID 17331945, Free PMC Article
    3. Collagen XXVII organises the pericellular matrix in the growth plate. Plumb DA, et al. PLoS One, 2011. PMID 22206015, 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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables extracellular matrix structural constituent ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in growth plate cartilage chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within growth plate cartilage chondrocyte development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of fibrillar collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of fibrillar collagen trimer ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-1(XXVII) chain
    Names
    collagen type XXVII proalpha 1 chain
    collagen, type XXVII, alpha 1
    procollagen, type XXVII, 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_001411859.2 → NP_001398788.1  collagen alpha-1(XXVII) chain precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8L2Q4D5
      Related
      ENSRNOP00000010333.4, ENSRNOT00000010333.5

    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_086023.1 Reference GRCr8

      Range
      81662822..81781502
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109470.2 → XP_038965398.1  collagen alpha-1(XXVII) chain isoform X3

      Conserved Domains (3) summary
      pfam05109
      Location:320 → 571
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam01391
      Location:745 → 801
      Collagen; Collagen triple helix repeat (20 copies)
      cl22861
      Location:43 → 221
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    2. XM_063287351.1 → XP_063143421.1  collagen alpha-1(XXVII) chain isoform X1

    3. XM_063287352.1 → XP_063143422.1  collagen alpha-1(XXVII) chain isoform X2

    4. XM_039109472.2 → XP_038965400.1  collagen alpha-1(XXVII) chain isoform X4

      Conserved Domains (2) summary
      pfam01391
      Location:570 → 624
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:889 → 1087
      COLFI; Fibrillar collagen C-terminal domain

    5. XM_039109471.2 → XP_038965399.1  collagen alpha-1(XXVII) chain isoform X4

      Conserved Domains (2) summary
      pfam01391
      Location:570 → 624
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:889 → 1087
      COLFI; Fibrillar collagen C-terminal domain

    6. XM_039109473.2 → XP_038965401.1  collagen alpha-1(XXVII) chain isoform X5

      Conserved Domains (2) summary
      pfam01391
      Location:453 → 507
      Collagen; Collagen triple helix repeat (20 copies)
      cl02436
      Location:772 → 970
      COLFI; Fibrillar collagen C-terminal domain

    RNA

    1. XR_005504389.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_198747.1: Suppressed sequence

      Description
      NM_198747.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q80ZF0.1 GenPept UniProtKB/Swiss-Prot:Q80ZF0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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