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    Plod1 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 116552, updated on 5-Mar-2024

    Summary

    Official Symbol
    Plod1provided by RGD
    Official Full Name
    procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1provided by RGD
    Primary source
    RGD:621382
    See related
    Ensembl:ENSRNOG00000007763 AllianceGenome:RGD:621382
    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
    Also known as
    Plod
    Summary
    Enables several functions, including L-ascorbic acid binding activity; ferrous iron binding activity; and procollagen-lysine 5-dioxygenase activity. Involved in cellular response to hormone stimulus; peptidyl-lysine hydroxylation; and response to hypoxia. Predicted to be located in rough endoplasmic reticulum membrane. Predicted to be part of catalytic complex. Predicted to be active in endoplasmic reticulum. Biomarker of hypothyroidism. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome kyphoscoliotic type 1. Orthologous to human PLOD1 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Heart (RPKM 165.6), Lung (RPKM 130.2) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Plod1 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (163623847..163650737, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (158340674..158367581, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (164720629..164747071, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene mitofusin 2 Neighboring gene uncharacterized LOC134487036 Neighboring gene RIKEN cDNA 2510039O18 gene like Neighboring gene natriuretic peptide B

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables L-ascorbic acid binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ferrous iron binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables peptide binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables peptide binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT enables procollagen glucosyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables procollagen-lysine 5-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables procollagen-lysine 5-dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables procollagen-lysine 5-dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables procollagen-lysine 5-dioxygenase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables procollagen-lysine 5-dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in cellular response to hormone stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in epidermis development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epidermis development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in peptidyl-lysine hydroxylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    NOT involved_in protein O-linked glycosylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to hypoxia ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of catalytic complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of catalytic complex ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in rough endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
    Names
    LH1
    lysyl hydroxylase 1
    procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1
    procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)
    NP_446279.2
    XP_038965072.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_053827.2NP_446279.2  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor

      See identical proteins and their annotated locations for NP_446279.2

      Status: VALIDATED

      Source sequence(s)
      CA513298, CB736258, CO397075, CV080837, FQ074486, FQ107796, FQ202794
      UniProtKB/Swiss-Prot
      Q63321
      UniProtKB/TrEMBL
      A6IU34, D3ZQ74
      Related
      ENSRNOP00000010433.6, ENSRNOT00000010433.8
      Conserved Domains (1) summary
      smart00702
      Location:563726
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    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
      163623847..163650737 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109144.2XP_038965072.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 isoform X1

      Conserved Domains (1) summary
      smart00702
      Location:340503
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues