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    Plod2 procollagen lysine, 2-oxoglutarate 5-dioxygenase 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 300901, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Plod2provided by RGD
    Official Full Name
    procollagen lysine, 2-oxoglutarate 5-dioxygenase 2provided by RGD
    Primary source
    RGD:3353
    See related
    Ensembl:ENSRNOG00000030183 AllianceGenome:RGD:3353
    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 procollagen-lysine 5-dioxygenase activity. Involved in cellular response to hormone stimulus and response to hypoxia. Predicted to be located in rough endoplasmic reticulum membrane. Predicted to be active in endoplasmic reticulum. Biomarker of hypothyroidism. Orthologous to human PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Uterus (RPKM 473.8), Kidney (RPKM 150.4) and 7 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    8q31
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (101964318..102047022)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (93084548..93167255)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (99977334..100059736)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480086 Neighboring gene ribosomal protein L39, pseudogene 5 Neighboring gene uncharacterized LOC102551814 Neighboring gene heterogeneous nuclear ribonucleoprotein A1, pseudogene 8

    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. Oxygen tension regulates the expression of a group of procollagen hydroxylases. Hofbauer KH, et al. Eur J Biochem, 2003 Nov. PMID 14622280
    2. Differential expression of procollagen lysine 2-oxoglutarate 5-deoxygenase and matrix metalloproteinase isoforms in hypothyroid rat ovary and disintegration of extracellular matrix. Saha SK, et al. Endocrinology, 2005 Jul. PMID 15817667
    3. PLOD2 regulated by transcription factor FOXA1 promotes metastasis in NSCLC. Du H, et al. Cell Death Dis, 2017 Oct 26. PMID 29072684, Free PMC Article
    4. Lysyl hydroxylase 3 is a multifunctional protein possessing collagen glucosyltransferase activity. Heikkinen J, et al. J Biol Chem, 2000 Nov 17. PMID 10934207
    5. Modulation of gene expression by hypoxia in human umbilical cord vein endothelial cells: A transcriptomic and proteomic study. Scheurer SB, et al. Proteomics, 2004 Jun. PMID 15174142

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circ-Plod2 destabilizes Mpo mRNA by binding to IGF2BP2 to promote osteogenic differentiation of bone marrow mesenchymal stem cells.
      Title: Circ-Plod2 destabilizes Mpo mRNA by binding to IGF2BP2 to promote osteogenic differentiation of bone marrow mesenchymal stem cells.
    2. N6-methyladenosine modification of PLOD2 causes spermatocyte damage in rats with varicocele.
      Title: N6-methyladenosine modification of PLOD2 causes spermatocyte damage in rats with varicocele.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 hydroxylysine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hydroxylysine biosynthetic process 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
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in rough endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
    Names
    LH2
    Procollagen-lysine, 2-oxoglutarate 5-dioxygenase (Lysine hydroxylase) 2
    lysyl hydroxylase 2
    NP_001136387.1
    NP_787065.2

    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_001142915.1 → NP_001136387.1  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001136387.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2), also known as the short variant, lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal 21 aa segment, compared to isoform 1.
      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      Q811A3, Q811A4
      UniProtKB/TrEMBL
      A6I245, G3V9I0
      Related
      ENSRNOP00000047828.3, ENSRNOT00000041859.5
      Conserved Domains (1) summary
      smart00702
      Location:572 → 735
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    2. NM_175869.3 → NP_787065.2  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_787065.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1), also known as the long variant, represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/Swiss-Prot
      Q811A3, Q811A4
      UniProtKB/TrEMBL
      A6I244, D3ZQR7
      Related
      ENSRNOP00000053546.1, ENSRNOT00000056704.4
      Conserved Domains (2) summary
      cd00761
      Location:309 → 422
      Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
      smart00702
      Location:593 → 756
      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_086026.1 Reference GRCr8

      Range
      101964318..102047022
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q811A3.1 GenPept UniProtKB/Swiss-Prot:Q811A3

    Gene LinkOut

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

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