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

Gene ID: 300901, updated on 18-Sep-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
EnsemblRapid: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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See Plod2 in Genome Data Viewer
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 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 collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
involved_in peptidyl-lysine hydroxylation ISO
Inferred from Sequence Orthology
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 Golgi apparatus 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
  
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
  
is_active_in extracellular space 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

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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, ENSRNOT00000041859.6
    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, ENSRNOT00000056704.5
    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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