Human Gene PLOD1 (uc010obb.2) Description and Page Index
  Description: Homo sapiens procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1), mRNA.
RefSeq Summary (NM_000302): Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015].
Transcript (Including UTRs)
   Position: hg19 chr1:11,994,724-12,035,599 Size: 40,876 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr1:11,994,837-12,034,865 Size: 40,029 Coding Exon Count: 20 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:11,994,724-12,035,599)mRNA (may differ from genome)Protein (774 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PLOD1
CDC HuGE Published Literature: PLOD1
Positive Disease Associations: bone density , longer forms of a repetitive sequence , Myocardial Infarction
Related Studies:
  1. bone density
    Spotila, L. D. et al. 2003, Association Analysis of Bone Mineral Density and Single Nucleotide Polymorphisms in Two Candidate Genes on Chromosome 1p36, Calcified tissue international. 2003 Aug;73(2):140-6. [PubMed 14565595]
    These findings strengthen the potential importance of chromosome 1p36.2-1p36.3 in contributing to BMD variation, and are consistent with genetic variation in either PLOD1, TNFRSF1B or nearby genes playing a role in the phenotype.
  2. bone density
    Yamada, Y. et al. 2007, Association of candidate gene polymorphisms with bone mineral density in community-dwelling Japanese women and men, Int J Mol Med 2007 19(5) 791-801. [PubMed 17390085]
  3. bone density
    Tasker, P. N. et al. 2006, Association of PLOD1 polymorphisms with bone mineral density in a population-based study of women from the UK, Osteoporos Int 2006 17(7) 1078-85. [PubMed 16758144]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PLOD1
Diseases sorted by gene-association score: ehlers-danlos syndrome, type vi* (1354), omphalocele* (400), abdominal wall defect* (400), ehlers-danlos syndrome, hypermobility type* (283), thoracic aortic aneurysms and aortic dissections* (163), ehlers-danlos syndrome, kyphoscoliotic form* (100), ehlers-danlos syndrome (59), hypomelanosis of ito (10), cervical incompetence (9), bruck syndrome (7), connective tissue disease (6), congenital contractures (5), collagen disease (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 90.78 RPKM in Cells - Cultured fibroblasts
Total median expression: 1221.72 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -49.00113-0.434 Picture PostScript Text
3' UTR -285.40734-0.389 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005123 - Oxoglu/Fe-dep_dioxygenase
IPR006620 - Pro_4_hyd_alph
IPR001006 - Procol_lys_dOase

Pfam Domains:
PF03171 - 2OG-Fe(II) oxygenase superfamily

ModBase Predicted Comparative 3D Structure on B4DR87
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK295254 - Homo sapiens cDNA FLJ52901 complete cds, highly similar to Procollagen-lysine,2-oxoglutarate5-dioxygenase 1 precursor (EC 1.14.11.4).
AK294688 - Homo sapiens cDNA FLJ53377 complete cds, highly similar to Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4).
AK316285 - Homo sapiens cDNA, FLJ79184 complete cds, highly similar to Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4).
AK312243 - Homo sapiens cDNA, FLJ92537, highly similar to Homo sapiens procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI) (PLOD), mRNA.
AK299150 - Homo sapiens cDNA FLJ59393 complete cds, highly similar to Procollagen-lysine,2-oxoglutarate5-dioxygenase 1 precursor (EC 1.14.11.4).
L06419 - Homo sapiens lysyl hydroxylase (PLOD) mRNA, complete cds.
M98252 - Homo sapiens lysyl hydroxylase (partial clone 2.2 Kb LH) RNA, complete mature peptide.
JD083786 - Sequence 64810 from Patent EP1572962.
BC016657 - Homo sapiens procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1, mRNA (cDNA clone MGC:8999 IMAGE:3917351), complete cds.
AB385110 - Synthetic construct DNA, clone: pF1KB5511, Homo sapiens PLOD1 gene for procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor, complete cds, without stop codon, in Flexi system.
KJ897345 - Synthetic construct Homo sapiens clone ccsbBroadEn_06739 PLOD1 gene, encodes complete protein.
KR709404 - Synthetic construct Homo sapiens clone CCSBHm_00001966 PLOD1 (PLOD1) mRNA, encodes complete protein.
KR709405 - Synthetic construct Homo sapiens clone CCSBHm_00001968 PLOD1 (PLOD1) mRNA, encodes complete protein.
KR709406 - Synthetic construct Homo sapiens clone CCSBHm_00001969 PLOD1 (PLOD1) mRNA, encodes complete protein.
KR709407 - Synthetic construct Homo sapiens clone CCSBHm_00001971 PLOD1 (PLOD1) mRNA, encodes complete protein.
AK124035 - Homo sapiens cDNA FLJ42041 fis, clone SPLEN2040222.
LP886337 - Sequence 229 from Patent WO2017201352.
LP978094 - Sequence 229 from Patent WO2017120612.
JD457955 - Sequence 438979 from Patent EP1572962.
JD127543 - Sequence 108567 from Patent EP1572962.
JD137595 - Sequence 118619 from Patent EP1572962.
JD193422 - Sequence 174446 from Patent EP1572962.
JD054127 - Sequence 35151 from Patent EP1572962.
JD539801 - Sequence 520825 from Patent EP1572962.
JD265295 - Sequence 246319 from Patent EP1572962.
JD061706 - Sequence 42730 from Patent EP1572962.
JD378701 - Sequence 359725 from Patent EP1572962.
JD444745 - Sequence 425769 from Patent EP1572962.
JD201082 - Sequence 182106 from Patent EP1572962.
JD082080 - Sequence 63104 from Patent EP1572962.
JD485944 - Sequence 466968 from Patent EP1572962.
JD218265 - Sequence 199289 from Patent EP1572962.
JD157525 - Sequence 138549 from Patent EP1572962.
JD422183 - Sequence 403207 from Patent EP1572962.
JD061886 - Sequence 42910 from Patent EP1572962.
JD544775 - Sequence 525799 from Patent EP1572962.
JD354312 - Sequence 335336 from Patent EP1572962.
MB419116 - JP 2019519516-A/78: MRNA COMBINATION THERAPIES FOR THE TREATMENT OF CANCER.
MB419981 - JP 2019519516-A/943: MRNA COMBINATION THERAPIES FOR THE TREATMENT OF CANCER.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00310 - Lysine degradation

-  Other Names for This Gene
  Alternate Gene Symbols: AK299150, B4DR87, B4DR87_HUMAN, NM_000302, NP_000293
UCSC ID: uc010obb.2
RefSeq Accession: NM_000302
Protein: B4DR87

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PLOD1:
eds6 (PLOD1-Related Kyphoscoliotic Ehlers-Danlos Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK299150.1
exon count: 20CDS single in 3' UTR: no RNA size: 2656
ORF size: 2325CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3690.00frame shift in genome: no % Coverage: 99.96
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.