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Aliases for PLOD3 Gene

Aliases for PLOD3 Gene

  • Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 2 3 5
  • Lysyl Hydroxylase 3 3 4
  • Lysyl Hydroxlase 3 2 3
  • EC 1.14.11.4 4 61
  • LH3 3 4
  • Lysine Hydroxylase 3 3

External Ids for PLOD3 Gene

Previous GeneCards Identifiers for PLOD3 Gene

  • GC07M099332
  • GC07M100395
  • GC07M100409
  • GC07M100442
  • GC07M100635
  • GC07M100849
  • GC07M095442

Summaries for PLOD3 Gene

Entrez Gene Summary for PLOD3 Gene

  • The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough 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 VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]

GeneCards Summary for PLOD3 Gene

PLOD3 (Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3) is a Protein Coding gene. Diseases associated with PLOD3 include Lysyl Hydroxylase 3 Deficiency and Ehlers-Danlos Syndrome. Among its related pathways are Collagen biosynthesis and modifying enzymes and Other types of O-glycan biosynthesis. GO annotations related to this gene include oxidoreductase activity and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. An important paralog of this gene is PLOD1.

UniProtKB/Swiss-Prot for PLOD3 Gene

  • Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.

Gene Wiki entry for PLOD3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLOD3 Gene

Genomics for PLOD3 Gene

Regulatory Elements for PLOD3 Gene

Enhancers for PLOD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07F101192 1.3 Ensembl ENCODE 13.7 +25.8 25834 1.2 HDGF ATF1 ARNT WRNIP1 ARID4B FEZF1 ZNF48 YY1 ZNF143 SP5 AP1S1 PLOD3 ZNHIT1 VGF NAT16
GH07F100835 1.7 FANTOM5 Ensembl ENCODE 10.3 +381.6 381585 2.5 PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 FEZF1 ZNF2 YY1 CBX5 EPHB4 MIR6875 RN7SL750P RN7SL416P GIGYF1 STAG3L5P NYAP1 ENSG00000242798 MBLAC1 SAP25
GH07F101185 1.1 Ensembl ENCODE 13.7 +33.0 33020 0.4 CBX3 SIN3A FOS CREM SMARCA5 SMAD5 JUNB CEBPB NR2F2 SMARCA4 ZNHIT1 PLOD3 AP1S1 NAT16 VGF
GH07F101282 1.1 Ensembl ENCODE 12.2 -64.6 -64606 0.4 ZNF76 ARID4B ZNF2 RAD21 RFX5 ZNF121 ZNF143 THAP11 ZNF263 SMARCA5 PLOD3 ZNHIT1 VGF AP1S1 NAT16 FIS1 LOC101927746 ENSG00000278683 AZGP1P2
GH07F101243 1.2 ENCODE 10.5 -26.1 -26098 2.5 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 FIS1 MIR6875 EPHB4 PCOLCE AGFG2 TRIM56 PLOD3 CLDN15 GC07M101250
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PLOD3 on UCSC Golden Path with GeneCards custom track

Promoters for PLOD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000631316 620 2801 PKNOX1 ARNT CREB3L1 ARID4B SIN3A ZNF2 YY1 FOS ZNF263 SP3

Genomic Location for PLOD3 Gene

Chromosome:
7
Start:
101,205,977 bp from pter
End:
101,218,420 bp from pter
Size:
12,444 bases
Orientation:
Minus strand

Genomic View for PLOD3 Gene

Genes around PLOD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLOD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLOD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLOD3 Gene

Proteins for PLOD3 Gene

  • Protein details for PLOD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60568-PLOD3_HUMAN
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
    Protein Accession:
    O60568
    Secondary Accessions:
    • B2R6W6
    • Q540C3

    Protein attributes for PLOD3 Gene

    Size:
    738 amino acids
    Molecular mass:
    84785 Da
    Cofactor:
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer.

neXtProt entry for PLOD3 Gene

Selected DME Specific Peptides for PLOD3 Gene

O60568:
  • HPGRLTHYHEGLPTT
  • DYEGGGCRFLRY
  • PCPDVYWFP
  • PHHDSST
  • LWSNFWG
  • GKRFLNSG
  • PTELLKKF
  • RVGVWNVPY
  • PRKGWAL
  • GTRYIMVSF
  • WGLAEQYPEVG
  • HGNGPTKLQ
  • IFQNLNG
  • WNVPYIS

Post-translational modifications for PLOD3 Gene

  • Glycosylation at Asn 63 and Asn 548
  • Modification sites at PhosphoSitePlus

Other Protein References for PLOD3 Gene

Antibody Products

  • Cloud-Clone Corp. Antibodies for PLOD3

Domains & Families for PLOD3 Gene

Suggested Antigen Peptide Sequences for PLOD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O60568

UniProtKB/Swiss-Prot:

PLOD3_HUMAN :
  • Contains 1 Fe2OG dioxygenase domain.
Domain:
  • Contains 1 Fe2OG dioxygenase domain.
genes like me logo Genes that share domains with PLOD3: view

No data available for Gene Families for PLOD3 Gene

Function for PLOD3 Gene

Molecular function for PLOD3 Gene

GENATLAS Biochemistry:
procollagen-lysine,2-oxoglutarate 5 dioxygenase 3,highly expressed in heart,placenta,pancreas
UniProtKB/Swiss-Prot CatalyticActivity:
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2).
UniProtKB/Swiss-Prot Function:
Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.

Enzyme Numbers (IUBMB) for PLOD3 Gene

Gene Ontology (GO) - Molecular Function for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0008475 procollagen-lysine 5-dioxygenase activity IEA,TAS --
GO:0016491 oxidoreductase activity IEA --
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen IEA --
genes like me logo Genes that share ontologies with PLOD3: view
genes like me logo Genes that share phenotypes with PLOD3: view

Human Phenotype Ontology for PLOD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PLOD3 Gene

MGI Knock Outs for PLOD3:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLOD3

miRNA for PLOD3 Gene

miRTarBase miRNAs that target PLOD3

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for PLOD3 Gene

Localization for PLOD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLOD3 Gene

Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PLOD3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0030867 rough endoplasmic reticulum membrane IEA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PLOD3: view

Pathways & Interactions for PLOD3 Gene

genes like me logo Genes that share pathways with PLOD3: view

Pathways by source for PLOD3 Gene

Gene Ontology (GO) - Biological Process for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001886 endothelial cell morphogenesis IEA --
GO:0008104 protein localization IEA --
GO:0021915 neural tube development IEA --
GO:0030199 collagen fibril organization IEA --
genes like me logo Genes that share ontologies with PLOD3: view

No data available for SIGNOR curated interactions for PLOD3 Gene

Drugs & Compounds for PLOD3 Gene

(10) Drugs for PLOD3 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Succinic acid Approved Nutra Full agonist, Agonist, Target 0
Vitamin C Approved Nutra Target 514,514
Carbon dioxide Approved, Vet_approved Pharma 0
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0

(4) Additional Compounds for PLOD3 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Hydroxylysine
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoate
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoic acid
  • (2S,5R)-5-hydroxylysine
  • (5R)-5-hydroxy-L-lysine
  • 5-Hydroxy-L-lysine
1190-94-9
Fe2+
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
15438-31-0
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
genes like me logo Genes that share compounds with PLOD3: view

Transcripts for PLOD3 Gene

Unigene Clusters for PLOD3 Gene

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLOD3 Gene

No ASD Table

Relevant External Links for PLOD3 Gene

GeneLoc Exon Structure for
PLOD3
ECgene alternative splicing isoforms for
PLOD3

Expression for PLOD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLOD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLOD3 Gene

This gene is overexpressed in Bone marrow stromal cell (32.2) and Testis (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLOD3 Gene



Protein tissue co-expression partners for PLOD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PLOD3 Gene:

PLOD3

SOURCE GeneReport for Unigene cluster for PLOD3 Gene:

Hs.153357
genes like me logo Genes that share expression patterns with PLOD3: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PLOD3 Gene

Orthologs for PLOD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLOD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLOD3 34 35
  • 99.55 (n)
cow
(Bos Taurus)
Mammalia PLOD3 34 35
  • 89.86 (n)
dog
(Canis familiaris)
Mammalia PLOD3 34 35
  • 89.51 (n)
oppossum
(Monodelphis domestica)
Mammalia PLOD3 35
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plod3 34 16 35
  • 85.77 (n)
rat
(Rattus norvegicus)
Mammalia Plod3 34
  • 85.55 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PLOD3 35
  • 77 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLOD3 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plod3 34
  • 69.04 (n)
Str.1520 34
African clawed frog
(Xenopus laevis)
Amphibia plod-prov 34
zebrafish
(Danio rerio)
Actinopterygii wu:fb72h05 34
  • 67.28 (n)
plod3 35
  • 65 (a)
OneToMany
PLOD3 (2 of 2) 35
  • 65 (a)
OneToMany
wufa10a05 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001507 34
  • 57.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta Plod 34 35
  • 55.14 (n)
CG6199 36
  • 46 (a)
worm
(Caenorhabditis elegans)
Secernentea let-268 36 34 35
  • 51.63 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 35
  • 50 (a)
OneToMany
Species where no ortholog for PLOD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PLOD3 Gene

ENSEMBL:
Gene Tree for PLOD3 (if available)
TreeFam:
Gene Tree for PLOD3 (if available)

Paralogs for PLOD3 Gene

Paralogs for PLOD3 Gene

(5) SIMAP similar genes for PLOD3 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PLOD3: view

Variants for PLOD3 Gene

Sequence variations from dbSNP and Humsavar for PLOD3 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs121434414 Pathogenic, Lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394] 101,215,100(-) CCTCA(A/G)CGGGG reference, missense
rs786205872 Pathogenic 101,206,427(-) GTGGC(-/T)GCCGC reference, frameshift-variant
rs10215517 -- 101,218,194(+) TGTGC(C/T)AATGG upstream-variant-2KB, utr-variant-5-prime
rs10215699 -- 101,219,487(+) agtgg(C/T)gcaat intron-variant, upstream-variant-2KB
rs10233414 -- 101,209,210(+) TACCt(C/T)ttttt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PLOD3 Gene

Variant ID Type Subtype PubMed ID
nsv970915 CNV duplication 23825009
nsv831076 CNV loss 17160897
nsv831075 CNV loss 17160897
nsv607974 CNV loss 21841781
nsv607973 CNV loss 21841781
nsv1030604 CNV gain 25217958
nsv1018841 CNV gain 25217958
esv3614321 CNV gain 21293372
esv3614319 CNV gain 21293372
esv3614318 CNV loss 21293372
esv2752134 CNV gain 17911159
esv2734888 CNV deletion 23290073
esv2422376 CNV duplication 17116639
esv2422326 CNV duplication 17116639
dgv11534n54 CNV loss 21841781

Variation tolerance for PLOD3 Gene

Residual Variation Intolerance Score: 90.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.90; 67.67% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLOD3 Gene

Human Gene Mutation Database (HGMD)
PLOD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLOD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLOD3 Gene

Disorders for PLOD3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PLOD3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lysyl hydroxylase 3 deficiency
  • bone fragility with contractures, arterial rupture, and deafness
ehlers-danlos syndrome
  • cutis hyperelastica
recessive dystrophic epidermolysis bullosa
  • autosomal recessive dystrophic epidermolysis bullosa generalisata gravis
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search PLOD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLOD3_HUMAN
  • Lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394]: Connective tissue disorder. The syndrome is characterized by congenital malformations severely affecting many tissues and organs and revealing features of several collagen disorders, most of them involving COL2A1 (type II collagen). The findings suggest that the failure of lysyl hydroxylation and hydroxylysyl carbohydrate addition, which affects many collagens, is the molecular basis of this syndrome. {ECO:0000269 PubMed:18834968}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PLOD3

Genetic Association Database (GAD)
PLOD3
Human Genome Epidemiology (HuGE) Navigator
PLOD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLOD3
genes like me logo Genes that share disorders with PLOD3: view

No data available for Genatlas for PLOD3 Gene

Publications for PLOD3 Gene

  1. Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3). (PMID: 9582318) Valtavaara M. … Myllylae R. (J. Biol. Chem. 1998) 2 3 4 22 64
  2. Cloning and characterization of a third human lysyl hydroxylase isoform. (PMID: 9724729) Passoja K. … Kivirikko K.I. (Proc. Natl. Acad. Sci. U.S.A. 1998) 2 3 4 22 64
  3. A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene. (PMID: 18834968) Salo A.M. … Myllylae R. (Am. J. Hum. Genet. 2008) 3 4 22 64
  4. Complete exon-intron organization of the gene for human lysyl hydroxylase 3 (LH3). (PMID: 10686427) Rautavuoma K. … Kivirikko K.I. (Matrix Biol. 2000) 3 4 22 64
  5. The glycosyltransferase activities of lysyl hydroxylase 3 (LH3) in the extracellular space are important for cell growth and viability. (PMID: 18298658) Wang C. … MyllylAo R. (J. Cell. Mol. Med. 2009) 3 22 64

Products for PLOD3 Gene

Sources for PLOD3 Gene

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