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PLOD3 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 3)

Identity

Alias_symbol (synonym)LH3
Other alias
HGNC (Hugo) PLOD3
LocusID (NCBI) 8985
Atlas_Id 72001
Location 7q22.1  [Link to chromosome band 7q22]
Location_base_pair Starts at 101205977 and ends at 101217730 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
JADE2 (5q31.1) / PLOD3 (7q22.1)PLOD3 (7q22.1) / MICA (6p21.33)PLOD3 (7q22.1) / MPV17 (2p23.3)
PLOD3 (7q22.1) / PLOD3 (7q22.1)PLOD3 (7q22.1) / SLC9A1 (1p36.11)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)PLOD3   9083
Cards
Entrez_Gene (NCBI)PLOD3  8985  procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
AliasesLH3
GeneCards (Weizmann)PLOD3
Ensembl hg19 (Hinxton)ENSG00000106397 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000106397 [Gene_View]  chr7:101205977-101217730 [Contig_View]  PLOD3 [Vega]
ICGC DataPortalENSG00000106397
TCGA cBioPortalPLOD3
AceView (NCBI)PLOD3
Genatlas (Paris)PLOD3
WikiGenes8985
SOURCE (Princeton)PLOD3
Genetics Home Reference (NIH)PLOD3
Genomic and cartography
GoldenPath hg38 (UCSC)PLOD3  -     chr7:101205977-101217730 -  7q22.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PLOD3  -     7q22.1   [Description]    (hg19-Feb_2009)
EnsemblPLOD3 - 7q22.1 [CytoView hg19]  PLOD3 - 7q22.1 [CytoView hg38]
Mapping of homologs : NCBIPLOD3 [Mapview hg19]  PLOD3 [Mapview hg38]
OMIM603066   612394   
Gene and transcription
Genbank (Entrez)AF046889 AF068229 AK075338 AK297559 AK298537
RefSeq transcript (Entrez)NM_001084
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PLOD3
Cluster EST : UnigeneHs.153357 [ NCBI ]
CGAP (NCI)Hs.153357
Alternative Splicing GalleryENSG00000106397
Gene ExpressionPLOD3 [ NCBI-GEO ]   PLOD3 [ EBI - ARRAY_EXPRESS ]   PLOD3 [ SEEK ]   PLOD3 [ MEM ]
Gene Expression Viewer (FireBrowse)PLOD3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8985
GTEX Portal (Tissue expression)PLOD3
Protein : pattern, domain, 3D structure
UniProt/SwissProtO60568   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO60568  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO60568
Splice isoforms : SwissVarO60568
PhosPhoSitePlusO60568
Domaine pattern : Prosite (Expaxy)FE2OG_OXY (PS51471)    LYS_HYDROXYLASE (PS01325)   
Domains : Interpro (EBI)Nucleotide-diphossugar_trans    Oxoglu/Fe-dep_dioxygenase    Pro_4_hyd_alph    Procol_lys_dOase   
Domain families : Pfam (Sanger)2OG-FeII_Oxy (PF03171)   
Domain families : Pfam (NCBI)pfam03171   
Domain families : Smart (EMBL)P4Hc (SM00702)  
Conserved Domain (NCBI)PLOD3
DMDM Disease mutations8985
Blocks (Seattle)PLOD3
SuperfamilyO60568
Human Protein AtlasENSG00000106397
Peptide AtlasO60568
HPRD04347
IPIIPI00030255   IPI00909548   IPI00908467   IPI00924424   IPI00927515   IPI00926796   IPI00926601   IPI00926874   
Protein Interaction databases
DIP (DOE-UCLA)O60568
IntAct (EBI)O60568
FunCoupENSG00000106397
BioGRIDPLOD3
STRING (EMBL)PLOD3
ZODIACPLOD3
Ontologies - Pathways
QuickGOO60568
Ontology : AmiGOin utero embryonic development  endothelial cell morphogenesis  iron ion binding  protein binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  protein O-linked glycosylation  protein localization  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  neural tube development  collagen fibril organization  rough endoplasmic reticulum membrane  L-ascorbic acid binding  cellular response to hormone stimulus  procollagen glucosyltransferase activity  procollagen glucosyltransferase activity  vasodilation  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  epidermis morphogenesis  procollagen galactosyltransferase activity  oxidation-reduction process  lung morphogenesis  extracellular exosome  basement membrane assembly  
Ontology : EGO-EBIin utero embryonic development  endothelial cell morphogenesis  iron ion binding  protein binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  protein O-linked glycosylation  protein localization  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  neural tube development  collagen fibril organization  rough endoplasmic reticulum membrane  L-ascorbic acid binding  cellular response to hormone stimulus  procollagen glucosyltransferase activity  procollagen glucosyltransferase activity  vasodilation  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  epidermis morphogenesis  procollagen galactosyltransferase activity  oxidation-reduction process  lung morphogenesis  extracellular exosome  basement membrane assembly  
Pathways : KEGGLysine degradation    Other types of O-glycan biosynthesis   
NDEx NetworkPLOD3
Atlas of Cancer Signalling NetworkPLOD3
Wikipedia pathwaysPLOD3
Orthology - Evolution
OrthoDB8985
GeneTree (enSembl)ENSG00000106397
Phylogenetic Trees/Animal Genes : TreeFamPLOD3
HOVERGENO60568
HOGENOMO60568
Homologs : HomoloGenePLOD3
Homology/Alignments : Family Browser (UCSC)PLOD3
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPLOD3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PLOD3
dbVarPLOD3
ClinVarPLOD3
1000_GenomesPLOD3 
Exome Variant ServerPLOD3
ExAC (Exome Aggregation Consortium)PLOD3 (select the gene name)
Genetic variants : HAPMAP8985
Genomic Variants (DGV)PLOD3 [DGVbeta]
DECIPHERPLOD3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPLOD3 
Mutations
ICGC Data PortalPLOD3 
TCGA Data PortalPLOD3 
Broad Tumor PortalPLOD3
OASIS PortalPLOD3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPLOD3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPLOD3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Ehlers Danlos Syndrome Variant Database
BioMutasearch PLOD3
DgiDB (Drug Gene Interaction Database)PLOD3
DoCM (Curated mutations)PLOD3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PLOD3 (select a term)
intoGenPLOD3
Cancer3DPLOD3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603066    612394   
Orphanet21104   
MedgenPLOD3
Genetic Testing Registry PLOD3
NextProtO60568 [Medical]
TSGene8985
GENETestsPLOD3
Huge Navigator PLOD3 [HugePedia]
snp3D : Map Gene to Disease8985
BioCentury BCIQPLOD3
ClinGenPLOD3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8985
Chemical/Pharm GKB GenePA33413
Clinical trialPLOD3
Miscellaneous
canSAR (ICR)PLOD3 (select the gene name)
Probes
Litterature
PubMed40 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePLOD3
EVEXPLOD3
GoPubMedPLOD3
iHOPPLOD3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri May 19 11:48:56 CEST 2017

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