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PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2)

Identity

Alias_namesprocollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2
procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2
Alias_symbol (synonym)LH2
Other aliasBRKS2
TLH
HGNC (Hugo) PLOD2
LocusID (NCBI) 5352
Atlas_Id 53907
Location 3q24  [Link to chromosome band 3q24]
Location_base_pair Starts at 146069441 and ends at 146161495 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
PLOD2 (3q24) / ABCG1 (21q22.3)PLOD2 (3q24) / PLOD2 (3q24)PLOD2 (3q24) / PLSCR4 (3q24)
PLOD2 3q24 / ABCG1 21q22.3PLOD2 3q24 / PLSCR4 3q24

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)PLOD2   9082
Cards
Entrez_Gene (NCBI)PLOD2  5352  procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
AliasesBRKS2; LH2; TLH
GeneCards (Weizmann)PLOD2
Ensembl hg19 (Hinxton)ENSG00000152952 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000152952 [Gene_View]  chr3:146069441-146161495 [Contig_View]  PLOD2 [Vega]
ICGC DataPortalENSG00000152952
TCGA cBioPortalPLOD2
AceView (NCBI)PLOD2
Genatlas (Paris)PLOD2
WikiGenes5352
SOURCE (Princeton)PLOD2
Genetics Home Reference (NIH)PLOD2
Genomic and cartography
GoldenPath hg38 (UCSC)PLOD2  -     chr3:146069441-146161495 -  3q24   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PLOD2  -     3q24   [Description]    (hg19-Feb_2009)
EnsemblPLOD2 - 3q24 [CytoView hg19]  PLOD2 - 3q24 [CytoView hg38]
Mapping of homologs : NCBIPLOD2 [Mapview hg19]  PLOD2 [Mapview hg38]
OMIM601865   609220   
Gene and transcription
Genbank (Entrez)AB209879 AK125700 AK130098 AK295084 AL832238
RefSeq transcript (Entrez)NM_000935 NM_182943
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PLOD2
Cluster EST : UnigeneHs.477866 [ NCBI ]
CGAP (NCI)Hs.477866
Alternative Splicing GalleryENSG00000152952
Gene ExpressionPLOD2 [ NCBI-GEO ]   PLOD2 [ EBI - ARRAY_EXPRESS ]   PLOD2 [ SEEK ]   PLOD2 [ MEM ]
Gene Expression Viewer (FireBrowse)PLOD2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5352
GTEX Portal (Tissue expression)PLOD2
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00469   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00469  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00469
Splice isoforms : SwissVarO00469
PhosPhoSitePlusO00469
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)PLOD2
DMDM Disease mutations5352
Blocks (Seattle)PLOD2
SuperfamilyO00469
Human Protein AtlasENSG00000152952
Peptide AtlasO00469
HPRD03519
IPIIPI00472165   IPI00337495   IPI00947400   IPI00939578   IPI00945245   IPI00947098   
Protein Interaction databases
DIP (DOE-UCLA)O00469
IntAct (EBI)O00469
FunCoupENSG00000152952
BioGRIDPLOD2
STRING (EMBL)PLOD2
ZODIACPLOD2
Ontologies - Pathways
QuickGOO00469
Ontology : AmiGOresponse to hypoxia  iron ion binding  endoplasmic reticulum  endoplasmic reticulum membrane  cellular protein modification process  protein O-linked glycosylation  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  rough endoplasmic reticulum membrane  L-ascorbic acid binding  procollagen glucosyltransferase activity  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  oxidation-reduction process  extracellular exosome  
Ontology : EGO-EBIresponse to hypoxia  iron ion binding  endoplasmic reticulum  endoplasmic reticulum membrane  cellular protein modification process  protein O-linked glycosylation  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  rough endoplasmic reticulum membrane  L-ascorbic acid binding  procollagen glucosyltransferase activity  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  oxidation-reduction process  extracellular exosome  
Pathways : KEGGLysine degradation   
NDEx NetworkPLOD2
Atlas of Cancer Signalling NetworkPLOD2
Wikipedia pathwaysPLOD2
Orthology - Evolution
OrthoDB5352
GeneTree (enSembl)ENSG00000152952
Phylogenetic Trees/Animal Genes : TreeFamPLOD2
HOVERGENO00469
HOGENOMO00469
Homologs : HomoloGenePLOD2
Homology/Alignments : Family Browser (UCSC)PLOD2
Gene fusions - Rearrangements
Fusion : MitelmanPLOD2/ABCG1 [3q24/21q22.3]  
Fusion: TCGAPLOD2 3q24 ABCG1 21q22.3 BRCA
Fusion: TCGAPLOD2 3q24 PLSCR4 3q24 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPLOD2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PLOD2
dbVarPLOD2
ClinVarPLOD2
1000_GenomesPLOD2 
Exome Variant ServerPLOD2
ExAC (Exome Aggregation Consortium)PLOD2 (select the gene name)
Genetic variants : HAPMAP5352
Genomic Variants (DGV)PLOD2 [DGVbeta]
DECIPHERPLOD2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPLOD2 
Mutations
ICGC Data PortalPLOD2 
TCGA Data PortalPLOD2 
Broad Tumor PortalPLOD2
OASIS PortalPLOD2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPLOD2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPLOD2
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Osteogenesis Imperfecta Variant Database
BioMutasearch PLOD2
DgiDB (Drug Gene Interaction Database)PLOD2
DoCM (Curated mutations)PLOD2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PLOD2 (select a term)
intoGenPLOD2
Cancer3DPLOD2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601865    609220   
Orphanet313   
MedgenPLOD2
Genetic Testing Registry PLOD2
NextProtO00469 [Medical]
TSGene5352
GENETestsPLOD2
Huge Navigator PLOD2 [HugePedia]
snp3D : Map Gene to Disease5352
BioCentury BCIQPLOD2
ClinGenPLOD2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5352
Chemical/Pharm GKB GenePA33412
Clinical trialPLOD2
Miscellaneous
canSAR (ICR)PLOD2 (select the gene name)
Probes
Litterature
PubMed54 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePLOD2
EVEXPLOD2
GoPubMedPLOD2
iHOPPLOD2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri May 19 12:31:41 CEST 2017

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