Atlas of Genetics and Cytogenetics in Oncology and Haematology


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PRKN (parkin RBR E3 ubiquitin protein ligase)

Identity

Other aliasAR-JP
LPRS2
PARK2
PDJ
HGNC (Hugo) PRKN
LocusID (NCBI) 5071
Atlas_Id 46408
Location 6q26  [Link to chromosome band 6q26]
Location_base_pair Starts at 161347558 and ends at 162727802 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ARID1B 6q25.3 / PARK2 6q26PARK2 6q26 / STRADA 17q23.3

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)PRKN   8607
Cards
Entrez_Gene (NCBI)PRKN  5071  parkin RBR E3 ubiquitin protein ligase
AliasesAR-JP; LPRS2; PARK2; PDJ
GeneCards (Weizmann)PRKN
Ensembl hg19 (Hinxton) [Gene_View]
Ensembl hg38 (Hinxton) [Gene_View]  chr6:161347558-162727802 [Contig_View]  PRKN [Vega]
TCGA cBioPortalPRKN
AceView (NCBI)PRKN
Genatlas (Paris)PRKN
WikiGenes5071
SOURCE (Princeton)PRKN
Genetics Home Reference (NIH)PRKN
Genomic and cartography
GoldenPath hg38 (UCSC)PRKN  -     chr6:161347558-162727802 -  6q26   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PRKN  -     6q26   [Description]    (hg19-Feb_2009)
EnsemblPRKN - 6q26 [CytoView hg19]  PRKN - 6q26 [CytoView hg38]
Mapping of homologs : NCBIPRKN [Mapview hg19]  PRKN [Mapview hg38]
OMIM167000   211980   600116   602544   607572   
Gene and transcription
Genbank (Entrez)###############################################################################################################################################################################################################################################################
RefSeq transcript (Entrez)NM_004562 NM_013987 NM_013988
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PRKN
Cluster EST : UnigeneHs.132954 [ NCBI ]
CGAP (NCI)Hs.132954
Gene ExpressionPRKN [ NCBI-GEO ]   PRKN [ EBI - ARRAY_EXPRESS ]   PRKN [ SEEK ]   PRKN [ MEM ]
Gene Expression Viewer (FireBrowse)PRKN [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5071
GTEX Portal (Tissue expression)PRKN
Protein : pattern, domain, 3D structure
UniProt/SwissProtO60260   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO60260  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO60260
Splice isoforms : SwissVarO60260
PhosPhoSitePlusO60260
Domaine pattern : Prosite (Expaxy)UBIQUITIN_2 (PS50053)   
Domains : Interpro (EBI)E3_UB_ligase_RBR    IBR_dom    Parkin    Ubiquitin-rel_dom    Ubiquitin_dom   
Domain families : Pfam (Sanger)IBR (PF01485)    ubiquitin (PF00240)   
Domain families : Pfam (NCBI)pfam01485    pfam00240   
Domain families : Smart (EMBL)IBR (SM00647)  UBQ (SM00213)  
Conserved Domain (NCBI)PRKN
DMDM Disease mutations5071
Blocks (Seattle)PRKN
PDB (SRS)1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
PDB (PDBSum)1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
PDB (IMB)1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
PDB (RSDB)1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
Structural Biology KnowledgeBase1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
SCOP (Structural Classification of Proteins)1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
CATH (Classification of proteins structures)1IYF    2JMO    4BM9    4I1F    4I1H    5C1Z    5C23    5C9V    5TR5   
SuperfamilyO60260
Peptide AtlasO60260
IPIIPI00005254   IPI00332282   IPI00984693   IPI00470428   IPI00470429   IPI00332283   IPI00470427   
Protein Interaction databases
DIP (DOE-UCLA)O60260
IntAct (EBI)O60260
BioGRIDPRKN
STRING (EMBL)PRKN
ZODIACPRKN
Ontologies - Pathways
QuickGOO60260
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  ubiquitin ligase complex  protein polyubiquitination  mitochondrial fission  mitophagy  mitophagy  macromitophagy  transcription regulatory region sequence-specific DNA binding  G-protein coupled receptor binding  negative regulation of protein phosphorylation  startle response  transcription factor activity, sequence-specific DNA binding  actin binding  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  protein binding  nucleus  cytoplasm  mitochondrion  mitochondrion  mitochondrion  endoplasmic reticulum  Golgi apparatus  cytosol  cytosol  cytosol  transcription, DNA-templated  protein monoubiquitination  protein monoubiquitination  response to oxidative stress  mitochondrion organization  central nervous system development  learning  beta-catenin binding  zinc ion binding  adult locomotory behavior  proteasomal protein catabolic process  regulation of autophagy  positive regulation of gene expression  negative regulation of gene expression  positive regulation of mitochondrial fusion  negative regulation of mitochondrial fusion  regulation of mitochondrion organization  regulation of mitochondrion organization  regulation of mitochondrion organization  regulation of glucose metabolic process  free ubiquitin chain polymerization  regulation of dopamine secretion  tubulin binding  aggresome  macroautophagy  protein ubiquitination  protein ubiquitination  protein deubiquitination  SH3 domain binding  SCF ubiquitin ligase complex  enzyme binding  kinase binding  protein kinase binding  PDZ domain binding  ubiquitin-dependent ERAD pathway  Hsp70 protein binding  heat shock protein binding  regulation of protein ubiquitination  regulation of protein ubiquitination  ubiquitin conjugating enzyme binding  ubiquitin conjugating enzyme binding  ubiquitin protein ligase binding  regulation of protein stability  protein destabilization  positive regulation of protein binding  negative regulation of actin filament bundle assembly  regulation of lipid transport  positive regulation of proteasomal ubiquitin-dependent protein catabolic process  negative regulation of glucokinase activity  cellular response to unfolded protein  response to endoplasmic reticulum stress  synaptic transmission, glutamatergic  protein K29-linked ubiquitination  ERAD pathway  regulation of dopamine metabolic process  norepinephrine metabolic process  dopamine metabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  identical protein binding  histone deacetylase binding  neuron projection  positive regulation of I-kappaB kinase/NF-kappaB signaling  positive regulation of I-kappaB kinase/NF-kappaB signaling  ubiquitin binding  proteasome-mediated ubiquitin-dependent protein catabolic process  protein complex  phospholipase binding  positive regulation of DNA binding  negative regulation of neuron apoptotic process  cellular protein catabolic process  cellular protein metabolic process  protein K27-linked ubiquitination  negative regulation by host of viral genome replication  positive regulation of protein catabolic process  positive regulation of transcription from RNA polymerase II promoter  negative regulation of JNK cascade  negative regulation of insulin secretion  perinuclear region of cytoplasm  protein stabilization  chaperone binding  positive regulation of neurotransmitter uptake  dopamine uptake involved in synaptic transmission  protein autoubiquitination  regulation of mitochondrial membrane potential  zinc ion homeostasis  negative regulation of cell death  regulation of canonical Wnt signaling pathway  ubiquitin protein ligase activity  ubiquitin protein ligase activity  ubiquitin protein ligase activity  parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization  neuron cellular homeostasis  protein K63-linked ubiquitination  protein K63-linked ubiquitination  protein K63-linked ubiquitination  protein localization to mitochondrion  aggresome assembly  protein K48-linked ubiquitination  protein K11-linked ubiquitination  cellular response to manganese ion  LUBAC complex  protein K6-linked ubiquitination  protein K6-linked ubiquitination  negative regulation of canonical Wnt signaling pathway  negative regulation of canonical Wnt signaling pathway  positive regulation of mitochondrial fission  negative regulation of release of cytochrome c from mitochondria  cellular response to toxic substance  Lewy body  cullin family protein binding  positive regulation of macromitophagy in response to mitochondrial depolarization  positive regulation of macromitophagy in response to mitochondrial depolarization  presynapse  mitochondrion-derived vesicle  mitochondrion to lysosome transport  regulation of cellular response to oxidative stress  regulation of cellular response to oxidative stress  regulation of cellular response to oxidative stress  negative regulation of neuron death  positive regulation of proteasomal protein catabolic process  negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator  negative regulation of primary amine oxidase activity  positive regulation of protein linear polyubiquitination  regulation of synaptic vesicle transport  negative regulation of oxidative stress-induced cell death  negative regulation of oxidative stress-induced cell death  regulation of protein targeting to mitochondrion  positive regulation of tumor necrosis factor-mediated signaling pathway  cellular response to dopamine  negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway  positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway  negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway  negative regulation of exosomal secretion  positive regulation of mitophagy  positive regulation of mitophagy  positive regulation of dendrite extension  negative regulation of spontaneous neurotransmitter secretion  ubiquitin protein ligase activity involved in ERAD pathway  positive regulation of retrograde transport, endosome to Golgi  negative regulation of intralumenal vesicle formation  positive regulation of protein localization to membrane  positive regulation of protein localization to membrane  ubiquitin-specific protease binding  F-box domain binding  Parkin-FBXW7-Cul1 ubiquitin ligase complex  regulation of reactive oxygen species metabolic process  negative regulation of reactive oxygen species metabolic process  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  ubiquitin ligase complex  protein polyubiquitination  mitochondrial fission  mitophagy  mitophagy  macromitophagy  transcription regulatory region sequence-specific DNA binding  G-protein coupled receptor binding  negative regulation of protein phosphorylation  startle response  transcription factor activity, sequence-specific DNA binding  actin binding  ubiquitin-protein transferase activity  ubiquitin-protein transferase activity  protein binding  nucleus  cytoplasm  mitochondrion  mitochondrion  mitochondrion  endoplasmic reticulum  Golgi apparatus  cytosol  cytosol  cytosol  transcription, DNA-templated  protein monoubiquitination  protein monoubiquitination  response to oxidative stress  mitochondrion organization  central nervous system development  learning  beta-catenin binding  zinc ion binding  adult locomotory behavior  proteasomal protein catabolic process  regulation of autophagy  positive regulation of gene expression  negative regulation of gene expression  positive regulation of mitochondrial fusion  negative regulation of mitochondrial fusion  regulation of mitochondrion organization  regulation of mitochondrion organization  regulation of mitochondrion organization  regulation of glucose metabolic process  free ubiquitin chain polymerization  regulation of dopamine secretion  tubulin binding  aggresome  macroautophagy  protein ubiquitination  protein ubiquitination  protein deubiquitination  SH3 domain binding  SCF ubiquitin ligase complex  enzyme binding  kinase binding  protein kinase binding  PDZ domain binding  ubiquitin-dependent ERAD pathway  Hsp70 protein binding  heat shock protein binding  regulation of protein ubiquitination  regulation of protein ubiquitination  ubiquitin conjugating enzyme binding  ubiquitin conjugating enzyme binding  ubiquitin protein ligase binding  regulation of protein stability  protein destabilization  positive regulation of protein binding  negative regulation of actin filament bundle assembly  regulation of lipid transport  positive regulation of proteasomal ubiquitin-dependent protein catabolic process  negative regulation of glucokinase activity  cellular response to unfolded protein  response to endoplasmic reticulum stress  synaptic transmission, glutamatergic  protein K29-linked ubiquitination  ERAD pathway  regulation of dopamine metabolic process  norepinephrine metabolic process  dopamine metabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  protein ubiquitination involved in ubiquitin-dependent protein catabolic process  identical protein binding  histone deacetylase binding  neuron projection  positive regulation of I-kappaB kinase/NF-kappaB signaling  positive regulation of I-kappaB kinase/NF-kappaB signaling  ubiquitin binding  proteasome-mediated ubiquitin-dependent protein catabolic process  protein complex  phospholipase binding  positive regulation of DNA binding  negative regulation of neuron apoptotic process  cellular protein catabolic process  cellular protein metabolic process  protein K27-linked ubiquitination  negative regulation by host of viral genome replication  positive regulation of protein catabolic process  positive regulation of transcription from RNA polymerase II promoter  negative regulation of JNK cascade  negative regulation of insulin secretion  perinuclear region of cytoplasm  protein stabilization  chaperone binding  positive regulation of neurotransmitter uptake  dopamine uptake involved in synaptic transmission  protein autoubiquitination  regulation of mitochondrial membrane potential  zinc ion homeostasis  negative regulation of cell death  regulation of canonical Wnt signaling pathway  ubiquitin protein ligase activity  ubiquitin protein ligase activity  ubiquitin protein ligase activity  parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization  neuron cellular homeostasis  protein K63-linked ubiquitination  protein K63-linked ubiquitination  protein K63-linked ubiquitination  protein localization to mitochondrion  aggresome assembly  protein K48-linked ubiquitination  protein K11-linked ubiquitination  cellular response to manganese ion  LUBAC complex  protein K6-linked ubiquitination  protein K6-linked ubiquitination  negative regulation of canonical Wnt signaling pathway  negative regulation of canonical Wnt signaling pathway  positive regulation of mitochondrial fission  negative regulation of release of cytochrome c from mitochondria  cellular response to toxic substance  Lewy body  cullin family protein binding  positive regulation of macromitophagy in response to mitochondrial depolarization  positive regulation of macromitophagy in response to mitochondrial depolarization  presynapse  mitochondrion-derived vesicle  mitochondrion to lysosome transport  regulation of cellular response to oxidative stress  regulation of cellular response to oxidative stress  regulation of cellular response to oxidative stress  negative regulation of neuron death  positive regulation of proteasomal protein catabolic process  negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator  negative regulation of primary amine oxidase activity  positive regulation of protein linear polyubiquitination  regulation of synaptic vesicle transport  negative regulation of oxidative stress-induced cell death  negative regulation of oxidative stress-induced cell death  regulation of protein targeting to mitochondrion  positive regulation of tumor necrosis factor-mediated signaling pathway  cellular response to dopamine  negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway  positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway  negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway  negative regulation of exosomal secretion  positive regulation of mitophagy  positive regulation of mitophagy  positive regulation of dendrite extension  negative regulation of spontaneous neurotransmitter secretion  ubiquitin protein ligase activity involved in ERAD pathway  positive regulation of retrograde transport, endosome to Golgi  negative regulation of intralumenal vesicle formation  positive regulation of protein localization to membrane  positive regulation of protein localization to membrane  ubiquitin-specific protease binding  F-box domain binding  Parkin-FBXW7-Cul1 ubiquitin ligase complex  regulation of reactive oxygen species metabolic process  negative regulation of reactive oxygen species metabolic process  
Pathways : KEGGUbiquitin mediated proteolysis    Protein processing in endoplasmic reticulum    Parkinson's disease   
NDEx NetworkPRKN
Atlas of Cancer Signalling NetworkPRKN
Wikipedia pathwaysPRKN
Orthology - Evolution
OrthoDB5071
Phylogenetic Trees/Animal Genes : TreeFamPRKN
HOVERGENO60260
HOGENOMO60260
Homologs : HomoloGenePRKN
Homology/Alignments : Family Browser (UCSC)PRKN
Gene fusions - Rearrangements
Fusion : MitelmanARID1B/PARK2 [6q25.3/6q26]  [t(6;6)(q25;q26)]  
Fusion : MitelmanPARK2/STRADA [6q26/17q23.3]  [t(6;17)(q26;q23)]  
Fusion: TCGAARID1B 6q25.3 PARK2 6q26 LUAD
Fusion: TCGAPARK2 6q26 STRADA 17q23.3 LGG
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPRKN [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRKN
dbVarPRKN
ClinVarPRKN
1000_GenomesPRKN 
Exome Variant ServerPRKN
ExAC (Exome Aggregation Consortium)PRKN (select the gene name)
Genetic variants : HAPMAP5071
Genomic Variants (DGV)PRKN [DGVbeta]
DECIPHERPRKN [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPRKN 
Mutations
ICGC Data PortalPRKN 
TCGA Data PortalPRKN 
Broad Tumor PortalPRKN
OASIS PortalPRKN [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDPRKN
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)Parkinson's disease Mutation Database
LOVD (Leiden Open Variation Database)SpainMDB
BioMutasearch PRKN
DgiDB (Drug Gene Interaction Database)PRKN
DoCM (Curated mutations)PRKN (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRKN (select a term)
intoGenPRKN
Cancer3DPRKN(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM167000    211980    600116    602544    607572   
Orphanet
MedgenPRKN
Genetic Testing Registry PRKN
NextProtO60260 [Medical]
TSGene5071
GENETestsPRKN
Target ValidationPRKN
Huge Navigator PRKN [HugePedia]
snp3D : Map Gene to Disease5071
BioCentury BCIQPRKN
ClinGenPRKN
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5071
Chemical/Pharm GKB GenePA32942
Clinical trialPRKN
Miscellaneous
canSAR (ICR)PRKN (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRKN
EVEXPRKN
GoPubMedPRKN
iHOPPRKN
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:51:07 CEST 2017

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