Human Gene PRKN (ENST00000366892.5) Description and Page Index
  Description: parkin RBR E3 ubiquitin protein ligase (from HGNC PRKN)
RefSeq Summary (NM_004562): The precise function of this gene is unknown; however, the encoded protein is a component of a multiprotein E3 ubiquitin ligase complex that mediates the targeting of substrate proteins for proteasomal degradation. Mutations in this gene are known to cause Parkinson disease and autosomal recessive juvenile Parkinson disease. Alternative splicing of this gene produces multiple transcript variants encoding distinct isoforms. Additional splice variants of this gene have been described but currently lack transcript support. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000366892.5
Gencode Gene: ENSG00000185345.21
Transcript (Including UTRs)
   Position: hg38 chr6:161,545,112-162,727,764 Size: 1,182,653 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg38 chr6:161,545,414-162,727,668 Size: 1,182,255 Coding Exon Count: 10 

Page IndexSequence and LinksMalaCardsRNA-Seq ExpressionMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
GeneReviewsMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:161,545,112-162,727,764)mRNA (may differ from genome)Protein (368 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblExonPrimerGeneCardsLynxMGIPubMed
Stanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: PRKN
Diseases sorted by gene-association score: parkinson disease, juvenile, type 2* (1550), ovarian cancer, somatic* (521), lung cancer* (408), leprosy* (406), lung cancer susceptibility 3* (284), parkinson disease, late-onset* (106), parkin type of early-onset parkinson disease* (100), synucleinopathy (19), early-onset parkinson disease (14), paratyphoid fever (12), tremor (10), movement disease (10), essential tremor (10), bell's palsy (9), dysautonomia (9), classic rett syndrome (9), multiple system atrophy (9), parkinson disease 10 (9), supranuclear palsy, progressive (8), dementia, lewy body (8), snca-related parkinson disease (8), autosomal recessive limb-girdle muscular dystrophy type 2h (7), muscular dystrophy, congenital, megaconial type (7), epilepsy, progressive myoclonic 2b (6), hypersomnia (6), amyotrophic lateral sclerosis-parkinsonism/dementia complex (6), parkinson disease 15, autosomal recessive (5), dementia (5), dystonia (4), angelman syndrome (2), motor neuron disease (2), dementia, frontotemporal (2), nervous system disease (1), central nervous system disease (1)
* = Manually curated disease association

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.26 RPKM in Muscle - Skeletal
Total median expression: 83.57 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 -44.8096-0.467 Picture PostScript Text
3' UTR -54.80302-0.181 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
IPR003977 - Parkin
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00240 - Ubiquitin family

ModBase Predicted Comparative 3D Structure on B1AKC3
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI     
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity
GO:0016874 ligase activity

Biological Process:
GO:0016567 protein ubiquitination

Cellular Component:
GO:0005739 mitochondrion
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  JA482182 - Sequence 165 from Patent WO2011072091.
JA482183 - Sequence 166 from Patent WO2011072091.
JA482184 - Sequence 167 from Patent WO2011072091.
JE980474 - Sequence 165 from Patent EP2862929.
JE980475 - Sequence 166 from Patent EP2862929.
JE980476 - Sequence 167 from Patent EP2862929.
AB009973 - Homo sapiens parkin mRNA for Parkin, complete cds.
AK294684 - Homo sapiens cDNA FLJ59199 complete cds, highly similar to Parkin (EC 6.3.2.-).
AB245403 - Homo sapiens mRNA for parkin 2, complete cds.
AK292590 - Homo sapiens cDNA FLJ75810 complete cds, highly similar to Homo sapiens Parkinson disease (autosomal recessive, juvenile) 2, parkin (PARK2), transcript variant 1, mRNA.
GU357501 - Homo sapiens nonfunctional truncated parkin variant SV2-4DEL (PARK2) mRNA, complete sequence, alternatively spliced.
GU345839 - Homo sapiens parkin variant SV5DEL (PARK2) mRNA, complete cds, alternatively spliced.
GU345840 - Homo sapiens parkin variant SV9DEL (PARK2) mRNA, complete cds, alternatively spliced.
GU361466 - Homo sapiens truncated parkin variant SV4,8DEL (PARK2) mRNA, complete cds, alternatively spliced.
GU361467 - Homo sapiens parkin variant SV5,9DEL (PARK2) mRNA, complete cds, alternatively spliced.
GU361468 - Homo sapiens truncated parkin variant SV3,8,9DEL (PARK2) mRNA, complete cds, alternatively spliced.
GU361470 - Homo sapiens nonfunctional truncated parkin variant SV1cINS (PARK2) mRNA, complete sequence, alternatively spliced.
GU361471 - Homo sapiens nonfunctional truncated parkin variant SV1cINS2-8DEL (PARK2) mRNA, complete sequence, alternatively spliced.
GU357502 - Homo sapiens nonfunctional truncated parkin variant SV2-4,8DEL (PARK2) mRNA, complete sequence, alternatively spliced.
GU345837 - Homo sapiens nonfunctional parkin variant SV2DEL (PARK2) mRNA, complete sequence; alternatively spliced.
GU345838 - Homo sapiens truncated parkin variant SV4DEL (PARK2) mRNA, complete cds, alternatively spliced.
GU361469 - Homo sapiens truncated parkin variant SV1bINS (PARK2) mRNA, complete cds, alternatively spliced.
KC357595 - Homo sapiens clone PP24 PARK2 splice variant (PARK2) mRNA, complete cds, alternatively spliced.
KC774171 - Homo sapiens clone PP32 E3 ubiquitin-protein ligase parkin isoform (PARK2) mRNA, complete cds, alternatively spliced.
AF381286 - Homo sapiens parkin isoform mRNA, complete cds, alternatively spliced.
AF381283 - Homo sapiens parkin isoform mRNA, complete cds, alternatively spliced.
AF381282 - Homo sapiens parkin isoform mRNA, complete cds, alternatively spliced.
AF381284 - Homo sapiens parkin isoform mRNA, complete cds, alternatively spliced.
EF375726 - Homo sapiens parkin 2 (PARK2) mRNA, complete cds.
AB527958 - Synthetic construct DNA, clone: pF1KB0407, Homo sapiens PARK2 gene for Parkinson disease (autosomal recessive, juvenile) 2, parkin, without stop codon, in Flexi system.
KJ534911 - Homo sapiens clone PARK2_iso-A_adult-A14 parkinson protein 2 isoform A (PARK2) mRNA, partial cds, alternatively spliced.
KJ534912 - Homo sapiens clone PARK2_iso-A_fetal-F14 parkinson protein 2 isoform A (PARK2) mRNA, partial cds, alternatively spliced.
BC022014 - Homo sapiens Parkinson disease (autosomal recessive, juvenile) 2, parkin, mRNA (cDNA clone MGC:26491 IMAGE:4824892), complete cds.
HQ447316 - Synthetic construct Homo sapiens clone IMAGE:100070632; CCSB001392_02 Parkinson disease (autosomal recessive, juvenile) 2, parkin (PARK2) gene, encodes complete protein.
KJ901621 - Synthetic construct Homo sapiens clone ccsbBroadEn_11015 PARK2 gene, encodes complete protein.
KR709488 - Synthetic construct Homo sapiens clone CCSBHm_00002623 PARK2 (PARK2) mRNA, encodes complete protein.
KR709489 - Synthetic construct Homo sapiens clone CCSBHm_00002644 PARK2 (PARK2) mRNA, encodes complete protein.
KU178240 - Homo sapiens parkinson protein 2 E3 ubiquitin protein ligase isoform 1 (PARK2) mRNA, partial cds, alternatively spliced.
KU178241 - Homo sapiens parkinson protein 2 E3 ubiquitin protein ligase isoform 2 (PARK2) mRNA, partial cds, alternatively spliced.
KU178242 - Homo sapiens parkinson protein 2 E3 ubiquitin protein ligase isoform 3 (PARK2) mRNA, partial cds, alternatively spliced.
CU692452 - Synthetic construct Homo sapiens gateway clone IMAGE:100019194 5' read PARK2 mRNA.
JD276280 - Sequence 257304 from Patent EP1572962.
JD217243 - Sequence 198267 from Patent EP1572962.
JD406141 - Sequence 387165 from Patent EP1572962.
JD478190 - Sequence 459214 from Patent EP1572962.
JD407088 - Sequence 388112 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04120 - Ubiquitin mediated proteolysis
hsa05012 - Parkinson's disease

-  Other Names for This Gene
  Alternate Gene Symbols: B1AKC3, B1AKC3_HUMAN, BC022014, KB-152G3.1-002, PARK2, uc063ssp.1
UCSC ID: uc063ssp.1
RefSeq Accession: NM_004562
Protein: B1AKC3

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PRKN:
dystonia-ov (Hereditary Dystonia Overview)
jpd (Parkin Type of Early-Onset Parkinson Disease)
parkinson-overview (Parkinson Disease Overview)

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