Human Gene PRKN (uc003qtv.4)
  Description: Homo sapiens parkinson protein 2, E3 ubiquitin protein ligase (parkin) (PRKN), transcript variant 1, mRNA.
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].
Transcript (Including UTRs)
   Position: hg19 chr6:161,768,590-162,683,797 Size: 915,208 Total Exon Count: 7 Strand: -


Page IndexSequence and LinksPrimersMalaCardsRNA-Seq ExpressionMicroarray Expression
Other SpeciesmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:161,768,590-162,683,797)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
EnsemblExonPrimerGeneNetworkH-INVLynxMalacards
PubMedTreefamWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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.

-  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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  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.
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.
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.
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.
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.
AK294684 - Homo sapiens cDNA FLJ59199 complete cds, highly similar to Parkin (EC 6.3.2.-).
GU357501 - Homo sapiens nonfunctional truncated parkin variant SV2-4DEL (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.
KC357594 - Homo sapiens clone PP47/PP50 PARK2 splice variant (PARK2) mRNA, complete cds, alternatively spliced.
AF381286 - Homo sapiens parkin isoform mRNA, complete cds, alternatively spliced.
JD308775 - Sequence 289799 from Patent EP1572962.
JD331825 - Sequence 312849 from Patent EP1572962.
JD084130 - Sequence 65154 from Patent EP1572962.
JD136717 - Sequence 117741 from Patent EP1572962.
JD279974 - Sequence 260998 from Patent EP1572962.
JD462398 - Sequence 443422 from Patent EP1572962.
JD049937 - Sequence 30961 from Patent EP1572962.
JD413551 - Sequence 394575 from Patent EP1572962.
JD118206 - Sequence 99230 from Patent EP1572962.
JD155570 - Sequence 136594 from Patent EP1572962.
JD100495 - Sequence 81519 from Patent EP1572962.
JD530106 - Sequence 511130 from Patent EP1572962.
JD305126 - Sequence 286150 from Patent EP1572962.
JD178241 - Sequence 159265 from Patent EP1572962.
JD381714 - Sequence 362738 from Patent EP1572962.
JD180406 - Sequence 161430 from Patent EP1572962.
JD557819 - Sequence 538843 from Patent EP1572962.
JD557817 - Sequence 538841 from Patent EP1572962.
JD490589 - Sequence 471613 from Patent EP1572962.
JD284938 - Sequence 265962 from Patent EP1572962.
JD315016 - Sequence 296040 from Patent EP1572962.
JD183466 - Sequence 164490 from Patent EP1572962.
JD566118 - Sequence 547142 from Patent EP1572962.
JD303074 - Sequence 284098 from Patent EP1572962.
JD317381 - Sequence 298405 from Patent EP1572962.
JD250712 - Sequence 231736 from Patent EP1572962.
JD411706 - Sequence 392730 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: AF381283, PARK2
UCSC ID: uc003qtv.4
RefSeq Accession: NM_004562

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

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: yes RNA accession: AF381283.1
exon count: 7CDS single in 3' UTR: no RNA size: 904
ORF size: 0CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 998.00frame shift in genome: no % Coverage: 99.23
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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