Human Gene PTPRR (uc001swi.2)
  Description: Homo sapiens protein tyrosine phosphatase, receptor type, R (PTPRR), transcript variant 1, mRNA.
RefSeq Summary (NM_002849): The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and a single intracellular catalytic domain, and thus represents a receptor-type PTP. Silencing of this gene has been associated with colorectal cancer. Multiple transcript variants encoding different isoforms have been found for this gene. This gene shares a symbol (PTPRQ) with another gene, protein tyrosine phosphatase, receptor type, Q (GeneID 374462), which is also located on chromosome 12. [provided by RefSeq, May 2011].
Transcript (Including UTRs)
   Position: hg19 chr12:71,031,853-71,314,584 Size: 282,732 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr12:71,032,964-71,314,170 Size: 281,207 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:71,031,853-71,314,584)mRNA (may differ from genome)Protein (657 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedTreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PTPRR_HUMAN
DESCRIPTION: RecName: Full=Receptor-type tyrosine-protein phosphatase R; Short=R-PTP-R; EC=3.1.3.48; AltName: Full=Ch-1PTPase; AltName: Full=NC-PTPCOM1; AltName: Full=Protein-tyrosine phosphatase PCPTP1; Flags: Precursor;
FUNCTION: Sequesters mitogen-activated protein kinases (MAPKs) such as MAPK1, MAPK3 and MAPK14 in the cytoplasm in an inactive form. The MAPKs bind to a dephosphorylated kinase interacting motif, phosphorylation of which by the protein kinase A complex releases the MAPKs for activation and translocation into the nucleus (By similarity).
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBUNIT: Interacts with MAPKs (By similarity).
SUBCELLULAR LOCATION: Isoform Alpha: Cell membrane; Single-pass type I membrane protein.
SUBCELLULAR LOCATION: Isoform Delta: Cytoplasm, perinuclear region. Note=Locates to the perinuclear areas within the cytoplasm.
SUBCELLULAR LOCATION: Isoform Gamma: Cytoplasm, perinuclear region. Note=Locates to the perinuclear areas within the cytoplasm.
TISSUE SPECIFICITY: Expressed in brain, placenta, small intestine, stomach, uterus and weakly in the prostate. Isoform alpha has been observed only in the brain. Isoform gamma is expressed in brain, placenta and uterus. Isoform delta is expressed in brain, kidney, placenta, prostate, small intestine and uterus.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Receptor class 7 subfamily.
SIMILARITY: Contains 1 tyrosine-protein phosphatase domain.
SEQUENCE CAUTION: Sequence=CAA57957.1; Type=Frameshift; Positions=651; Sequence=CAB01957.1; Type=Frameshift; Positions=651;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PTPRR
CDC HuGE Published Literature: PTPRR
Positive Disease Associations: Parkinson Disease , Waist-Hip Ratio
Related Studies:
  1. Parkinson Disease
    Hon-Chung Fung et al. Lancet neurology 2006, Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data., Lancet neurology. [PubMed 17052657]
    We generated publicly available genotype data for Parkinsons disease patients and controls so that these data can be mined and augmented by other researchers to identify common genetic variability that results in minor and moderate risk for disease.
  2. Waist-Hip Ratio
    , , . [PubMed 0]
  3. Waist-Hip Ratio
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.78 RPKM in Brain - Cerebellum
Total median expression: 41.56 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -171.60414-0.414 Picture PostScript Text
3' UTR -278.901111-0.251 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
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR008356 - Tyr_Pase_KIM-con
IPR000242 - Tyr_Pase_rcpt/non-rcpt
IPR016334 - Tyr_Pase_rcpt_R/non-rcpt_5

Pfam Domains:
PF00102 - Protein-tyrosine phosphatase

SCOP Domains:
52799 - (Phosphotyrosine protein) phosphatases II

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2A8B - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15256
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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004721 phosphoprotein phosphatase activity
GO:0004725 protein tyrosine phosphatase activity
GO:0005001 transmembrane receptor protein tyrosine phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0019901 protein kinase binding

Biological Process:
GO:0001701 in utero embryonic development
GO:0006470 protein dephosphorylation
GO:0010633 negative regulation of epithelial cell migration
GO:0016311 dephosphorylation
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0038128 ERBB2 signaling pathway
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:1903385 regulation of homophilic cell adhesion

Cellular Component:
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  U42361 - Human protein tyrosine phosphatase Cr1PTPase precursor (Ch-1PTPase alpha) mRNA, complete cds.
D64053 - Homo sapiens mRNA for tyrosine phosphatase, complete cds.
Z79693 - H.sapiens mRNA for protein-tyrosine phosphatase NC-PTPCOM1.
AK312376 - Homo sapiens cDNA, FLJ92701, Homo sapiens protein tyrosine phosphatase, receptor type, R(PTPRR), transcript variant 1, mRNA.
BC110900 - Homo sapiens protein tyrosine phosphatase, receptor type, R, mRNA (cDNA clone MGC:131968 IMAGE:4538615), complete cds.
X82635 - H.sapiens mRNA for protein-tyrosine-phosphatase.
CR749836 - Homo sapiens mRNA; cDNA DKFZp781C1038 (from clone DKFZp781C1038).
BC072386 - Homo sapiens protein tyrosine phosphatase, receptor type, R, mRNA (cDNA clone IMAGE:5585629), partial cds.
BX571751 - Homo sapiens mRNA; cDNA DKFZp686K0257 (from clone DKFZp686K0257); complete cds.
AK091647 - Homo sapiens cDNA FLJ34328 fis, clone FEBRA2009074, moderately similar to Human Ch-1PTPase delta form mRNA.
U77917 - Human Ch-1PTPase gamma minus form mRNA, complete cds.
AK295951 - Homo sapiens cDNA FLJ56093 complete cds, highly similar to Receptor-type tyrosine-protein phosphatase R precursor (EC 3.1.3.48).
BC119777 - Homo sapiens protein tyrosine phosphatase, receptor type, R, mRNA (cDNA clone MGC:148171 IMAGE:40109494), complete cds.
BC122866 - Homo sapiens protein tyrosine phosphatase, receptor type, R, mRNA (cDNA clone MGC:148170 IMAGE:40109492), complete cds.
AK304457 - Homo sapiens cDNA FLJ55167 complete cds, highly similar to Receptor-type tyrosine-protein phosphatase R precursor (EC 3.1.3.48).
E09724 - cDNA encoding novel human tyrosine phosphatase.
E10497 - cDNA encoding human tyrosine phosphatase.
U77916 - Human Ch-1PTPase delta form mRNA, complete cds.
KJ891952 - Synthetic construct Homo sapiens clone ccsbBroadEn_01346 PTPRR gene, encodes complete protein.
KJ897425 - Synthetic construct Homo sapiens clone ccsbBroadEn_06819 PTPRR gene, encodes complete protein.
JD048870 - Sequence 29894 from Patent EP1572962.
JD238695 - Sequence 219719 from Patent EP1572962.
JD261212 - Sequence 242236 from Patent EP1572962.
JD323675 - Sequence 304699 from Patent EP1572962.
JD237023 - Sequence 218047 from Patent EP1572962.
JD436204 - Sequence 417228 from Patent EP1572962.
JD284959 - Sequence 265983 from Patent EP1572962.
JD436219 - Sequence 417243 from Patent EP1572962.
JD161213 - Sequence 142237 from Patent EP1572962.
AK304672 - Homo sapiens cDNA FLJ55273 complete cds, highly similar to Receptor-type tyrosine-protein phosphatase R precursor (EC 3.1.3.48).
BC092469 - Homo sapiens protein tyrosine phosphatase, receptor type, R, mRNA (cDNA clone IMAGE:5314937), partial cds.
JD467601 - Sequence 448625 from Patent EP1572962.
JD462200 - Sequence 443224 from Patent EP1572962.
JD235692 - Sequence 216716 from Patent EP1572962.
JD206479 - Sequence 187503 from Patent EP1572962.
JD420644 - Sequence 401668 from Patent EP1572962.
JD330179 - Sequence 311203 from Patent EP1572962.
JD130487 - Sequence 111511 from Patent EP1572962.
JD150179 - Sequence 131203 from Patent EP1572962.
JD398357 - Sequence 379381 from Patent EP1572962.
JD185145 - Sequence 166169 from Patent EP1572962.
JD143131 - Sequence 124155 from Patent EP1572962.
JD217745 - Sequence 198769 from Patent EP1572962.
JD406958 - Sequence 387982 from Patent EP1572962.
JD508360 - Sequence 489384 from Patent EP1572962.
JD462103 - Sequence 443127 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_erkPathway - Erk1/Erk2 Mapk Signaling pathway

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5Z7, ECPTP, NM_002849, NP_570897, O00342, PTPRQ, PTPRR_HUMAN, Q15256, Q92682, Q9UE65
UCSC ID: uc001swi.2
RefSeq Accession: NM_002849
Protein: Q15256 (aka PTPRR_HUMAN or PTPR_HUMAN)
CCDS: CCDS8998.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002849.3
exon count: 14CDS single in 3' UTR: no RNA size: 3516
ORF size: 1974CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3971.50frame shift in genome: no % Coverage: 99.52
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.