Human Gene PTPRD (uc003zkk.3) Description and Page Index
  Description: Homo sapiens protein tyrosine phosphatase, receptor type, D (PTPRD), transcript variant 1, mRNA.
RefSeq Summary (NM_002839): 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 contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010].
Transcript (Including UTRs)
   Position: hg19 chr9:8,314,246-10,612,723 Size: 2,298,478 Total Exon Count: 46 Strand: -
Coding Region
   Position: hg19 chr9:8,317,874-8,733,843 Size: 415,970 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:8,314,246-10,612,723)mRNA (may differ from genome)Protein (1912 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PTPRD_HUMAN
DESCRIPTION: RecName: Full=Receptor-type tyrosine-protein phosphatase delta; Short=Protein-tyrosine phosphatase delta; Short=R-PTP-delta; EC=3.1.3.48; Flags: Precursor;
CATALYTIC ACTIVITY: Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
SUBUNIT: Interacts with IL1RAPL1 (via extracellular region); interaction is required for IL1RAPL1-mediated synapse formation (By similarity). Interacts with PPFIA1, PPFIA2 and PPFIA3.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
PTM: A cleavage occurs, separating the extracellular domain from the transmembrane segment. This process called 'ectodomain shedding' is thought to be involved in receptor desensitization, signal transduction and/or membrane localization.
SIMILARITY: Belongs to the protein-tyrosine phosphatase family. Receptor class 2A subfamily.
SIMILARITY: Contains 8 fibronectin type-III domains.
SIMILARITY: Contains 3 Ig-like C2-type (immunoglobulin-like) domains.
SIMILARITY: Contains 2 tyrosine-protein phosphatase domains.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PTPRDID41927ch9p23.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PTPRD
CDC HuGE Published Literature: PTPRD
Positive Disease Associations: Arteries , Asthma , Attention deficit hyperactivity disorder and conduct disorder , Body Height , Body Mass Index , Body Weight , Brain , Breath Tests , Cholesterol , Cholesterol, HDL , Cholesterol, LDL , Coronary Disease , Creatinine , Diabetes Mellitus , Diabetes Mellitus, Type 2 , Echocardiography , Electrocardiography , Eosinophils , Epilepsies, Partial , Erythrocyte Count , Forced Expiratory Volume , Glomerular Filtration Rate , Heart Failure , Hematocrit , Hemoglobins , Hip , Insulin , Iron , Leukocyte Count , Lipids , Lipoproteins , Lipoproteins, VLDL , Lymphocytes , Maximal Midexpiratory Flow Rate , monocyte chemoattractant protein 1 (66-77) , Neutrophils , Respiratory Function Tests , Restless Legs Syndrome , smoking cessation , Stroke , Triglycerides , Tunica Media , type 2 diabetes , Vitamin D
Related Studies:
  1. Arteries
    , , . [PubMed 0]
  2. Asthma
    , , . [PubMed 0]
  3. Attention deficit hyperactivity disorder and conduct disorder
    Anney ,et al. 2008, Conduct disorder and ADHD: Evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study, American journal of medical genetics. Part B, Neuropsychiatric genetics 2008 147B- 8 : 1369-78. [PubMed 18951430]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PTPRD
Diseases sorted by gene-association score: restless legs syndrome (11), central nervous system mesenchymal non-meningothelial tumor (6)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 27.50 RPKM in Brain - Cerebellum
Total median expression: 222.14 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 -267.74743-0.360 Picture PostScript Text
3' UTR -926.273628-0.255 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
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003598 - Ig_sub2
IPR000387 - Tyr/Dual-specificity_Pase
IPR016130 - Tyr_Pase_AS
IPR000242 - Tyr_Pase_rcpt/non-rcpt

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00102 - Protein-tyrosine phosphatase
PF07679 - Immunoglobulin I-set domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
49265 - Fibronectin type III
52799 - (Phosphotyrosine protein) phosphatases II

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1X5Z
- NMR MuPIT

2DLH
- NMR MuPIT

2YD6
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2YD7 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P23468
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 orthologNo orthologNo orthologGenome BrowserNo orthologNo ortholog
   Gene Details  
   Gene Sorter  
   FlyBase  
   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:0005102 receptor binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0016791 phosphatase activity
GO:0050839 cell adhesion molecule binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0006796 phosphate-containing compound metabolic process
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007185 transmembrane receptor protein tyrosine phosphatase signaling pathway
GO:0016311 dephosphorylation
GO:0030182 neuron differentiation
GO:0035335 peptidyl-tyrosine dephosphorylation
GO:0050775 positive regulation of dendrite morphogenesis
GO:0051965 positive regulation of synapse assembly
GO:0097105 presynaptic membrane assembly

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AB208869 - Homo sapiens mRNA for protein tyrosine phosphatase, receptor type, D isoform 4 precursor variant protein.
L38929 - Homo sapiens protein tyrosine phosphatase delta mRNA, complete cds.
AB211400 - Homo sapiens PTPRD mRNA for protein tyrosine phosphatase receptor type D, complete cds.
BC106715 - Homo sapiens protein tyrosine phosphatase, receptor type, D, mRNA (cDNA clone MGC:119752 IMAGE:40027584), complete cds.
BC106713 - Homo sapiens protein tyrosine phosphatase, receptor type, D, mRNA (cDNA clone MGC:119750 IMAGE:40027581), complete cds.
BC106714 - Homo sapiens protein tyrosine phosphatase, receptor type, D, mRNA (cDNA clone MGC:119751 IMAGE:40027582), complete cds.
BC106716 - Homo sapiens protein tyrosine phosphatase, receptor type, D, mRNA (cDNA clone MGC:119753 IMAGE:40027585), complete cds.
AK296392 - Homo sapiens cDNA FLJ53604 complete cds, highly similar to Receptor-type tyrosine-protein phosphatase delta precursor (EC 3.1.3.48).
X54133 - Human HPTP delta mRNA for protein tyrosine phosphatase delta.
BC028038 - Homo sapiens, Similar to protein tyrosine phosphatase, receptor type, D, clone IMAGE:5247444, mRNA.
BC037801 - Homo sapiens cDNA clone IMAGE:4796517.
BC045786 - Homo sapiens cDNA clone IMAGE:4795393.
JD142758 - Sequence 123782 from Patent EP1572962.
LC106313 - Homo sapiens PTPRD mRNA for rceptor-type tyrosine-protein phosphatase delta, partial cds.
JD452316 - Sequence 433340 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P23468 (Reactome details) participates in the following event(s):

R-HSA-6797803 PTPRD binds SLITRK1-6
R-HSA-6797810 PTPRD binds IL1RAPL1
R-HSA-6800380 PTPRD binds IL1RAP-1
R-HSA-388824 PTPRF, PTPRS, PTPRD bind Liprins
R-HSA-6798258 PRTPRF, PTPRS, PTPRD bind LRRC4B
R-HSA-8855648 SALM3 binds LAR-RPTP
R-HSA-388844 Receptor-type tyrosine-protein phosphatases
R-HSA-8849932 Synaptic adhesion-like molecules
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: B1ALA0, NM_002839, NP_002830, P23468, PTPRD_HUMAN, Q3KPJ0, Q3KPJ1, Q3KPJ2
UCSC ID: uc003zkk.3
RefSeq Accession: NM_002839
Protein: P23468 (aka PTPRD_HUMAN)
CCDS: CCDS43786.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002839.3
exon count: 46CDS single in 3' UTR: no RNA size: 10127
ORF size: 5739CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 11301.00frame shift in genome: no % Coverage: 99.83
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.