Human Gene PTPRD (uc003zkt.1) 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 chr9:8,528,152-10,612,723 Size: 2,084,572 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr9:8,528,425-8,733,843 Size: 205,419 Coding Exon Count: 5 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:8,528,152-10,612,723)mRNA (may differ from genome)Protein (202 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsHGNC
LynxMGIPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: C9J8S8_HUMAN
DESCRIPTION: SubName: Full=Receptor-type tyrosine-protein phosphatase delta;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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 -291.54815-0.358 Picture PostScript Text
3' UTR -48.79273-0.179 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003598 - Ig_sub2

Pfam Domains:
PF07679 - Immunoglobulin I-set domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on C9J8S8
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  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.
BC028038 - Homo sapiens, Similar to protein tyrosine phosphatase, receptor type, D, clone IMAGE:5247444, mRNA.
JD452316 - Sequence 433340 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC028038, C9J8S8, C9J8S8_HUMAN
UCSC ID: uc003zkt.1
RefSeq Accession: NM_002839
Protein: C9J8S8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC028038.1
exon count: 17CDS single in 3' UTR: no RNA size: 1815
ORF size: 609CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 1186.00frame shift in genome: no % Coverage: 93.50
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.