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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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3'-UTR located exon skipping events lost miRNA binding sites

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for PTPRS

check button Gene summary
Gene informationGene symbol

PTPRS

Gene ID

5802

Gene nameprotein tyrosine phosphatase receptor type S
SynonymsPTPSIGMA|R-PTP-S|R-PTP-sigma
Cytomap

19p13.3

Type of geneprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase Sprotein tyrosine phosphatase PTPsigmareceptor-type tyrosine-protein phosphatase sigma
Modification date20200322
UniProtAcc

A0A0A0MR60,

A8E4L7,

D6W632,

D6W633,

G8JL96,

K7ERX4,

K7ESP0,

L8E8Y3,

L8EAN4,

Q13332,

Q8NHS7,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
PTPRS

GO:0006470

protein dephosphorylation

8524829

PTPRS

GO:0099560

synaptic membrane adhesion

23345436


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Gene structures and expression levels for PTPRS

check buttonSkipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

ENSG00000105426
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
PCCDOWNENST00000353284.7PTPRS-202:protein_coding:PTPRS2.466541e+02-8.001532e-015.527735e-041.760728e-02
PGUPENST00000588012.5PTPRS-205:protein_coding:PTPRS2.200098e+021.137139e+009.760048e-052.696370e-03
TCUPENST00000588012.5PTPRS-205:protein_coding:PTPRS1.514802e+028.066275e-016.966467e-051.213165e-03

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PTPRS

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_101594chr195215498:5215595:5216720:5216767:5218420:52185325216720:5216767
exon_skip_117017chr195222123:5222220:5222689:5223297:5225727:52258445222689:5223297
exon_skip_124991chr195215505:5215595:5216720:5216767:5218420:52185325216720:5216767
exon_skip_143036chr195208237:5208391:5210469:5210594:5210679:52108055210469:5210594
exon_skip_155468chr195215367:5215412:5215498:5215595:5218420:52185325215498:5215595
exon_skip_156141chr195229491:5229684:5231310:5231615:5238919:52390635231310:5231615
exon_skip_180289chr195218420:5218532:5218787:5218798:5219310:52194055218787:5218798
exon_skip_205442chr195225727:5225844:5229491:5229684:5231310:52314245229491:5229684
exon_skip_215183chr195225727:5225844:5229316:5229342:5229491:52296845229316:5229342
exon_skip_222378chr195225727:5225844:5229316:5229342:5229491:52295215229316:5229342
exon_skip_236960chr195260805:5260822:5262964:5262972:5265008:52651965262964:5262972
exon_skip_242514chr195229316:5229342:5229491:5229684:5231310:52314245229491:5229684
exon_skip_262622chr195218787:5218798:5219310:5219467:5219939:52200165219310:5219467
exon_skip_267151chr195243901:5244482:5245776:5246045:5258017:52581275245776:5246045
exon_skip_279208chr195265008:5265196:5273442:5273583:5274199:52743445273442:5273583
exon_skip_296278chr195207922:5208057:5208237:5208391:5210469:52105945208237:5208391
exon_skip_33281chr195206774:5206842:5207922:5208057:5208237:52083915207922:5208057
exon_skip_3471chr195218420:5218532:5218787:5218798:5219310:52194675218787:5218798
exon_skip_35412chr195229316:5229342:5229491:5229684:5231310:52316155229491:5229684
exon_skip_48866chr195240199:5240332:5243901:5244482:5245776:52460455243901:5244482
exon_skip_88905chr195245776:5246045:5256108:5256119:5258017:52581275256108:5256119

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
psi tcga
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value
exon_skip_101594MSBB_PG2.956391e-011.907273e-011.049118e-016.621448e-07
exon_skip_215183Mayo_TC3.436250e-014.882258e-01-1.446008e-012.687869e-06


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Open reading frame (ORF) annotation in the exon skipping event for PTPRS

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000058730352079225208057Frame-shift
ENST0000058730352294915229684Frame-shift
ENST0000058730352734425273583Frame-shift
ENST0000058730352104695210594In-frame
ENST0000058730352167205216767In-frame
ENST0000058730352187875218798In-frame
ENST0000058730352293165229342In-frame
ENST0000058730352313105231615In-frame
ENST0000058730352439015244482In-frame
ENST0000058730352561085256119In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000058730352167205216767In-frame
ENST0000058730352187875218798In-frame
ENST0000058730352226895223297In-frame
ENST0000058730352293165229342In-frame
ENST0000058730352561085256119In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000058730352082375208391Frame-shift
ENST0000058730352193105219467Frame-shift
ENST0000058730352294915229684Frame-shift
ENST0000058730352734425273583Frame-shift
ENST0000058730352167205216767In-frame
ENST0000058730352187875218798In-frame
ENST0000058730352293165229342In-frame
ENST0000058730352561085256119In-frame
ENST0000058730352629645262972In-frame

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Infer the effects of exon skipping event on protein functional features for PTPRS

p-ENSG00000105426_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000587303637019485243901524448210891669329523
ENST00000587303637019485231310523161519502254616718
ENST0000058730363701948521672052167674149419513491365
ENST0000058730363701948521046952105945462558617871828

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000005873036370194852226895223297259532028311034
ENST0000058730363701948521672052167674149419513491365

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000058730363701948521672052167674149419513491365

check button Lost protein functional features of individual exon skipping events in ROSMAP.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q13332329523339343Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523348351Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523361370Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523377382Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523384389Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523397405Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523410413Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523417420Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523431441Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523443448Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523457466Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523475479Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523482488Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523496507Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523516524Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q13332329523334424DomainNote=Fibronectin type-III 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q13332329523429523DomainNote=Fibronectin type-III 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q13332329523472474HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4PBX
Q13332329523428429Sequence conflictNote=SA->RP;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q13332329523301282Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q133326167186171034Alternative sequenceID=VSP_050023;Note=In isoform PTPS-F4-7 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q13332616718301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q13332616718641644Compositional biasNote=Poly-Pro
Q13332616718527616DomainNote=Fibronectin type-III 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q13332616718621718DomainNote=Fibronectin type-III 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q13332616718301282Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q133321349136513501365Alternative sequenceID=VSP_050026;Note=In isoform PTPS-MEB%2C isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8992885;Dbxref=PMID:15489334,PMID:8992885
Q1333213491365301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q133321349136513041948Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q133321787182817961798Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7
Q133321787182818001802Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7
Q133321787182818051814Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7
Q133321787182818161827Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7
Q1333217871828301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q133321787182816801939DomainNote=Tyrosine-protein phosphatase 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q133321787182813041948Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q133321787182818281830TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2FH7

check button Lost protein functional features of individual exon skipping events in MSBB.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q1333283110346171034Alternative sequenceID=VSP_050023;Note=In isoform PTPS-F4-7 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
Q133328311034301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q133328311034723831DomainNote=Fibronectin type-III 5;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q133328311034832930DomainNote=Fibronectin type-III 6;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q1333283110349311033DomainNote=Fibronectin type-III 7;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00316
Q133328311034940940GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q133328311034996996Natural variantID=VAR_035649;Note=In a colorectal cancer sample%3B somatic mutation. T->M;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=dbSNP:rs775778266,PMID:16959974
Q133328311034910910Sequence conflictNote=R->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q133328311034995995Sequence conflictNote=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q133328311034301282Topological domainNote=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q133321349136513501365Alternative sequenceID=VSP_050026;Note=In isoform PTPS-MEB%2C isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8992885;Dbxref=PMID:15489334,PMID:8992885
Q1333213491365301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q133321349136513041948Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255

check button Lost protein functional features of individual exon skipping events in Mayo.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q133321349136513501365Alternative sequenceID=VSP_050026;Note=In isoform PTPS-MEB%2C isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8992885;Dbxref=PMID:15489334,PMID:8992885
Q1333213491365301948ChainID=PRO_0000025462;Note=Receptor-type tyrosine-protein phosphatase S
Q133321349136513041948Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255


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3'-UTR located exon skipping events that lost miRNA binding sites in PTPRS

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda

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SNVs in the skipped exons for PTPRS

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for PTPRS

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPRS

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for PTPRS

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
DLPFCRBFOX2exon_skip_101594-6.891958e-014.266881e-48
HCCHNRNPFexon_skip_215183-4.246304e-014.220527e-12
HCCRBM6exon_skip_88905-4.687485e-014.802952e-16
IFGRBFOX2exon_skip_101594-6.897886e-014.888553e-05
PCCRBFOX2exon_skip_101594-5.768743e-015.023076e-20
PCCHNRNPFexon_skip_1015945.141488e-011.444070e-15
PGRBFOX2exon_skip_101594-6.739776e-012.991903e-26
PGPCBP1exon_skip_101594-4.772294e-014.384872e-12
PGILF2exon_skip_101594-4.817569e-012.572229e-12
PGHNRNPKexon_skip_101594-4.786278e-013.721976e-12
PGSRSF9exon_skip_101594-4.056868e-017.663841e-09
TCRBFOX2exon_skip_101594-7.536655e-013.106391e-30
TCHNRNPH2exon_skip_2151835.036711e-011.667034e-10
TCHNRNPFexon_skip_215183-4.405113e-014.109678e-08

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RelatedDrugs for PTPRS

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
Q13332approvedDB00630Alendronic acidsmall moleculeQ13332
Q13332approvedDB01077Etidronic acidsmall moleculeQ13332

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RelatedDiseases for PTPRS

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource