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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 PTPN12

check button Gene summary
Gene informationGene symbol

PTPN12

Gene ID

5782

Gene nameprotein tyrosine phosphatase non-receptor type 12
SynonymsPTP-PEST|PTPG1
Cytomap

7q11.23

Type of geneprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 12protein-tyrosine phosphatase G1
Modification date20200329
UniProtAcc

C9J1X8,

C9JJC1,

C9JYA4,

F8WB51,

H0YB59,

H0YC15,

H3BM04,

Q05209,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
PTPN12

GO:0006470

protein dephosphorylation

27134172

PTPN12

GO:0035335

peptidyl-tyrosine dephosphorylation

27134172


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Gene structures and expression levels for PTPN12

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

ENSG00000127947
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
CBUPENST00000519553.1PTPN12-213:retained_intron:PTPN121.997862e+001.104129e+001.087366e-047.948976e-04
CBUPENST00000407343.3PTPN12-202:protein_coding:PTPN121.040179e+011.048833e+001.688363e-041.153248e-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 PTPN12

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_108325chr777571153:77571186:77581427:77581503:77585543:7758557177581427:77581503
exon_skip_109776chr777571153:77571186:77583555:77583650:77585543:7758557177583555:77583650
exon_skip_128406chr777581427:77581503:77583555:77583650:77585543:7758557177583555:77583650
exon_skip_136764chr777571153:77571186:77581427:77581503:77583555:7758364977581427:77581503
exon_skip_139053chr777632348:77632425:77635782:77635849:77637018:7763704877635782:77635849
exon_skip_152872chr777592185:77592256:77597842:77597901:77600664:7760072877597842:77597901
exon_skip_184588chr777571153:77571186:77581427:77581503:77583555:7758359577581427:77581503
exon_skip_189162chr777583555:77583650:77585543:77585581:77592185:7759225677585543:77585581
exon_skip_194335chr777618480:77618565:77626705:77627675:77632348:7763242577626705:77627675
exon_skip_195079chr777600664:77600806:77607235:77607301:77610765:7761080277607235:77607301
exon_skip_197178chr777627156:77627675:77632348:77632425:77635782:7763584977632348:77632425
exon_skip_207891chr777637018:77637048:77638624:77638731:77639219:7763928077638624:77638731
exon_skip_214111chr777537554:77537645:77571078:77571186:77581427:7758146577571078:77571186
exon_skip_233454chr777585546:77585581:77592185:77592256:77597842:7759790177592185:77592256
exon_skip_248469chr777600664:77600806:77604879:77604935:77607235:7760730177604879:77604935
exon_skip_256732chr777537554:77537645:77563936:77564195:77571078:7757110977563936:77564195
exon_skip_263834chr777581427:77581503:77583555:77583650:77585543:7758558177583555:77583650
exon_skip_268637chr777635782:77635849:77637018:77637048:77638624:7763870877637018:77637048
exon_skip_50398chr777571153:77571186:77581427:77581503:77583555:7758365077581427:77581503
exon_skip_5122chr777600781:77600806:77604879:77604935:77607235:7760730177604879:77604935
exon_skip_59084chr777610948:77611046:77618480:77618565:77626705:7762767577618480:77618565
exon_skip_85417chr777537554:77537645:77563936:77564195:77571078:7757118677563936:77564195
exon_skip_87283chr777583574:77583650:77585543:77585581:77592185:7759225677585543:77585581
exon_skip_88758chr777597842:77597901:77600664:77600806:77607235:7760730177600664:77600806

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value


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Open reading frame (ORF) annotation in the exon skipping event for PTPN12

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
ENST000002485947758142777581503Frame-shift
ENST000002485947760066477600806Frame-shift
ENST000002485947760723577607301Frame-shift
ENST000002485947761848077618565Frame-shift
ENST000002485947763578277635849Frame-shift
ENST000002485947763701877637048Frame-shift
ENST000002485947758355577583650In-frame
ENST000002485947758554377585581In-frame
ENST000002485947759218577592256In-frame
ENST000002485947759784277597901In-frame
ENST000002485947763234877632425In-frame
ENST000002485947763862477638731In-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
ENST000002485947760066477600806Frame-shift
ENST000002485947760723577607301Frame-shift
ENST000002485947763701877637048Frame-shift
ENST000002485947758355577583650In-frame
ENST000002485947759784277597901In-frame
ENST000002485947763234877632425In-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
ENST000002485947758142777581503Frame-shift
ENST000002485947760066477600806Frame-shift
ENST000002485947760723577607301Frame-shift
ENST000002485947761848077618565Frame-shift
ENST000002485947762670577627675Frame-shift
ENST000002485947763578277635849Frame-shift
ENST000002485947763701877637048Frame-shift
ENST000002485947758355577583650In-frame
ENST000002485947758554377585581In-frame
ENST000002485947759218577592256In-frame
ENST000002485947759784277597901In-frame
ENST000002485947763234877632425In-frame
ENST000002485947763862477638731In-frame

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Infer the effects of exon skipping event on protein functional features for PTPN12

p-ENSG00000127947_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
ENST000002485943423780775835557758365055965395127
ENST0000024859434237807758554377585581655692127140
ENST0000024859434237807759218577592256694764140164
ENST0000024859434237807759784277597901766824164184
ENST000002485943423780776323487763242522702346666691
ENST000002485943423780776386247763873124472553725760

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
ENST000002485943423780775835557758365055965395127
ENST0000024859434237807759784277597901766824164184
ENST000002485943423780776323487763242522702346666691

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
ENST000002485943423780775835557758365055965395127
ENST0000024859434237807758554377585581655692127140
ENST0000024859434237807759218577592256694764140164
ENST0000024859434237807759784277597901766824164184
ENST000002485943423780776323487763242522702346666691
ENST000002485943423780776386247763873124472553725760

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
Q05209951271130Alternative sequenceID=VSP_046274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q05209951271119Alternative sequenceID=VSP_054168;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127102106Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209951271780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q052099512728293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q0520995127114123HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q0520995127121121Sequence conflictNote=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127121121Sequence conflictNote=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127111113TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091271401130Alternative sequenceID=VSP_046274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q05209127140128131Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209127140135137Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091271401780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520912714028293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q05209140164155157Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209140164160170Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091401641780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520914016428293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q05209164184160170Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209164184173182Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091641841780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520916418428293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q052096666911780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q05209666691673673Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163,E
Q05209666691689689Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18220336,ECO:0000244|PubMed:18669648;Dbxref=PMID:18220336,PMID:18669648
Q052097257601780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12

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
Q05209951271130Alternative sequenceID=VSP_046274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q05209951271119Alternative sequenceID=VSP_054168;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127102106Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209951271780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q052099512728293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q0520995127114123HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q0520995127121121Sequence conflictNote=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127121121Sequence conflictNote=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127111113TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209164184160170Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209164184173182Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091641841780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520916418428293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q052096666911780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q05209666691673673Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163,E
Q05209666691689689Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18220336,ECO:0000244|PubMed:18669648;Dbxref=PMID:18220336,PMID:18669648

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
Q05209951271130Alternative sequenceID=VSP_046274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q05209951271119Alternative sequenceID=VSP_054168;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127102106Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209951271780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q052099512728293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q0520995127114123HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q0520995127121121Sequence conflictNote=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127121121Sequence conflictNote=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q0520995127111113TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091271401130Alternative sequenceID=VSP_046274;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q05209127140128131Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209127140135137Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091271401780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520912714028293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q05209140164155157Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209140164160170Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091401641780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520914016428293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q05209164184160170Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q05209164184173182Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5HDE
Q052091641841780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q0520916418428293DomainNote=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160
Q052096666911780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12
Q05209666691673673Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163,E
Q05209666691689689Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18220336,ECO:0000244|PubMed:18669648;Dbxref=PMID:18220336,PMID:18669648
Q052097257601780ChainID=PRO_0000094771;Note=Tyrosine-protein phosphatase non-receptor type 12


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3'-UTR located exon skipping events that lost miRNA binding sites in PTPN12

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 PTPN12

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 PTPN12

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 PTPN12

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 PTPN12

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value

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RelatedDrugs for PTPN12

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

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RelatedDiseases for PTPN12

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