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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 TCGA

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Exon skipping events with PSIs in GTEx

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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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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for PTPRD

check button Gene summary
Gene informationGene symbol

PTPRD

Gene ID

5789

Gene nameprotein tyrosine phosphatase, receptor type D
SynonymsHPTP|HPTPD|HPTPDELTA|PTPD|RPTPDELTA
Cytomap

9p24.1-p23

Type of geneprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase deltaR-PTP-deltaprotein tyrosine phosphatase, receptor type, delta polypeptiderceptor-type tyrosine-protein phosphatase delta
Modification date20180522
UniProtAcc

P23468

ContextPubMed: PTPRD [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

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

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Exon skipping events across known transcript of Ensembl for PTPRD from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx 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

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Gene isoform structures and expression levels for PTPRD

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for PTPRD

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_50255798317703:8317942:8319830:8319966:8331581:83317368319830:8319966ENSG00000153707.11ENST00000381196.4,ENST00000486161.1,ENST00000397611.3,ENST00000537002.1,ENST00000355233.5,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000397617.3,ENST00000540109.1,ENST00000397606.3
exon_skip_50255898319830:8319966:8331581:8331736:8338921:83390478331581:8331736ENSG00000153707.11ENST00000381196.4,ENST00000486161.1,ENST00000397611.3,ENST00000537002.1,ENST00000355233.5,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000397617.3,ENST00000540109.1,ENST00000397606.3
exon_skip_50255998340342:8340469:8341089:8341268:8341692:83419788341089:8341268ENSG00000153707.11ENST00000381196.4,ENST00000486161.1,ENST00000397611.3,ENST00000537002.1,ENST00000355233.5,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000397617.3,ENST00000540109.1,ENST00000397606.3
exon_skip_50256198436591:8436689:8437197:8437239:8449724:84498378437197:8437239ENSG00000153707.11ENST00000397617.3,ENST00000397606.3
exon_skip_50256298449724:8449837:8454579:8454591:8460410:84605688454579:8454591ENSG00000153707.11ENST00000486161.1,ENST00000397611.3
exon_skip_50256398449724:8449837:8454579:8454594:8460410:84605688454579:8454594ENSG00000153707.11ENST00000355233.5
exon_skip_50256498492861:8492979:8497241:8497268:8499646:84998408497241:8497268ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000540109.1
exon_skip_50256598499646:8499840:8500753:8501059:8504260:85044058500753:8501059ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000540109.1
exon_skip_50256698521276:8521546:8523512:8523524:8524924:85250358523512:8523524ENSG00000153707.11ENST00000381196.4,ENST00000486161.1,ENST00000397611.3,ENST00000355233.5,ENST00000356435.5,ENST00000540109.1
exon_skip_50256898524948:8525035:8526626:8526644:8527344:85273538526626:8526644ENSG00000153707.11ENST00000381196.4,ENST00000486161.1,ENST00000355233.5,ENST00000356435.5,ENST00000540109.1
exon_skip_50256998524948:8525035:8526626:8526644:8528590:85287798526626:8526644ENSG00000153707.11ENST00000397611.3
exon_skip_50257098524948:8525035:8527344:8527353:8528590:85287798527344:8527353ENSG00000153707.11ENST00000397606.3
exon_skip_50257198526626:8526644:8527344:8527353:8528590:85287798527344:8527353ENSG00000153707.11ENST00000381196.4,ENST00000486161.1,ENST00000355233.5,ENST00000356435.5,ENST00000540109.1
exon_skip_50257298636698:8636844:8733779:8733946:8857637:88577768733779:8733946ENSG00000153707.11ENST00000481079.1
exon_skip_50257399397448:9397482:9414751:9414823:9574731:95747819414751:9414823ENSG00000153707.11ENST00000463477.1
exon_skip_50257599574731:9574781:9734532:9734571:9766809:97668519734532:9734571ENSG00000153707.11ENST00000381196.4,ENST00000463477.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for PTPRD

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_50255798317703:8317942:8319830:8319966:8331581:83317368319830:8319966ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000355233.5,ENST00000397617.3,ENST00000397611.3,ENST00000537002.1,ENST00000540109.1,ENST00000486161.1,ENST00000397606.3
exon_skip_50255898319830:8319966:8331581:8331736:8338921:83390478331581:8331736ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000355233.5,ENST00000397617.3,ENST00000397611.3,ENST00000537002.1,ENST00000540109.1,ENST00000486161.1,ENST00000397606.3
exon_skip_50255998340342:8340469:8341089:8341268:8341692:83419788341089:8341268ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000355233.5,ENST00000397617.3,ENST00000397611.3,ENST00000537002.1,ENST00000540109.1,ENST00000486161.1,ENST00000397606.3
exon_skip_50256198436591:8436689:8437197:8437239:8449724:84498378437197:8437239ENSG00000153707.11ENST00000397617.3,ENST00000397606.3
exon_skip_50256298449724:8449837:8454579:8454591:8460410:84605688454579:8454591ENSG00000153707.11ENST00000397611.3,ENST00000486161.1
exon_skip_50256398449724:8449837:8454579:8454594:8460410:84605688454579:8454594ENSG00000153707.11ENST00000355233.5
exon_skip_50256498492861:8492979:8497241:8497268:8499646:84998408497241:8497268ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000540109.1
exon_skip_50256598499646:8499840:8500753:8501059:8504260:85044058500753:8501059ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000360074.4,ENST00000358503.5,ENST00000540109.1
exon_skip_50256698521276:8521546:8523512:8523524:8524924:85250358523512:8523524ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000355233.5,ENST00000397611.3,ENST00000540109.1,ENST00000486161.1
exon_skip_50256898524948:8525035:8526626:8526644:8527344:85273538526626:8526644ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000355233.5,ENST00000540109.1,ENST00000486161.1
exon_skip_50256998524948:8525035:8526626:8526644:8528590:85287798526626:8526644ENSG00000153707.11ENST00000397611.3
exon_skip_50257098524948:8525035:8527344:8527353:8528590:85287798527344:8527353ENSG00000153707.11ENST00000397606.3
exon_skip_50257198526626:8526644:8527344:8527353:8528590:85287798527344:8527353ENSG00000153707.11ENST00000381196.4,ENST00000356435.5,ENST00000355233.5,ENST00000540109.1,ENST00000486161.1
exon_skip_50257298636698:8636844:8733779:8733946:8857637:88577768733779:8733946ENSG00000153707.11ENST00000481079.1
exon_skip_50257399397448:9397482:9414751:9414823:9574731:95747819414751:9414823ENSG00000153707.11ENST00000463477.1
exon_skip_50257599574731:9574781:9734532:9734571:9766809:97668519734532:9734571ENSG00000153707.11ENST00000381196.4,ENST00000463477.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF

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

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

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

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

check button Lost protein functional features of individual exon skipping events in TCGA.
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


check button Lost protein functional features of individual exon skipping events in GTEx.
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


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SNVs in the skipped exons for PTPRD

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.
PTPRD_THCA_exon_skip_502562_psi_boxplot.png
boxplot
PTPRD_THCA_exon_skip_502563_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SKCMTCGA-3N-A9WD-06exon_skip_502558
8331582833173683317068331706Nonsense_MutationGAp.Q1804*
SKCMTCGA-D3-A5GN-06exon_skip_502558
8331582833173683317068331706Nonsense_MutationGAp.Q1394X
SKCMTCGA-D3-A5GN-06exon_skip_502558
8331582833173683317068331706Nonsense_MutationGAp.Q1804*
SKCMTCGA-EE-A2A2-06exon_skip_502558
8331582833173683317068331706Nonsense_MutationGAp.Q1394X
SKCMTCGA-EE-A2A2-06exon_skip_502558
8331582833173683317068331706Nonsense_MutationGAp.Q1804*
HNSCTCGA-F7-A624-01exon_skip_502558
8331582833173683317128331712Nonsense_MutationGAp.Q1802*
SKCMTCGA-BF-AAOX-01exon_skip_502565
8500754850105985007698500769Nonsense_MutationGAp.R705*
BRCATCGA-E2-A15A-01exon_skip_502565
8500754850105985009018500901Nonsense_MutationCAp.E661*
BRCATCGA-E2-A15A-06exon_skip_502565
8500754850105985009018500901Nonsense_MutationCAp.E661*
THCATCGA-ET-A3BT-01exon_skip_502562
8454580845459184545798454579Splice_SiteCA.
THCATCGA-ET-A3BT-01exon_skip_502563
8454580845459484545798454579Splice_SiteCA.
LUSCTCGA-33-4566-01exon_skip_502564
8497242849726884972418497241Splice_SiteCAp.H783_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
PTPRD_8449724_8449837_8454579_8454594_8460410_8460568_TCGA-ET-A3BT-01Sample: TCGA-ET-A3BT-01
Cancer type: THCA
ESID: exon_skip_502563
Skipped exon start: 8454580
Skipped exon end: 8454594
Mutation start: 8454579
Mutation end: 8454579
Mutation type: Splice_Site
Reference seq: C
Mutation seq: A
AAchange: .
PTPRD_8449724_8449837_8454579_8454594_8460410_8460568_TCGA-ET-A3BT-01Sample: TCGA-ET-A3BT-01
Cancer type: THCA
ESID: exon_skip_502562
Skipped exon start: 8454580
Skipped exon end: 8454591
Mutation start: 8454579
Mutation end: 8454579
Mutation type: Splice_Site
Reference seq: C
Mutation seq: A
AAchange: .
exon_skip_502562_THCA_TCGA-ET-A3BT-01.png
boxplot
exon_skip_502563_THCA_TCGA-ET-A3BT-01.png
boxplot
PTPRD_8449724_8449837_8454579_8454591_8460410_8460568_TCGA-ET-A3BT-01Sample: TCGA-ET-A3BT-01
Cancer type: THCA
ESID: exon_skip_502563
Skipped exon start: 8454580
Skipped exon end: 8454594
Mutation start: 8454579
Mutation end: 8454579
Mutation type: Splice_Site
Reference seq: C
Mutation seq: A
AAchange: .
PTPRD_8449724_8449837_8454579_8454591_8460410_8460568_TCGA-ET-A3BT-01Sample: TCGA-ET-A3BT-01
Cancer type: THCA
ESID: exon_skip_502562
Skipped exon start: 8454580
Skipped exon end: 8454591
Mutation start: 8454579
Mutation end: 8454579
Mutation type: Splice_Site
Reference seq: C
Mutation seq: A
AAchange: .
exon_skip_502562_THCA_TCGA-ET-A3BT-01.png
boxplot
exon_skip_502563_THCA_TCGA-ET-A3BT-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HEC108_ENDOMETRIUM8319831831996683198708319870Missense_MutationTAp.K1877N
AGS_STOMACH8319831831996683198908319890Missense_MutationCGp.D1871H
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE8319831831996683199268319926Missense_MutationTCp.I1859V
HEC59_ENDOMETRIUM8319831831996683199408319940Missense_MutationAGp.F1854S
BIN67_OVARY8319831831996683199628319962Missense_MutationCTp.G1847S
SW684_SOFT_TISSUE8331582833173683316228331622Missense_MutationCTp.E1832K
HCC1428_BREAST8331582833173683316498331649Missense_MutationATp.F1823I
PECAPJ49_UPPER_AERODIGESTIVE_TRACT8331582833173683316558331655Missense_MutationTCp.I1821V
HCC33_LUNG8331582833173683317138331713Missense_MutationCAp.R1801S
HCC1419_BREAST8331582833173683317138331713Missense_MutationCAp.R1801S
SW684_SOFT_TISSUE8331582833173683317268331726Missense_MutationGAp.S1797F
EOL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE8341090834126883411488341148Missense_MutationGTp.P1690T
SNUC5_LARGE_INTESTINE8341090834126883411488341148Missense_MutationGAp.P1690S
SNU407_LARGE_INTESTINE8341090834126883411548341154Missense_MutationGTp.L1688M
NCIH1623_LUNG8341090834126883412288341228Missense_MutationCAp.S1663I
NCIH322_LUNG8341090834126883412458341245Missense_MutationGCp.H1657Q
CORL23_LUNG8497242849726884972598497259Missense_MutationCGp.D778H
BICR18_UPPER_AERODIGESTIVE_TRACT8500754850105985007638500763Missense_MutationTCp.N707D
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE8500754850105985007638500763Missense_MutationTCp.N707D
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE8500754850105985007638500763Missense_MutationTCp.N707D
MM426_SKIN8500754850105985007688500768Missense_MutationCTp.R705Q
L82_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE8500754850105985008178500817Missense_MutationCAp.A689S
NCIH1155_LUNG8500754850105985008258500825Missense_MutationGAp.T686I
OSC19_UPPER_AERODIGESTIVE_TRACT8500754850105985008268500826Missense_MutationTCp.T686A
MM386_SKIN8500754850105985008918500891Missense_MutationCTp.G664E
COLO792_SKIN8500754850105985009018500901Missense_MutationCTp.E661K
BICR18_UPPER_AERODIGESTIVE_TRACT8500754850105985009348500935Missense_MutationTGCAp.T650A
BICR18_UPPER_AERODIGESTIVE_TRACT8500754850105985009438500943Missense_MutationTGp.I647L
HCC202_BREAST8500754850105985009688500968Missense_MutationCGp.Q638H
HCT15_LARGE_INTESTINE8500754850105985010148501014Missense_MutationGAp.S623F
MEWO_SKIN8526627852664485266298526629Missense_MutationCTp.R189K
SARC9371_BONE8526627852664485266358526635Missense_MutationGAp.P187L
MFE319_ENDOMETRIUM8319831831996683198998319899Nonsense_MutationCAp.G1868*
JHUEM7_ENDOMETRIUM8500754850105985007698500769Nonsense_MutationGAp.R705*
RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE8523513852352485235198523519Nonsense_MutationGAp.R229*
SNU349_KIDNEY8319831831996683199658319965Splice_SiteCAp.A1846S
HEC108_ENDOMETRIUM8341090834126883410918341091Splice_SiteTCp.R1709G
SNU1040_LARGE_INTESTINE8341090834126883412688341268Splice_SiteGAp.R1650C

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

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPRD


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPRD


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RelatedDrugs for PTPRD

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

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RelatedDiseases for PTPRD

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
PTPRDC0009404Colorectal Neoplasms2CTD_human
PTPRDC0023893Liver Cirrhosis, Experimental1CTD_human
PTPRDC0035258Restless Legs Syndrome1CTD_human
PTPRDC1263846Attention deficit hyperactivity disorder1CTD_human
PTPRDC1458155Mammary Neoplasms1CTD_human