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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for PTPRD |
 Gene summary |
| Gene information | Gene symbol | PTPRD | Gene ID | 5789 |
| Gene name | protein tyrosine phosphatase receptor type D | |
| Synonyms | HPTP|HPTPD|HPTPDELTA|PTPD|R-PTP-delta|RPTPDELTA | |
| Cytomap | 9p24.1-p23 | |
| Type of gene | protein-coding | |
| Description | receptor-type tyrosine-protein phosphatase deltaprotein tyrosine phosphatase, receptor type, delta polypeptiderceptor-type tyrosine-protein phosphatase delta | |
| Modification date | 20200320 | |
| UniProtAcc | A0A1B0GU15, | |
| Context | - 28322283(Susceptibility to neurofibrillary tangles: role of the PTPRD locus and limited pleiotropy with other neuropathologies) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PTPRD | GO:0099545 | trans-synaptic signaling by trans-synaptic complex | 21926414 |
| PTPRD | GO:0099560 | synaptic membrane adhesion | 23345436 |
| PTPRD | GO:1905606 | regulation of presynapse assembly | 21926414 |
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Gene structures and expression levels for PTPRD |
| Skipped 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. |
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ENSG00000153707
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | DOWN | ENST00000429581.2 | PTPRD-AS2-201:lncRNA:PTPRD | 7.109576e+00 | -9.243185e-01 | 5.340005e-11 | 4.139231e-08 |
| PG | DOWN | ENST00000486161.5 | PTPRD-211:protein_coding:PTPRD | 1.459464e+02 | -1.526843e+00 | 4.244049e-03 | 4.074282e-02 |
| PG | UP | ENST00000356435.9 | PTPRD-202:protein_coding:PTPRD | 4.279050e+00 | 5.292461e+00 | 5.660348e-03 | 4.979620e-02 |
| CB | UP | ENST00000356435.9 | PTPRD-202:protein_coding:PTPRD | 1.160212e+03 | 8.303866e-01 | 2.236541e-05 | 2.080356e-04 |
| CB | DOWN | ENST00000397617.7 | PTPRD-206:protein_coding:PTPRD | 3.219438e+02 | -1.789638e+00 | 7.415975e-04 | 4.018225e-03 |
| TC | UP | ENST00000397606.7 | PTPRD-204:protein_coding:PTPRD | 1.615148e+01 | 9.753413e-01 | 1.329074e-04 | 2.026600e-03 |
| TC | DOWN | ENST00000397611.7 | PTPRD-205:protein_coding:PTPRD | 6.666637e+02 | -9.488981e-01 | 1.326455e-03 | 1.225152e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PTPRD |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_101746 | chr9 | 8526627:8526644:8527345:8527353:8528591:8528695 | 8527345:8527353 |
| exon_skip_103849 | chr9 | 8524925:8525035:8527345:8527353:8528591:8528776 | 8527345:8527353 |
| exon_skip_120149 | chr9 | 8340343:8340469:8341090:8341268:8341693:8341978 | 8341090:8341268 |
| exon_skip_132351 | chr9 | 8524949:8525035:8526627:8526644:8528591:8528776 | 8526627:8526644 |
| exon_skip_132864 | chr9 | 8521277:8521546:8523513:8523524:8524925:8525035 | 8523513:8523524 |
| exon_skip_141062 | chr9 | 8528591:8528779:8633317:8633458:8636699:8636844 | 8633317:8633458 |
| exon_skip_148453 | chr9 | 8317704:8317942:8319831:8319966:8331582:8331736 | 8319831:8319966 |
| exon_skip_150533 | chr9 | 8524949:8525035:8527345:8527353:8528591:8528779 | 8527345:8527353 |
| exon_skip_16566 | chr9 | 8733780:8733946:9018697:9018735:9183304:9183363 | 9018697:9018735 |
| exon_skip_169693 | chr9 | 8524925:8525035:8526627:8526644:8527345:8527353 | 8526627:8526644 |
| exon_skip_172609 | chr9 | 8404537:8404660:8436592:8436689:8449725:8449837 | 8436592:8436689 |
| exon_skip_184750 | chr9 | 8449725:8449837:8454580:8454594:8460411:8460568 | 8454580:8454594 |
| exon_skip_186837 | chr9 | 8504261:8504405:8507301:8507434:8517848:8518429 | 8507301:8507434 |
| exon_skip_190421 | chr9 | 8376607:8376726:8389232:8389407:8404537:8404660 | 8389232:8389407 |
| exon_skip_194975 | chr9 | 9574732:9574781:9734533:9734571:9766810:9766851 | 9734533:9734571 |
| exon_skip_20602 | chr9 | 8524949:8525035:8526627:8526644:8527345:8527353 | 8526627:8526644 |
| exon_skip_208629 | chr9 | 8526627:8526644:8527345:8527353:8528591:8528776 | 8527345:8527353 |
| exon_skip_209020 | chr9 | 8436647:8436689:8437198:8437239:8449725:8449837 | 8437198:8437239 |
| exon_skip_215562 | chr9 | 8524949:8525035:8527345:8527353:8528591:8528695 | 8527345:8527353 |
| exon_skip_219134 | chr9 | 8436647:8436689:8438701:8438820:8449725:8449833 | 8438701:8438820 |
| exon_skip_23212 | chr9 | 8499647:8499840:8500754:8501059:8504261:8504405 | 8500754:8501059 |
| exon_skip_233535 | chr9 | 9397449:9397482:9574732:9574781:9734533:9734571 | 9574732:9574781 |
| exon_skip_23449 | chr9 | 9397449:9397482:9414752:9414823:9574732:9574781 | 9414752:9414823 |
| exon_skip_250214 | chr9 | 8524949:8525035:8526627:8526644:8528591:8528779 | 8526627:8526644 |
| exon_skip_252427 | chr9 | 8436647:8436689:8437198:8437239:8449725:8449813 | 8437198:8437239 |
| exon_skip_2810 | chr9 | 8449725:8449837:8454580:8454591:8460411:8460568 | 8454580:8454591 |
| exon_skip_290526 | chr9 | 8436647:8436689:8438701:8438820:8449725:8449837 | 8438701:8438820 |
| exon_skip_3138 | chr9 | 8492862:8492979:8497242:8497268:8499647:8499840 | 8497242:8497268 |
| exon_skip_43111 | chr9 | 8319831:8319966:8331582:8331736:8338922:8339047 | 8331582:8331736 |
| exon_skip_43794 | chr9 | 8492866:8492979:8497242:8497268:8499647:8499840 | 8497242:8497268 |
| exon_skip_44758 | chr9 | 8317704:8317942:8319831:8319966:8331582:8331727 | 8319831:8319966 |
| exon_skip_45611 | chr9 | 8526627:8526644:8527345:8527353:8528591:8528779 | 8527345:8527353 |
| exon_skip_51868 | chr9 | 8436647:8436689:8438701:8438820:8449725:8449813 | 8438701:8438820 |
| exon_skip_54374 | chr9 | 9183304:9183363:9397449:9397482:9574732:9574781 | 9397449:9397482 |
| exon_skip_62408 | chr9 | 8436647:8436689:8437198:8437239:8449725:8449833 | 8437198:8437239 |
| exon_skip_81011 | chr9 | 8524949:8525035:8526627:8526644:8528591:8528695 | 8526627:8526644 |
| exon_skip_93459 | chr9 | 8389232:8389407:8404537:8404660:8436592:8436689 | 8404537:8404660 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_209020 | MSBB_STG | 4.294203e-01 | 3.220833e-01 | 1.073370e-01 | 1.476973e-02 |
| exon_skip_62408 | MSBB_PG | 5.032667e-01 | 3.417544e-01 | 1.615123e-01 | 8.195645e-08 |
| exon_skip_2810 | MSBB_PG | 2.357047e-01 | 3.689286e-01 | -1.332239e-01 | 4.062514e-07 |
| exon_skip_132864 | MSBB_PG | 3.938281e-01 | 5.822000e-01 | -1.883719e-01 | 6.552120e-05 |
| exon_skip_20602 | MSBB_PG | 3.816964e-01 | 6.061224e-01 | -2.244260e-01 | 2.733921e-02 |
| exon_skip_150533 | MSBB_PG | 5.579130e-01 | 4.538636e-01 | 1.040494e-01 | 1.505120e-02 |
| exon_skip_252427 | Mayo_TC | 7.012195e-01 | 5.648000e-01 | 1.364195e-01 | 7.921217e-04 |
| exon_skip_132864 | Mayo_TC | 2.369512e-01 | 3.894203e-01 | -1.524691e-01 | 1.274152e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for PTPRD |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
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Infer the effects of exon skipping event on protein functional features for PTPRD |
p-ENSG00000153707_img4.png |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| 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 feature | Description of feature |
| 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 feature | Description of feature |
| 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 feature | Description of feature |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTPRD |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for PTPRD |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for PTPRD |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
| ADstage | MSBB | IFG | exon_skip_209020 | 4.134581e-01 | 2.874344e-02 | chr9 | - | 8436647 | 8436689 | 8437198 | 8437239 | 8449725 | 8449837 |
| CDR | MSBB | STG | exon_skip_209020 | 3.485833e-01 | 6.165760e-04 | chr9 | - | 8436647 | 8436689 | 8437198 | 8437239 | 8449725 | 8449837 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPRD |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_23212 | rs16928124 | chr9:8557264 | 9.393773e-08 | 1.896293e-05 |
| HCC | exon_skip_3138 | rs16928124 | chr9:8557264 | 1.297452e-04 | 1.139182e-02 |
| HCC | exon_skip_250214 | rs16928124 | chr9:8557264 | 5.815300e-04 | 3.815697e-02 |
| PCC | exon_skip_20602 | rs13294631 | chr9:8562080 | 1.695978e-04 | 2.614333e-02 |
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Correlation with RNA binding proteins (RBPs) for PTPRD |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | UNK | exon_skip_23212 | -4.307929e-01 | 3.467363e-07 |
| CB | RBM45 | exon_skip_23212 | -4.714767e-01 | 1.704334e-08 |
| CB | NUP42 | exon_skip_23212 | -5.559283e-01 | 7.971585e-12 |
| CB | RALYL | exon_skip_23212 | -4.616670e-01 | 3.654382e-08 |
| HCC | MSI1 | exon_skip_23212 | 4.913371e-01 | 8.826599e-17 |
| HCC | SAMD4A | exon_skip_23212 | 4.250007e-01 | 1.613805e-12 |
| HCC | SRSF1 | exon_skip_250214 | -4.277378e-01 | 6.701485e-13 |
| IFG | NOVA1 | exon_skip_209020 | -5.539259e-01 | 2.226497e-03 |
| IFG | DAZAP1 | exon_skip_23212 | 5.547862e-01 | 6.004191e-03 |
| IFG | RBM25 | exon_skip_23212 | 4.307618e-01 | 4.017183e-02 |
| IFG | ZNF326 | exon_skip_23212 | 4.605492e-01 | 2.699964e-02 |
| IFG | RBM6 | exon_skip_23212 | 4.569735e-01 | 2.836834e-02 |
| IFG | SAMD4A | exon_skip_23212 | 5.230085e-01 | 1.044517e-02 |
| IFG | IGF2BP2 | exon_skip_23212 | 6.350121e-01 | 1.132631e-03 |
| IFG | UNK | exon_skip_23212 | 5.064295e-01 | 1.366763e-02 |
| IFG | FUBP1 | exon_skip_23212 | 4.815732e-01 | 1.998200e-02 |
| IFG | NUP42 | exon_skip_20602 | 4.519311e-01 | 1.576394e-02 |
| IFG | EWSR1 | exon_skip_20602 | 4.319366e-01 | 2.171604e-02 |
| IFG | SRSF9 | exon_skip_20602 | 4.042466e-01 | 3.287837e-02 |
| IFG | ESRP1 | exon_skip_20602 | 5.636958e-01 | 1.785233e-03 |
| IFG | ESRP1 | exon_skip_150533 | -4.214882e-01 | 2.549206e-02 |
| PCC | MSI1 | exon_skip_23212 | 4.680151e-01 | 2.383148e-11 |
| PCC | SAMD4A | exon_skip_23212 | 4.893021e-01 | 2.086787e-12 |
| PCC | ILF2 | exon_skip_23212 | -4.353571e-01 | 7.318906e-10 |
| PCC | HNRNPK | exon_skip_23212 | -4.007983e-01 | 1.884956e-08 |
| PCC | RALYL | exon_skip_23212 | -5.735358e-01 | 2.142573e-17 |
| PCC | RBM23 | exon_skip_23212 | -4.324998e-01 | 9.710214e-10 |
| PG | NOVA1 | exon_skip_62408 | -4.136319e-01 | 5.837424e-10 |
| PG | HNRNPL | exon_skip_20602 | 4.061365e-01 | 9.024607e-08 |
| PG | ESRP1 | exon_skip_20602 | 4.144365e-01 | 4.618008e-08 |
| STG | NOVA1 | exon_skip_209020 | -5.272817e-01 | 5.630158e-08 |
| TC | NOVA1 | exon_skip_252427 | -6.208221e-01 | 4.203631e-18 |
| TC | NUP42 | exon_skip_2810 | 6.552553e-01 | 2.976973e-20 |
| TC | NUP42 | exon_skip_20602 | 6.503681e-01 | 3.706376e-19 |
| TC | ESRP1 | exon_skip_20602 | 5.729572e-01 | 2.753164e-14 |
| TC | NUP42 | exon_skip_81011 | 6.360358e-01 | 1.144793e-16 |
| TC | ESRP1 | exon_skip_81011 | 5.240673e-01 | 6.890408e-11 |
| TC | NUP42 | exon_skip_173964 | 6.352360e-01 | 4.502232e-17 |
| TC | ESRP1 | exon_skip_173964 | 5.507939e-01 | 2.139801e-12 |
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RelatedDrugs for PTPRD |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PTPRD |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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