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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for PTPDC1 |
 Gene summary |
| Gene information | Gene symbol | PTPDC1 | Gene ID | 138639 |
| Gene name | protein tyrosine phosphatase domain containing 1 | |
| Synonyms | PTP9Q22 | |
| Cytomap | 9q22.32 | |
| Type of gene | protein-coding | |
| Description | protein tyrosine phosphatase domain-containing protein 1protein tyrosine phosphatase PTP9Q22 | |
| Modification date | 20180523 | |
| UniProtAcc | A2A3K4 | |
| Context | PubMed: PTPDC1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Exon skipping events across known transcript of Ensembl for PTPDC1 from UCSC genome browser |
| Skipped 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. |
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Gene isoform structures and expression levels for PTPDC1 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PTPDC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_497376 | 9 | 96847532:96847704:96850112:96850193:96850426:96850545 | 96850112:96850193 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497380 | 9 | 96850112:96850193:96850426:96850545:96857598:96857736 | 96850426:96850545 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497383 | 9 | 96857598:96857736:96859602:96860861:96863847:96864033 | 96859602:96860861 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497389 | 9 | 96859602:96860861:96863847:96864033:96866556:96866667 | 96863847:96864033 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497393 | 9 | 96863847:96864033:96866556:96866667:96870109:96870194 | 96866556:96866667 | ENSG00000158079.10 | ENST00000375360.3,ENST00000467049.1,ENST00000288976.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PTPDC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_497376 | 9 | 96847532:96847704:96850112:96850193:96850426:96850545 | 96850112:96850193 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497380 | 9 | 96850112:96850193:96850426:96850545:96857598:96857736 | 96850426:96850545 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497383 | 9 | 96857598:96857736:96859602:96860861:96863847:96864033 | 96859602:96860861 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497389 | 9 | 96859602:96860861:96863847:96864033:96866556:96866667 | 96863847:96864033 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3 |
| exon_skip_497393 | 9 | 96863847:96864033:96866556:96866667:96870109:96870194 | 96866556:96866667 | ENSG00000158079.10 | ENST00000375360.3,ENST00000288976.3,ENST00000467049.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PTPDC1 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000375360 | 96850426 | 96850545 | Frame-shift |
| ENST00000375360 | 96859602 | 96860861 | Frame-shift |
| ENST00000375360 | 96850112 | 96850193 | In-frame |
| ENST00000375360 | 96863847 | 96864033 | In-frame |
| ENST00000375360 | 96866556 | 96866667 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000375360 | 96850426 | 96850545 | Frame-shift |
| ENST00000375360 | 96859602 | 96860861 | Frame-shift |
| ENST00000375360 | 96850112 | 96850193 | In-frame |
| ENST00000375360 | 96863847 | 96864033 | In-frame |
| ENST00000375360 | 96866556 | 96866667 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPDC1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000375360 | 4534 | 754 | 96850112 | 96850193 | 595 | 675 | 85 | 111 |
| ENST00000375360 | 4534 | 754 | 96863847 | 96864033 | 2192 | 2377 | 617 | 679 |
| ENST00000375360 | 4534 | 754 | 96866556 | 96866667 | 2378 | 2488 | 679 | 716 |
| Loci of skipped exons in GTEx 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 |
| ENST00000375360 | 4534 | 754 | 96850112 | 96850193 | 595 | 675 | 85 | 111 |
| ENST00000375360 | 4534 | 754 | 96863847 | 96864033 | 2192 | 2377 | 617 | 679 |
| ENST00000375360 | 4534 | 754 | 96866556 | 96866667 | 2378 | 2488 | 679 | 716 |
| 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 feature | Description of feature |
| A2A3K4 | 85 | 111 | 1 | 754 | Chain | ID=PRO_0000312212;Note=Protein tyrosine phosphatase domain-containing protein 1 |
| A2A3K4 | 617 | 679 | 1 | 754 | Chain | ID=PRO_0000312212;Note=Protein tyrosine phosphatase domain-containing protein 1 |
| A2A3K4 | 679 | 716 | 1 | 754 | Chain | ID=PRO_0000312212;Note=Protein tyrosine phosphatase domain-containing protein 1 |
| 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 feature | Description of feature |
| A2A3K4 | 85 | 111 | 1 | 754 | Chain | ID=PRO_0000312212;Note=Protein tyrosine phosphatase domain-containing protein 1 |
| A2A3K4 | 617 | 679 | 1 | 754 | Chain | ID=PRO_0000312212;Note=Protein tyrosine phosphatase domain-containing protein 1 |
| A2A3K4 | 679 | 716 | 1 | 754 | Chain | ID=PRO_0000312212;Note=Protein tyrosine phosphatase domain-containing protein 1 |
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SNVs in the skipped exons for PTPDC1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_497383 | 96859603 | 96860861 | 96860715 | 96860715 | Frame_Shift_Del | A | - | p.K569fs |
| UCEC | TCGA-AP-A0LG-01 | exon_skip_497383 | 96859603 | 96860861 | 96860837 | 96860837 | Frame_Shift_Del | A | - | p.L663fs |
| HNSC | TCGA-CN-A63W-01 | exon_skip_497389 | 96863848 | 96864033 | 96863913 | 96863922 | Frame_Shift_Del | ATGCAGCTTG | - | p.LCSL639fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_497389 | 96863848 | 96864033 | 96863965 | 96863965 | Frame_Shift_Del | A | - | p.K657fs |
| STAD | TCGA-BR-6452-01 | exon_skip_497389 | 96863848 | 96864033 | 96864017 | 96864017 | Frame_Shift_Del | T | - | p.L728fs |
| STAD | TCGA-KB-A93J-01 | exon_skip_497383 | 96859603 | 96860861 | 96860420 | 96860421 | Frame_Shift_Ins | - | G | p.N524fs |
| STAD | TCGA-KB-A93J-01 | exon_skip_497383 | 96859603 | 96860861 | 96860420 | 96860421 | Frame_Shift_Ins | - | G | p.V471fs |
| STAD | TCGA-F1-6177-01 | exon_skip_497389 | 96863848 | 96864033 | 96864016 | 96864017 | Frame_Shift_Ins | - | T | p.L674fs |
| STAD | TCGA-F1-6177-01 | exon_skip_497389 | 96863848 | 96864033 | 96864016 | 96864017 | Frame_Shift_Ins | - | T | p.L728fs |
| STAD | TCGA-F1-6177-01 | exon_skip_497389 | 96863848 | 96864033 | 96864017 | 96864018 | Frame_Shift_Ins | - | T | p.L728fs |
| SKCM | TCGA-D3-A8GM-06 | exon_skip_497383 | 96859603 | 96860861 | 96859619 | 96859619 | Nonsense_Mutation | T | A | p.C203* |
| LUAD | TCGA-55-6968-01 | exon_skip_497383 | 96859603 | 96860861 | 96859842 | 96859842 | Nonsense_Mutation | G | T | p.E278* |
| SARC | TCGA-DX-A8BP-01 | exon_skip_497383 | 96859603 | 96860861 | 96860235 | 96860235 | Nonsense_Mutation | G | T | p.E409* |
| PRAD | TCGA-KC-A7FA-01 | exon_skip_497383 | 96859603 | 96860861 | 96860386 | 96860386 | Nonsense_Mutation | C | G | p.S459* |
| COAD | TCGA-AZ-4615-01 | exon_skip_497383 | 96859603 | 96860861 | 96860646 | 96860646 | Nonsense_Mutation | C | T | p.R598X |
| STAD | TCGA-BR-4280-01 | exon_skip_497383 | 96859603 | 96860861 | 96860859 | 96860859 | Nonsense_Mutation | C | T | p.Q617* |
| STAD | TCGA-BR-4280-01 | exon_skip_497383 | 96859603 | 96860861 | 96860859 | 96860859 | Nonsense_Mutation | C | T | p.Q671X |
| LUSC | TCGA-37-3783-01 | exon_skip_497393 | 96866557 | 96866667 | 96866629 | 96866629 | Nonsense_Mutation | G | T | p.E758* |
| UCEC | TCGA-D1-A15X-01 | exon_skip_497383 | 96859603 | 96860861 | 96860863 | 96860863 | Splice_Site | T | C | e6+2 |
| STAD | TCGA-IN-7808-01 | exon_skip_497389 | 96863848 | 96864033 | 96864034 | 96864034 | Splice_Site | G | A | . |
| STAD | TCGA-IN-7808-01 | exon_skip_497389 | 96863848 | 96864033 | 96864034 | 96864034 | Splice_Site | G | A | p.K679_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| SNU1040_LARGE_INTESTINE | 96863848 | 96864033 | 96864017 | 96864017 | Frame_Shift_Del | T | - | p.L674fs |
| IM95_STOMACH | 96863848 | 96864033 | 96864027 | 96864028 | Frame_Shift_Del | AG | - | p.E678fs |
| KG1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96863848 | 96864033 | 96864016 | 96864017 | Frame_Shift_Ins | - | T | p.L674fs |
| SNU719_STOMACH | 96863848 | 96864033 | 96864016 | 96864017 | Frame_Shift_Ins | - | T | p.L674fs |
| SNU1040_LARGE_INTESTINE | 96850427 | 96850545 | 96850459 | 96850459 | Missense_Mutation | G | A | p.R123H |
| SNGM_ENDOMETRIUM | 96859603 | 96860861 | 96859647 | 96859647 | Missense_Mutation | G | A | p.A213T |
| SKMEL28_SKIN | 96859603 | 96860861 | 96859690 | 96859690 | Missense_Mutation | C | T | p.S227F |
| SF295_CENTRAL_NERVOUS_SYSTEM | 96859603 | 96860861 | 96859749 | 96859749 | Missense_Mutation | C | A | p.L247I |
| ISTMES2_PLEURA | 96859603 | 96860861 | 96859801 | 96859801 | Missense_Mutation | C | G | p.P264R |
| JHUEM7_ENDOMETRIUM | 96859603 | 96860861 | 96859815 | 96859815 | Missense_Mutation | C | T | p.R269C |
| KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96859603 | 96860861 | 96859815 | 96859815 | Missense_Mutation | C | T | p.R269C |
| SNU1196_BILIARY_TRACT | 96859603 | 96860861 | 96859815 | 96859815 | Missense_Mutation | C | T | p.R269C |
| MET2B | 96859603 | 96860861 | 96859815 | 96859815 | Missense_Mutation | C | T | p.R269C |
| KURAMOCHI_OVARY | 96859603 | 96860861 | 96859821 | 96859821 | Missense_Mutation | C | T | p.R271C |
| CHLA57_BONE | 96859603 | 96860861 | 96859857 | 96859857 | Missense_Mutation | A | C | p.K283Q |
| FEPD_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96859603 | 96860861 | 96859900 | 96859900 | Missense_Mutation | T | C | p.L297P |
| HCC2450_LUNG | 96859603 | 96860861 | 96860145 | 96860145 | Missense_Mutation | G | C | p.E379Q |
| HCC2218_BREAST | 96859603 | 96860861 | 96860261 | 96860261 | Missense_Mutation | G | C | p.Q417H |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 96859603 | 96860861 | 96860305 | 96860305 | Missense_Mutation | A | G | p.H432R |
| DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96859603 | 96860861 | 96860358 | 96860358 | Missense_Mutation | C | T | p.R450C |
| HCT15_LARGE_INTESTINE | 96859603 | 96860861 | 96860454 | 96860454 | Missense_Mutation | A | G | p.K482E |
| HEC251_ENDOMETRIUM | 96859603 | 96860861 | 96860530 | 96860530 | Missense_Mutation | G | C | p.S507T |
| MM383_SKIN | 96859603 | 96860861 | 96860674 | 96860674 | Missense_Mutation | C | T | p.P555L |
| 42MGBA_CENTRAL_NERVOUS_SYSTEM | 96859603 | 96860861 | 96860685 | 96860685 | Missense_Mutation | T | A | p.F559I |
| COV504_OVARY | 96859603 | 96860861 | 96860687 | 96860687 | Missense_Mutation | C | A | p.F559L |
| NCIH820_LUNG | 96859603 | 96860861 | 96860721 | 96860721 | Missense_Mutation | C | G | p.L571V |
| AN3CA_ENDOMETRIUM | 96859603 | 96860861 | 96860731 | 96860731 | Missense_Mutation | C | T | p.A574V |
| JHU011_UPPER_AERODIGESTIVE_TRACT | 96859603 | 96860861 | 96860769 | 96860769 | Missense_Mutation | G | A | p.E587K |
| NCIH345_LUNG | 96859603 | 96860861 | 96860818 | 96860818 | Missense_Mutation | C | T | p.S603F |
| SNU81_LARGE_INTESTINE | 96863848 | 96864033 | 96863882 | 96863882 | Missense_Mutation | G | T | p.R629I |
| GIMEN_AUTONOMIC_GANGLIA | 96866557 | 96866667 | 96866648 | 96866648 | Missense_Mutation | C | G | p.A710G |
| SW48_LARGE_INTESTINE | 96859603 | 96860861 | 96860112 | 96860112 | Nonsense_Mutation | C | T | p.Q368* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPDC1 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPDC1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPDC1 |
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RelatedDrugs for PTPDC1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for PTPDC1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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