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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 PTPN12 |
 Gene summary |
| Gene information | Gene symbol | PTPN12 | Gene ID | 5782 |
| Gene name | protein tyrosine phosphatase, non-receptor type 12 | |
| Synonyms | PTP-PEST|PTPG1 | |
| Cytomap | 7q11.23 | |
| Type of gene | protein-coding | |
| Description | tyrosine-protein phosphatase non-receptor type 12protein-tyrosine phosphatase G1 | |
| Modification date | 20180522 | |
| UniProtAcc | Q05209 | |
| Context | PubMed: PTPN12 [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 |
| PTPN12 | GO:0006470 | protein dephosphorylation | 27134172 |
| PTPN12 | GO:0035335 | peptidyl-tyrosine dephosphorylation | 27134172 |
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Exon skipping events across known transcript of Ensembl for PTPN12 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 PTPN12 |
| 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 PTPN12 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_467609 | 7 | 77166870:77166962:77193252:77193512:77200394:77200503 | 77193252:77193512 | ENSG00000127947.11 | ENST00000523952.1 |
| exon_skip_467611 | 7 | 77166870:77166962:77200394:77200503:77210743:77210782 | 77200394:77200503 | ENSG00000127947.11 | ENST00000460731.1 |
| exon_skip_467623 | 7 | 77167385:77167423:77168081:77168162:77200394:77200503 | 77168081:77168162 | ENSG00000127947.11 | ENST00000433369.2 |
| exon_skip_467625 | 7 | 77200469:77200503:77210743:77210820:77212871:77212967 | 77210743:77210820 | ENSG00000127947.11 | ENST00000418110.1,ENST00000460731.1,ENST00000248594.6,ENST00000433369.2,ENST00000522115.2,ENST00000415482.2 |
| exon_skip_467627 | 7 | 77200469:77200503:77210743:77210820:77214859:77214888 | 77210743:77210820 | ENSG00000127947.11 | ENST00000435495.2 |
| exon_skip_467628 | 7 | 77200469:77200503:77212871:77212967:77214859:77214888 | 77212871:77212967 | ENSG00000127947.11 | ENST00000440186.1 |
| exon_skip_467632 | 7 | 77210743:77210820:77212871:77212967:77214859:77214888 | 77212871:77212967 | ENSG00000127947.11 | ENST00000418110.1,ENST00000248594.6,ENST00000433369.2,ENST00000522115.2,ENST00000415482.2 |
| exon_skip_467634 | 7 | 77212871:77212967:77214859:77214898:77221501:77221573 | 77214859:77214898 | ENSG00000127947.11 | ENST00000418110.1,ENST00000248594.6,ENST00000447995.2,ENST00000433369.2,ENST00000415482.2 |
| exon_skip_467635 | 7 | 77212871:77212967:77214859:77214898:77227158:77227218 | 77214859:77214898 | ENSG00000127947.11 | ENST00000522115.2 |
| exon_skip_467640 | 7 | 77214862:77214898:77221501:77221573:77227158:77227218 | 77221501:77221573 | ENSG00000127947.11 | ENST00000418110.1,ENST00000248594.6,ENST00000447995.2,ENST00000435495.2,ENST00000415482.2,ENST00000494248.1 |
| exon_skip_467643 | 7 | 77221501:77221573:77227158:77227218:77229980:77230045 | 77227158:77227218 | ENSG00000127947.11 | ENST00000418110.1,ENST00000248594.6,ENST00000447995.2,ENST00000435495.2,ENST00000415482.2,ENST00000494248.1 |
| exon_skip_467646 | 7 | 77227158:77227218:77229980:77230123:77234195:77234252 | 77229980:77230123 | ENSG00000127947.11 | ENST00000447995.2 |
| exon_skip_467647 | 7 | 77227158:77227218:77229980:77230123:77236551:77236618 | 77229980:77230123 | ENSG00000127947.11 | ENST00000248594.6,ENST00000435495.2,ENST00000522115.2,ENST00000415482.2 |
| exon_skip_467655 | 7 | 77229980:77230123:77234195:77234252:77236551:77236618 | 77234195:77234252 | ENSG00000127947.11 | ENST00000447995.2 |
| exon_skip_467657 | 7 | 77229980:77230123:77236551:77236618:77240081:77240119 | 77236551:77236618 | ENSG00000127947.11 | ENST00000248594.6,ENST00000435495.2,ENST00000522115.2,ENST00000415482.2 |
| exon_skip_467662 | 7 | 77240264:77240363:77247796:77247882:77256021:77256992 | 77247796:77247882 | ENSG00000127947.11 | ENST00000248594.6,ENST00000435495.2,ENST00000415482.2 |
| exon_skip_467668 | 7 | 77256472:77256992:77261664:77261742:77265098:77265166 | 77261664:77261742 | ENSG00000127947.11 | ENST00000248594.6,ENST00000435495.2,ENST00000415482.2 |
| exon_skip_467671 | 7 | 77265098:77265166:77266334:77266365:77267940:77268025 | 77266334:77266365 | ENSG00000127947.11 | ENST00000248594.6,ENST00000435495.2,ENST00000407343.3,ENST00000415482.2 |
| exon_skip_467675 | 7 | 77266334:77266365:77267940:77268048:77268535:77268597 | 77267940:77268048 | ENSG00000127947.11 | ENST00000248594.6,ENST00000435495.2,ENST00000520947.1,ENST00000415482.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PTPN12 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_467609 | 7 | 77166870:77166962:77193252:77193512:77200394:77200503 | 77193252:77193512 | ENSG00000127947.11 | ENST00000523952.1 |
| exon_skip_467611 | 7 | 77166870:77166962:77200394:77200503:77210743:77210782 | 77200394:77200503 | ENSG00000127947.11 | ENST00000460731.1 |
| exon_skip_467623 | 7 | 77167385:77167423:77168081:77168162:77200394:77200503 | 77168081:77168162 | ENSG00000127947.11 | ENST00000433369.2 |
| exon_skip_467625 | 7 | 77200469:77200503:77210743:77210820:77212871:77212967 | 77210743:77210820 | ENSG00000127947.11 | ENST00000248594.6,ENST00000460731.1,ENST00000433369.2,ENST00000415482.2,ENST00000418110.1,ENST00000522115.2 |
| exon_skip_467627 | 7 | 77200469:77200503:77210743:77210820:77214859:77214888 | 77210743:77210820 | ENSG00000127947.11 | ENST00000435495.2 |
| exon_skip_467628 | 7 | 77200469:77200503:77212871:77212967:77214859:77214888 | 77212871:77212967 | ENSG00000127947.11 | ENST00000440186.1 |
| exon_skip_467632 | 7 | 77210743:77210820:77212871:77212967:77214859:77214888 | 77212871:77212967 | ENSG00000127947.11 | ENST00000248594.6,ENST00000433369.2,ENST00000415482.2,ENST00000418110.1,ENST00000522115.2 |
| exon_skip_467634 | 7 | 77212871:77212967:77214859:77214898:77221501:77221573 | 77214859:77214898 | ENSG00000127947.11 | ENST00000248594.6,ENST00000433369.2,ENST00000415482.2,ENST00000418110.1,ENST00000447995.2 |
| exon_skip_467635 | 7 | 77212871:77212967:77214859:77214898:77227158:77227218 | 77214859:77214898 | ENSG00000127947.11 | ENST00000522115.2 |
| exon_skip_467640 | 7 | 77214862:77214898:77221501:77221573:77227158:77227218 | 77221501:77221573 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2,ENST00000418110.1,ENST00000447995.2,ENST00000494248.1 |
| exon_skip_467643 | 7 | 77221501:77221573:77227158:77227218:77229980:77230045 | 77227158:77227218 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2,ENST00000418110.1,ENST00000447995.2,ENST00000494248.1 |
| exon_skip_467646 | 7 | 77227158:77227218:77229980:77230123:77234195:77234252 | 77229980:77230123 | ENSG00000127947.11 | ENST00000447995.2 |
| exon_skip_467647 | 7 | 77227158:77227218:77229980:77230123:77236551:77236618 | 77229980:77230123 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2,ENST00000522115.2 |
| exon_skip_467655 | 7 | 77229980:77230123:77234195:77234252:77236551:77236618 | 77234195:77234252 | ENSG00000127947.11 | ENST00000447995.2 |
| exon_skip_467657 | 7 | 77229980:77230123:77236551:77236618:77240081:77240119 | 77236551:77236618 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2,ENST00000522115.2 |
| exon_skip_467662 | 7 | 77240264:77240363:77247796:77247882:77256021:77256992 | 77247796:77247882 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2 |
| exon_skip_467668 | 7 | 77256472:77256992:77261664:77261742:77265098:77265166 | 77261664:77261742 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2 |
| exon_skip_467671 | 7 | 77265098:77265166:77266334:77266365:77267940:77268025 | 77266334:77266365 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2,ENST00000407343.3 |
| exon_skip_467675 | 7 | 77266334:77266365:77267940:77268048:77268535:77268597 | 77267940:77268048 | ENSG00000127947.11 | ENST00000248594.6,ENST00000415482.2,ENST00000435495.2,ENST00000520947.1 |
| 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 PTPN12 |
| 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 |
| ENST00000248594 | 77210743 | 77210820 | Frame-shift |
| ENST00000248594 | 77229980 | 77230123 | Frame-shift |
| ENST00000248594 | 77236551 | 77236618 | Frame-shift |
| ENST00000248594 | 77247796 | 77247882 | Frame-shift |
| ENST00000248594 | 77266334 | 77266365 | Frame-shift |
| ENST00000248594 | 77212871 | 77212967 | In-frame |
| ENST00000248594 | 77214859 | 77214898 | In-frame |
| ENST00000248594 | 77221501 | 77221573 | In-frame |
| ENST00000248594 | 77227158 | 77227218 | In-frame |
| ENST00000248594 | 77261664 | 77261742 | In-frame |
| ENST00000248594 | 77267940 | 77268048 | 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 |
| ENST00000248594 | 77210743 | 77210820 | Frame-shift |
| ENST00000248594 | 77229980 | 77230123 | Frame-shift |
| ENST00000248594 | 77236551 | 77236618 | Frame-shift |
| ENST00000248594 | 77247796 | 77247882 | Frame-shift |
| ENST00000248594 | 77266334 | 77266365 | Frame-shift |
| ENST00000248594 | 77212871 | 77212967 | In-frame |
| ENST00000248594 | 77214859 | 77214898 | In-frame |
| ENST00000248594 | 77221501 | 77221573 | In-frame |
| ENST00000248594 | 77227158 | 77227218 | In-frame |
| ENST00000248594 | 77261664 | 77261742 | In-frame |
| ENST00000248594 | 77267940 | 77268048 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPN12 |
| 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 |
| ENST00000248594 | 3423 | 780 | 77212871 | 77212967 | 558 | 653 | 95 | 127 |
| ENST00000248594 | 3423 | 780 | 77214859 | 77214898 | 654 | 692 | 127 | 140 |
| ENST00000248594 | 3423 | 780 | 77221501 | 77221573 | 693 | 764 | 140 | 164 |
| ENST00000248594 | 3423 | 780 | 77227158 | 77227218 | 765 | 824 | 164 | 184 |
| ENST00000248594 | 3423 | 780 | 77261664 | 77261742 | 2269 | 2346 | 665 | 691 |
| ENST00000248594 | 3423 | 780 | 77267940 | 77268048 | 2446 | 2553 | 724 | 760 |
| 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 |
| ENST00000248594 | 3423 | 780 | 77212871 | 77212967 | 558 | 653 | 95 | 127 |
| ENST00000248594 | 3423 | 780 | 77214859 | 77214898 | 654 | 692 | 127 | 140 |
| ENST00000248594 | 3423 | 780 | 77221501 | 77221573 | 693 | 764 | 140 | 164 |
| ENST00000248594 | 3423 | 780 | 77227158 | 77227218 | 765 | 824 | 164 | 184 |
| ENST00000248594 | 3423 | 780 | 77261664 | 77261742 | 2269 | 2346 | 665 | 691 |
| ENST00000248594 | 3423 | 780 | 77267940 | 77268048 | 2446 | 2553 | 724 | 760 |
| 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 |
| 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 |
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SNVs in the skipped exons for PTPN12 |
| - 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-DD-A39Y-01 | exon_skip_467611 | 77200395 | 77200503 | 77200473 | 77200473 | Frame_Shift_Del | A | - | p.K61fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_467632 exon_skip_467628 | 77212872 | 77212967 | 77212934 | 77212934 | Frame_Shift_Del | T | - | p.D116fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_467646 exon_skip_467647 | 77229981 | 77230123 | 77230002 | 77230002 | Frame_Shift_Del | T | - | p.F192fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_467657 | 77236552 | 77236618 | 77236603 | 77236603 | Frame_Shift_Del | T | - | p.N249fs |
| STAD | TCGA-BR-8368-01 | exon_skip_467662 | 77247797 | 77247882 | 77247840 | 77247840 | Frame_Shift_Del | A | - | p.E328fs |
| STAD | TCGA-MX-A666-01 | exon_skip_467675 | 77267941 | 77268048 | 77268032 | 77268033 | Frame_Shift_Del | AG | - | p.755_755del |
| STAD | TCGA-MX-A666-01 | exon_skip_467675 | 77267941 | 77268048 | 77268032 | 77268033 | Frame_Shift_Del | AG | - | p.TE755fs |
| UCEC | TCGA-AX-A05Z-01 | exon_skip_467611 | 77200395 | 77200503 | 77200461 | 77200461 | Nonsense_Mutation | G | T | p.E56* |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_467611 | 77200395 | 77200503 | 77200464 | 77200464 | Nonsense_Mutation | G | T | p.E57* |
| LUSC | TCGA-33-4566-01 | exon_skip_467625 exon_skip_467627 | 77210744 | 77210820 | 77210755 | 77210755 | Nonsense_Mutation | C | T | p.R74* |
| COAD | TCGA-G4-6586-01 | exon_skip_467635 exon_skip_467634 | 77214860 | 77214898 | 77214878 | 77214878 | Nonsense_Mutation | C | T | p.R4X |
| PRAD | TCGA-FC-A5OB-01 | exon_skip_467640 | 77221502 | 77221573 | 77221501 | 77221502 | Splice_Site | - | A | . |
| LIHC | TCGA-BC-A112-01 | exon_skip_467662 | 77247797 | 77247882 | 77247882 | 77247883 | Splice_Site | - | GT | p.I342_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 |
| FLO1_OESOPHAGUS | 77229981 | 77230123 | 77230084 | 77230086 | In_Frame_Del | ATC | - | p.219_220YQ>* |
| RF48_STOMACH | 77210744 | 77210820 | 77210767 | 77210767 | Missense_Mutation | A | C | p.T78P |
| JVM3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 77212872 | 77212967 | 77212917 | 77212917 | Missense_Mutation | G | A | p.A111T |
| SARC9371_BONE | 77212872 | 77212967 | 77212946 | 77212946 | Missense_Mutation | G | A | p.M120I |
| DOV13_OVARY | 77221502 | 77221573 | 77221523 | 77221523 | Missense_Mutation | C | T | p.P148S |
| OC316_OVARY | 77221502 | 77221573 | 77221548 | 77221548 | Missense_Mutation | C | T | p.T156M |
| OC314_OVARY | 77221502 | 77221573 | 77221548 | 77221548 | Missense_Mutation | C | T | p.T156M |
| NCIH1838_LUNG | 77227159 | 77227218 | 77227191 | 77227191 | Missense_Mutation | C | G | p.I175M |
| NCIH358_LUNG | 77227159 | 77227218 | 77227213 | 77227213 | Missense_Mutation | C | G | p.Q183E |
| SW48_LARGE_INTESTINE | 77229981 | 77230123 | 77230029 | 77230029 | Missense_Mutation | G | A | p.D201N |
| WM88_SKIN | 77229981 | 77230123 | 77230035 | 77230035 | Missense_Mutation | C | T | p.P203S |
| RXF393_KIDNEY | 77229981 | 77230123 | 77230039 | 77230039 | Missense_Mutation | C | T | p.S204L |
| HMC18_BREAST | 77229981 | 77230123 | 77230081 | 77230081 | Missense_Mutation | A | C | p.K218T |
| HCC1395_BREAST | 77229981 | 77230123 | 77230116 | 77230116 | Missense_Mutation | C | T | p.H230Y |
| COLO678_LARGE_INTESTINE | 77247797 | 77247882 | 77247812 | 77247812 | Missense_Mutation | G | A | p.E319K |
| CHLA06ATRT_SOFT_TISSUE | 77247797 | 77247882 | 77247827 | 77247827 | Missense_Mutation | T | C | p.S324P |
| LS411N_LARGE_INTESTINE | 77247797 | 77247882 | 77247879 | 77247879 | Missense_Mutation | G | A | p.R341H |
| NCIH630_LARGE_INTESTINE | 77247797 | 77247882 | 77247879 | 77247879 | Missense_Mutation | G | A | p.R341H |
| DJM1_SKIN | 77261665 | 77261742 | 77261736 | 77261736 | Missense_Mutation | G | A | p.E690K |
| HCC2998_LARGE_INTESTINE | 77200395 | 77200503 | 77200461 | 77200461 | Nonsense_Mutation | G | T | p.E56* |
| UMUC6_URINARY_TRACT | 77227159 | 77227218 | 77227213 | 77227213 | Nonsense_Mutation | C | T | p.Q183* |
| LS513_LARGE_INTESTINE | 77221502 | 77221573 | 77221503 | 77221503 | Splice_Site | A | G | p.K141R |
| HCC1588_LUNG | 77221502 | 77221573 | 77221503 | 77221503 | Splice_Site | A | G | p.K141R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN12 |
| 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 |
| exon_skip_467611 | 7 | 77166870:77166962:77200394:77200503:77210743:77210782 | 77200394:77200503 | ENST00000460731.1 | COAD | rs17155183 | chr7:77200392 | A/T | 1.28e-03 |
| exon_skip_467611 | 7 | 77166870:77166962:77200394:77200503:77210743:77210782 | 77200394:77200503 | ENST00000460731.1 | OV | rs17155183 | chr7:77200392 | A/T | 3.69e-04 |
| exon_skip_467611 | 7 | 77166870:77166962:77200394:77200503:77210743:77210782 | 77200394:77200503 | ENST00000460731.1 | OV | rs17155183 | chr7:77200392 | A/T | 3.69e-04 |
| exon_skip_467662 | 7 | 77240264:77240363:77247796:77247882:77256021:77256992 | 77247796:77247882 | ENST00000248594.6,ENST00000435495.2,ENST00000415482.2 | LGG | rs9640663 | chr7:77247821 | G/A | 2.72e-03 |
| exon_skip_467662 | 7 | 77240264:77240363:77247796:77247882:77256021:77256992 | 77247796:77247882 | ENST00000248594.6,ENST00000435495.2,ENST00000415482.2 | STAD | rs9640663 | chr7:77247821 | G/A | 1.03e-04 |
| exon_skip_467662 | 7 | 77240264:77240363:77247796:77247882:77256021:77256992 | 77247796:77247882 | ENST00000248594.6,ENST00000435495.2,ENST00000415482.2 | STAD | rs9640663 | chr7:77247821 | G/A | 1.03e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPN12 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPN12 |
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RelatedDrugs for PTPN12 |
| 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 PTPN12 |
| 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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