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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 PTPN3 |
 Gene summary |
| Gene information | Gene symbol | PTPN3 | Gene ID | 5774 |
| Gene name | protein tyrosine phosphatase, non-receptor type 3 | |
| Synonyms | PTP-H1|PTPH1 | |
| Cytomap | 9q31.3 | |
| Type of gene | protein-coding | |
| Description | tyrosine-protein phosphatase non-receptor type 3cytoskeletal-associated protein tyrosine phosphataseprotein-tyrosine phosphatase H1 | |
| Modification date | 20180527 | |
| UniProtAcc | P26045 | |
| Context | PubMed: PTPN3 [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 |
| PTPN3 | GO:0006470 | protein dephosphorylation | 10364224 |
| PTPN3 | GO:0045930 | negative regulation of mitotic cell cycle | 10364224 |
| PTPN3 | GO:0098902 | regulation of membrane depolarization during action potential | 16930557 |
| PTPN3 | GO:2000649 | regulation of sodium ion transmembrane transporter activity | 16930557 |
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Exon skipping events across known transcript of Ensembl for PTPN3 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 PTPN3 |
| 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 PTPN3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_505609 | 9 | 112170600:112170657:112172278:112172356:112172508:112172695 | 112172278:112172356 | ENSG00000070159.9 | ENST00000412145.1,ENST00000446349.1,ENST00000262539.3,ENST00000374541.2,ENST00000394827.3 |
| exon_skip_505610 | 9 | 112182703:112182880:112184997:112185132:112189229:112189303 | 112184997:112185132 | ENSG00000070159.9 | ENST00000412145.1,ENST00000374541.2 |
| exon_skip_505616 | 9 | 112207519:112207572:112211090:112211135:112219452:112219495 | 112211090:112211135 | ENSG00000070159.9 | ENST00000262539.3 |
| exon_skip_505630 | 9 | 112211090:112211135:112216775:112216854:112219452:112219495 | 112216775:112216854 | ENSG00000070159.9 | ENST00000374541.2 |
| exon_skip_505632 | 9 | 112211090:112211135:112219452:112219495:112219571:112219679 | 112219452:112219495 | ENSG00000070159.9 | ENST00000262539.3 |
| exon_skip_505642 | 9 | 112216775:112216854:112219452:112219495:112219571:112219679 | 112219452:112219495 | ENSG00000070159.9 | ENST00000374541.2 |
| exon_skip_505643 | 9 | 112219452:112219495:112219571:112219679:112225576:112225731 | 112219571:112219679 | ENSG00000070159.9 | ENST00000262539.3,ENST00000374541.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PTPN3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_505609 | 9 | 112170600:112170657:112172278:112172356:112172508:112172695 | 112172278:112172356 | ENSG00000070159.9 | ENST00000412145.1,ENST00000446349.1,ENST00000374541.2,ENST00000394827.3,ENST00000262539.3 |
| exon_skip_505610 | 9 | 112182703:112182880:112184997:112185132:112189229:112189303 | 112184997:112185132 | ENSG00000070159.9 | ENST00000412145.1,ENST00000374541.2 |
| exon_skip_505616 | 9 | 112207519:112207572:112211090:112211135:112219452:112219495 | 112211090:112211135 | ENSG00000070159.9 | ENST00000262539.3 |
| exon_skip_505630 | 9 | 112211090:112211135:112216775:112216854:112219452:112219495 | 112216775:112216854 | ENSG00000070159.9 | ENST00000374541.2 |
| exon_skip_505632 | 9 | 112211090:112211135:112219452:112219495:112219571:112219679 | 112219452:112219495 | ENSG00000070159.9 | ENST00000262539.3 |
| exon_skip_505642 | 9 | 112216775:112216854:112219452:112219495:112219571:112219679 | 112219452:112219495 | ENSG00000070159.9 | ENST00000374541.2 |
| exon_skip_505643 | 9 | 112219452:112219495:112219571:112219679:112225576:112225731 | 112219571:112219679 | ENSG00000070159.9 | ENST00000374541.2,ENST00000262539.3 |
| 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 PTPN3 |
| 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 |
| ENST00000374541 | 112216775 | 112216854 | Frame-shift |
| ENST00000374541 | 112219452 | 112219495 | Frame-shift |
| ENST00000374541 | 112172278 | 112172356 | In-frame |
| ENST00000374541 | 112184997 | 112185132 | In-frame |
| ENST00000374541 | 112219571 | 112219679 | 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 |
| ENST00000374541 | 112216775 | 112216854 | Frame-shift |
| ENST00000374541 | 112219452 | 112219495 | Frame-shift |
| ENST00000374541 | 112172278 | 112172356 | In-frame |
| ENST00000374541 | 112184997 | 112185132 | In-frame |
| ENST00000374541 | 112219571 | 112219679 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPN3 |
| 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 |
| ENST00000374541 | 6720 | 913 | 112219571 | 112219679 | 244 | 351 | 46 | 82 |
| ENST00000374541 | 6720 | 913 | 112184997 | 112185132 | 1107 | 1241 | 334 | 378 |
| ENST00000374541 | 6720 | 913 | 112172278 | 112172356 | 1606 | 1683 | 500 | 526 |
| 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 |
| ENST00000374541 | 6720 | 913 | 112219571 | 112219679 | 244 | 351 | 46 | 82 |
| ENST00000374541 | 6720 | 913 | 112184997 | 112185132 | 1107 | 1241 | 334 | 378 |
| ENST00000374541 | 6720 | 913 | 112172278 | 112172356 | 1606 | 1683 | 500 | 526 |
| 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 |
| P26045 | 46 | 82 | 1 | 131 | Alternative sequence | ID=VSP_046309;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| P26045 | 46 | 82 | 1 | 913 | Chain | ID=PRO_0000219433;Note=Tyrosine-protein phosphatase non-receptor type 3 |
| P26045 | 46 | 82 | 29 | 312 | Domain | Note=FERM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00084 |
| P26045 | 46 | 82 | 77 | 77 | Natural variant | ID=VAR_055252;Note=D->N;Dbxref=dbSNP:rs35285139 |
| P26045 | 334 | 378 | 335 | 379 | Alternative sequence | ID=VSP_046310;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| P26045 | 334 | 378 | 1 | 913 | Chain | ID=PRO_0000219433;Note=Tyrosine-protein phosphatase non-receptor type 3 |
| P26045 | 334 | 378 | 357 | 357 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P26045 | 334 | 378 | 359 | 359 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| P26045 | 334 | 378 | 367 | 367 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| P26045 | 334 | 378 | 376 | 376 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| P26045 | 500 | 526 | 1 | 913 | Chain | ID=PRO_0000219433;Note=Tyrosine-protein phosphatase non-receptor type 3 |
| P26045 | 500 | 526 | 510 | 582 | Domain | Note=PDZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| 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 |
| P26045 | 46 | 82 | 1 | 131 | Alternative sequence | ID=VSP_046309;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| P26045 | 46 | 82 | 1 | 913 | Chain | ID=PRO_0000219433;Note=Tyrosine-protein phosphatase non-receptor type 3 |
| P26045 | 46 | 82 | 29 | 312 | Domain | Note=FERM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00084 |
| P26045 | 46 | 82 | 77 | 77 | Natural variant | ID=VAR_055252;Note=D->N;Dbxref=dbSNP:rs35285139 |
| P26045 | 334 | 378 | 335 | 379 | Alternative sequence | ID=VSP_046310;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| P26045 | 334 | 378 | 1 | 913 | Chain | ID=PRO_0000219433;Note=Tyrosine-protein phosphatase non-receptor type 3 |
| P26045 | 334 | 378 | 357 | 357 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P26045 | 334 | 378 | 359 | 359 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| P26045 | 334 | 378 | 367 | 367 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| P26045 | 334 | 378 | 376 | 376 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
| P26045 | 500 | 526 | 1 | 913 | Chain | ID=PRO_0000219433;Note=Tyrosine-protein phosphatase non-receptor type 3 |
| P26045 | 500 | 526 | 510 | 582 | Domain | Note=PDZ;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
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SNVs in the skipped exons for PTPN3 |
| - 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 |
| STAD | TCGA-HU-A4GQ-01 | exon_skip_505610 | 112184998 | 112185132 | 112185106 | 112185106 | Frame_Shift_Del | T | - | p.K343fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_505630 | 112216776 | 112216854 | 112216802 | 112216802 | Frame_Shift_Del | G | - | p.P114fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_505630 | 112216776 | 112216854 | 112216814 | 112216814 | Frame_Shift_Del | A | - | p.F110fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_505630 | 112216776 | 112216854 | 112216814 | 112216814 | Frame_Shift_Del | A | - | p.F110fs |
| KIRP | TCGA-MH-A561-01 | exon_skip_505642 exon_skip_505632 | 112219453 | 112219495 | 112219466 | 112219466 | Frame_Shift_Del | C | - | p.K93fs |
| KIRP | TCGA-MH-A561-01 | exon_skip_505642 exon_skip_505632 | 112219453 | 112219495 | 112219466 | 112219466 | Frame_Shift_Del | C | - | p.R92fs |
| KICH | TCGA-KM-8477-01 | exon_skip_505643 | 112219572 | 112219679 | 112219611 | 112219612 | Frame_Shift_Del | AT | - | p.Y69fs |
| - 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 |
| A253_SALIVARY_GLAND | 112172279 | 112172356 | 112172323 | 112172323 | Missense_Mutation | G | A | p.R512C |
| SARC9371_BONE | 112184998 | 112185132 | 112185064 | 112185064 | Missense_Mutation | G | A | p.S357F |
| NCIH2110_LUNG | 112184998 | 112185132 | 112185092 | 112185092 | Missense_Mutation | T | A | p.M348L |
| HEC151_ENDOMETRIUM | 112184998 | 112185132 | 112185107 | 112185107 | Missense_Mutation | T | C | p.K343E |
| SNUC5_LARGE_INTESTINE | 112184998 | 112185132 | 112185112 | 112185112 | Missense_Mutation | C | T | p.C341Y |
| CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 112211091 | 112211135 | 112211094 | 112211094 | Missense_Mutation | C | G | p.G137A |
| M14_SKIN | 112216776 | 112216854 | 112216852 | 112216852 | Missense_Mutation | C | T | p.G98S |
| MDAMB435S_SKIN | 112216776 | 112216854 | 112216852 | 112216852 | Missense_Mutation | C | T | p.G98S |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 112184998 | 112185132 | 112185084 | 112185084 | Nonsense_Mutation | C | T | p.W350* |
| TGBC11TKB_STOMACH | 112216776 | 112216854 | 112216783 | 112216783 | Nonsense_Mutation | G | A | p.Q121* |
| LS411N_LARGE_INTESTINE | 112219453 | 112219495 | 112219454 | 112219454 | Splice_Site | T | G | p.K96N |
| SNU81_LARGE_INTESTINE | 112219572 | 112219679 | 112219678 | 112219678 | Splice_Site | T | G | p.K47T |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN3 |
| 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 PTPN3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPN3 |
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RelatedDrugs for PTPN3 |
| 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 PTPN3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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