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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 PTPN13 |
 Gene summary |
| Gene information | Gene symbol | PTPN13 | Gene ID | 5783 |
| Gene name | protein tyrosine phosphatase non-receptor type 13 | |
| Synonyms | FAP-1|PNP1|PTP-BAS|PTP-BL|PTP1E|PTPL1|PTPLE|hPTP1E | |
| Cytomap | 4q21.3 | |
| Type of gene | protein-coding | |
| Description | tyrosine-protein phosphatase non-receptor type 13fas-associated protein-tyrosine phosphatase 1hPTPE1protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)protein-tyrosine phosphatase 1Eprotein-tyrosine phosphatas | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PTPN13 | GO:0006470 | protein dephosphorylation | 17657516|19307596 |
| PTPN13 | GO:0014066 | regulation of phosphatidylinositol 3-kinase signaling | 23604317 |
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Gene structures and expression levels for PTPN13 |
| 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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ENSG00000163629
| 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 |
| IFG | UP | ENST00000436978.5 | PTPN13-204:protein_coding:PTPN13 | 1.971581e+01 | 2.251159e+01 | 3.605922e-19 | 9.095795e-15 |
| TC | UP | ENST00000511105.1 | PTPN13-208:retained_intron:PTPN13 | 4.931851e+00 | 8.104567e-01 | 5.866993e-04 | 6.527866e-03 |
| 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 PTPN13 |
| 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_124582 | chr4 | 86751027:86751124:86753009:86753065:86758260:86758349 | 86753009:86753065 |
| exon_skip_134794 | chr4 | 86753009:86753065:86758260:86758349:86758678:86758785 | 86758260:86758349 |
| exon_skip_150571 | chr4 | 86689005:86689190:86693587:86693674:86701241:86701801 | 86693587:86693674 |
| exon_skip_152988 | chr4 | 86693587:86693674:86701241:86701801:86716530:86716625 | 86701241:86701801 |
| exon_skip_154464 | chr4 | 86635252:86635371:86672365:86672543:86686710:86686775 | 86672365:86672543 |
| exon_skip_158590 | chr4 | 86672365:86672543:86686710:86686775:86689005:86689061 | 86686710:86686775 |
| exon_skip_159308 | chr4 | 86716530:86716625:86717024:86717117:86722212:86722434 | 86717024:86717117 |
| exon_skip_169009 | chr4 | 86796874:86796929:86799101:86799204:86803709:86803857 | 86799101:86799204 |
| exon_skip_181611 | chr4 | 86769769:86769983:86770101:86770199:86771171:86771535 | 86770101:86770199 |
| exon_skip_18583 | chr4 | 86693591:86693674:86701241:86701801:86716530:86716625 | 86701241:86701801 |
| exon_skip_210374 | chr4 | 86769904:86769983:86770101:86770199:86771171:86771535 | 86770101:86770199 |
| exon_skip_240091 | chr4 | 86758942:86759073:86762727:86763190:86764593:86764724 | 86762727:86763190 |
| exon_skip_254645 | chr4 | 86722212:86722434:86732400:86732474:86732592:86732766 | 86732400:86732474 |
| exon_skip_273819 | chr4 | 86741634:86741816:86744966:86745128:86750470:86750887 | 86744966:86745128 |
| exon_skip_288293 | chr4 | 86744966:86745128:86758260:86758349:86758678:86758785 | 86758260:86758349 |
| exon_skip_33676 | chr4 | 86782201:86782262:86784465:86784558:86785231:86785368 | 86784465:86784558 |
| exon_skip_47509 | chr4 | 86767817:86767976:86769769:86769983:86770101:86770199 | 86769769:86769983 |
| exon_skip_53620 | chr4 | 86594732:86594789:86635252:86635371:86672365:86672543 | 86635252:86635371 |
| exon_skip_6674 | chr4 | 86765395:86765488:86766432:86766517:86767817:86767976 | 86766432:86766517 |
| exon_skip_72033 | chr4 | 86758678:86758785:86758942:86759073:86762727:86762934 | 86758942:86759073 |
| exon_skip_92788 | chr4 | 86766432:86766517:86767817:86767976:86769769:86769983 | 86767817:86767976 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for PTPN13 |
| 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 |
| ENST00000411767 | 86635252 | 86635371 | 5CDS-5UTR |
| ENST00000411767 | 86672365 | 86672543 | Frame-shift |
| ENST00000411767 | 86693587 | 86693674 | Frame-shift |
| ENST00000411767 | 86744966 | 86745128 | Frame-shift |
| ENST00000411767 | 86767817 | 86767976 | Frame-shift |
| ENST00000411767 | 86769769 | 86769983 | Frame-shift |
| ENST00000411767 | 86701241 | 86701801 | In-frame |
| ENST00000411767 | 86753009 | 86753065 | In-frame |
| ENST00000411767 | 86758942 | 86759073 | In-frame |
| ENST00000411767 | 86770101 | 86770199 | In-frame |
| 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 |
| ENST00000411767 | 86635252 | 86635371 | 5CDS-5UTR |
| ENST00000411767 | 86672365 | 86672543 | Frame-shift |
| ENST00000411767 | 86693587 | 86693674 | Frame-shift |
| ENST00000411767 | 86717024 | 86717117 | Frame-shift |
| ENST00000411767 | 86762727 | 86763190 | Frame-shift |
| ENST00000411767 | 86784465 | 86784558 | Frame-shift |
| ENST00000411767 | 86686710 | 86686775 | In-frame |
| ENST00000411767 | 86701241 | 86701801 | In-frame |
| ENST00000411767 | 86753009 | 86753065 | In-frame |
| ENST00000411767 | 86770101 | 86770199 | In-frame |
| 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 |
| ENST00000411767 | 86635252 | 86635371 | 5CDS-5UTR |
| ENST00000411767 | 86693587 | 86693674 | Frame-shift |
| ENST00000411767 | 86744966 | 86745128 | Frame-shift |
| ENST00000411767 | 86766432 | 86766517 | Frame-shift |
| ENST00000411767 | 86767817 | 86767976 | Frame-shift |
| ENST00000411767 | 86769769 | 86769983 | Frame-shift |
| ENST00000411767 | 86784465 | 86784558 | Frame-shift |
| ENST00000411767 | 86799101 | 86799204 | Frame-shift |
| ENST00000411767 | 86701241 | 86701801 | In-frame |
| ENST00000411767 | 86732400 | 86732474 | In-frame |
| ENST00000411767 | 86753009 | 86753065 | In-frame |
| ENST00000411767 | 86758260 | 86758349 | In-frame |
| ENST00000411767 | 86770101 | 86770199 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPN13 |
p-ENSG00000163629_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 |
| ENST00000411767 | 8136 | 2485 | 86701241 | 86701801 | 699 | 1258 | 212 | 398 |
| ENST00000411767 | 8136 | 2485 | 86753009 | 86753065 | 3231 | 3286 | 1056 | 1074 |
| ENST00000411767 | 8136 | 2485 | 86758942 | 86759073 | 3486 | 3616 | 1141 | 1184 |
| ENST00000411767 | 8136 | 2485 | 86770101 | 86770199 | 4769 | 4866 | 1568 | 1601 |
| 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 |
| ENST00000411767 | 8136 | 2485 | 86686710 | 86686775 | 359 | 423 | 98 | 120 |
| ENST00000411767 | 8136 | 2485 | 86701241 | 86701801 | 699 | 1258 | 212 | 398 |
| ENST00000411767 | 8136 | 2485 | 86753009 | 86753065 | 3231 | 3286 | 1056 | 1074 |
| ENST00000411767 | 8136 | 2485 | 86770101 | 86770199 | 4769 | 4866 | 1568 | 1601 |
| 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 |
| ENST00000411767 | 8136 | 2485 | 86701241 | 86701801 | 699 | 1258 | 212 | 398 |
| ENST00000411767 | 8136 | 2485 | 86732400 | 86732474 | 1673 | 1746 | 536 | 561 |
| ENST00000411767 | 8136 | 2485 | 86753009 | 86753065 | 3231 | 3286 | 1056 | 1074 |
| ENST00000411767 | 8136 | 2485 | 86758260 | 86758349 | 3288 | 3376 | 1075 | 1104 |
| ENST00000411767 | 8136 | 2485 | 86770101 | 86770199 | 4769 | 4866 | 1568 | 1601 |
| 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 |
| Q12923 | 212 | 398 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 212 | 398 | 240 | 240 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q12923 | 212 | 398 | 301 | 301 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64512 |
| Q12923 | 212 | 398 | 302 | 302 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64512 |
| Q12923 | 1056 | 1074 | 884 | 1074 | Alternative sequence | ID=VSP_000496;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8287977;Dbxref=PMID:8287977 |
| Q12923 | 1056 | 1074 | 1056 | 1074 | Alternative sequence | ID=VSP_000497;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7929060,ECO:0000303|PubMed:8287977;Dbxref=PMID:15489334,PMID:7929060,PMID:8287977 |
| Q12923 | 1056 | 1074 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1141 | 1184 | 1143 | 1147 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5GLJ |
| Q12923 | 1141 | 1184 | 1169 | 1177 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5GLJ |
| Q12923 | 1141 | 1184 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1141 | 1184 | 1093 | 1178 | Domain | Note=PDZ 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| Q12923 | 1141 | 1184 | 1157 | 1166 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5GLJ |
| Q12923 | 1568 | 1601 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1568 | 1601 | 1501 | 1588 | Domain | Note=PDZ 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| 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 |
| Q12923 | 98 | 120 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 98 | 120 | 3 | 190 | Domain | Note=KIND;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00709 |
| Q12923 | 212 | 398 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 212 | 398 | 240 | 240 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q12923 | 212 | 398 | 301 | 301 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64512 |
| Q12923 | 212 | 398 | 302 | 302 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64512 |
| Q12923 | 1056 | 1074 | 884 | 1074 | Alternative sequence | ID=VSP_000496;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8287977;Dbxref=PMID:8287977 |
| Q12923 | 1056 | 1074 | 1056 | 1074 | Alternative sequence | ID=VSP_000497;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7929060,ECO:0000303|PubMed:8287977;Dbxref=PMID:15489334,PMID:7929060,PMID:8287977 |
| Q12923 | 1056 | 1074 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1568 | 1601 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1568 | 1601 | 1501 | 1588 | Domain | Note=PDZ 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| 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 |
| Q12923 | 212 | 398 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 212 | 398 | 240 | 240 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q12923 | 212 | 398 | 301 | 301 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64512 |
| Q12923 | 212 | 398 | 302 | 302 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64512 |
| Q12923 | 536 | 561 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1056 | 1074 | 884 | 1074 | Alternative sequence | ID=VSP_000496;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:8287977;Dbxref=PMID:8287977 |
| Q12923 | 1056 | 1074 | 1056 | 1074 | Alternative sequence | ID=VSP_000497;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7929060,ECO:0000303|PubMed:8287977;Dbxref=PMID:15489334,PMID:7929060,PMID:8287977 |
| Q12923 | 1056 | 1074 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1075 | 1104 | 1090 | 1097 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5GLJ |
| Q12923 | 1075 | 1104 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1075 | 1104 | 1093 | 1178 | Domain | Note=PDZ 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| Q12923 | 1075 | 1104 | 1085 | 1085 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q12923 | 1075 | 1104 | 1100 | 1102 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5GLJ |
| Q12923 | 1568 | 1601 | 1 | 2485 | Chain | ID=PRO_0000219435;Note=Tyrosine-protein phosphatase non-receptor type 13 |
| Q12923 | 1568 | 1601 | 1501 | 1588 | Domain | Note=PDZ 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTPN13 |
| 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 PTPN13 |
| - 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 PTPN13 |
| 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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN13 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| PCC | exon_skip_53620 | rs12505291 | chr4:86590418 | 1.615328e-06 | 5.193387e-04 |
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Correlation with RNA binding proteins (RBPs) for PTPN13 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | MSI1 | exon_skip_152988 | 4.675686e-01 | 1.211173e-02 |
| IFG | NOVA1 | exon_skip_124582 | -4.192991e-01 | 4.139335e-02 |
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RelatedDrugs for PTPN13 |
| 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 PTPN13 |
| 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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