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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 PTPRR |
 Gene summary |
| Gene information | Gene symbol | PTPRR | Gene ID | 5801 |
| Gene name | protein tyrosine phosphatase receptor type R | |
| Synonyms | EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ | |
| Cytomap | 12q15 | |
| Type of gene | protein-coding | |
| Description | receptor-type tyrosine-protein phosphatase RCh-1 PTPaseNC-PTPCOM1R-PTP-Rch-1PTPaseprotein tyrosine phosphatase Cr1PTPaseprotein-tyrosine phosphatase NC-PTPCOM1protein-tyrosine phosphatase PCPTP1 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 27131904(Transcriptomic gene-network analysis of exposure to silver nanoparticle reveals potentially neurodegenerative progression in mouse brain neural cells) |
| 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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Gene structures and expression levels for PTPRR |
| 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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ENSG00000153233
| 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 |
| PCC | UP | ENST00000547752.5 | PTPRR-206:lncRNA:PTPRR | 1.396464e+01 | 1.756547e+00 | 1.139600e-03 | 2.755942e-02 |
| STG | DOWN | ENST00000537619.6 | PTPRR-205:lncRNA:PTPRR | 2.996825e+01 | -9.385689e-01 | 1.311515e-03 | 4.432912e-02 |
| PG | DOWN | ENST00000537619.6 | PTPRR-205:lncRNA:PTPRR | 1.737189e+01 | -9.157250e-01 | 7.264856e-06 | 3.967426e-04 |
| CB | UP | ENST00000548220.1 | PTPRR-207:lncRNA:PTPRR | 9.339018e+00 | 1.383521e+00 | 1.391987e-09 | 5.722966e-08 |
| 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 PTPRR |
| 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_102709 | chr12 | 70745818:70746086:70754191:70754301:70761471:70761626 | 70754191:70754301 |
| exon_skip_145204 | chr12 | 70764665:70764778:70892679:70892977:70920333:70920738 | 70892679:70892977 |
| exon_skip_177621 | chr12 | 70639130:70639277:70639519:70639672:70656704:70656812 | 70639519:70639672 |
| exon_skip_206410 | chr12 | 70698265:70698349:70701137:70701323:70745818:70746086 | 70701137:70701323 |
| exon_skip_226153 | chr12 | 70639130:70639277:70656704:70656817:70660940:70661097 | 70656704:70656817 |
| exon_skip_235503 | chr12 | 70662495:70662605:70672720:70672976:70684127:70684264 | 70672720:70672976 |
| exon_skip_49215 | chr12 | 70639130:70639277:70639519:70639672:70656704:70656817 | 70639519:70639672 |
| 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 PTPRR |
| 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 |
| ENST00000283228 | 70701137 | 70701323 | Frame-shift |
| ENST00000283228 | 70754191 | 70754301 | 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 |
| ENST00000283228 | 70701137 | 70701323 | Frame-shift |
| 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 |
| ENST00000283228 | 70701137 | 70701323 | Frame-shift |
| ENST00000283228 | 70892679 | 70892977 | Frame-shift |
| ENST00000283228 | 70656704 | 70656817 | In-frame |
| ENST00000283228 | 70754191 | 70754301 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPRR |
p-ENSG00000153233_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 |
| ENST00000283228 | 3546 | 657 | 70754191 | 70754301 | 1081 | 1190 | 209 | 245 |
| 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 |
| ENST00000283228 | 3546 | 657 | 70754191 | 70754301 | 1081 | 1190 | 209 | 245 |
| ENST00000283228 | 3546 | 657 | 70656704 | 70656817 | 2220 | 2332 | 589 | 626 |
| 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 |
| Q15256 | 209 | 245 | 1 | 245 | Alternative sequence | ID=VSP_005156;Note=In isoform Gamma. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10705342;Dbxref=PMID:10705342 |
| Q15256 | 209 | 245 | 207 | 209 | Alternative sequence | ID=VSP_005158;Note=In isoform Delta. SPE->MNQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10705342;Dbxref=PMID:10705342 |
| Q15256 | 209 | 245 | 22 | 657 | Chain | ID=PRO_0000025459;Note=Receptor-type tyrosine-protein phosphatase R |
| Q15256 | 209 | 245 | 22 | 227 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q15256 | 209 | 245 | 228 | 248 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q15256 | 209 | 245 | 1 | 245 | Alternative sequence | ID=VSP_005156;Note=In isoform Gamma. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10705342;Dbxref=PMID:10705342 |
| Q15256 | 209 | 245 | 207 | 209 | Alternative sequence | ID=VSP_005158;Note=In isoform Delta. SPE->MNQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10705342;Dbxref=PMID:10705342 |
| Q15256 | 209 | 245 | 22 | 657 | Chain | ID=PRO_0000025459;Note=Receptor-type tyrosine-protein phosphatase R |
| Q15256 | 209 | 245 | 22 | 227 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q15256 | 209 | 245 | 228 | 248 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q15256 | 589 | 626 | 589 | 592 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2A8B |
| Q15256 | 589 | 626 | 612 | 614 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2A8B |
| Q15256 | 589 | 626 | 22 | 657 | Chain | ID=PRO_0000025459;Note=Receptor-type tyrosine-protein phosphatase R |
| Q15256 | 589 | 626 | 393 | 647 | Domain | Note=Tyrosine-protein phosphatase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
| Q15256 | 589 | 626 | 593 | 611 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2A8B |
| Q15256 | 589 | 626 | 616 | 626 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2A8B |
| Q15256 | 589 | 626 | 588 | 594 | Region | Note=Substrate binding;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q15256 | 589 | 626 | 249 | 657 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTPRR |
| 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 PTPRR |
| - 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 PTPRR |
| 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 PTPRR |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for PTPRR |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PTPRR |
| 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 PTPRR |
| 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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