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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 PTPRM |
 Gene summary |
| Gene information | Gene symbol | PTPRM | Gene ID | 5797 |
| Gene name | protein tyrosine phosphatase receptor type M | |
| Synonyms | PTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu | |
| Cytomap | 18p11.23 | |
| Type of gene | protein-coding | |
| Description | receptor-type tyrosine-protein phosphatase muprotein tyrosine phosphatase muprotein tyrosine phosphatase, receptor type, mu polypeptide | |
| 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 |
| PTPRM | GO:0006470 | protein dephosphorylation | 8393854|10809770 |
| PTPRM | GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | 8393854 |
| PTPRM | GO:0007165 | signal transduction | 15080886 |
| PTPRM | GO:0031175 | neuron projection development | 16380380 |
| PTPRM | GO:0031290 | retinal ganglion cell axon guidance | 15080886 |
| PTPRM | GO:0042493 | response to drug | 18566238 |
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Gene structures and expression levels for PTPRM |
| 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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ENSG00000173482
| 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 |
| TC | UP | ENST00000400053.8 | PTPRM-202:protein_coding:PTPRM | 1.421874e+02 | 8.311849e-01 | 7.632470e-03 | 4.587286e-02 |
| 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 PTPRM |
| 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_191987 | chr18 | 8114791:8114827:8122242:8122316:8143647:8143778 | 8122242:8122316 |
| exon_skip_206443 | chr18 | 8379167:8379340:8380296:8380427:8384561:8384686 | 8380296:8380427 |
| exon_skip_244243 | chr18 | 8343423:8343520:8370890:8371006:8376046:8376200 | 8370890:8371006 |
| exon_skip_260052 | chr18 | 8247874:8247919:8248150:8248176:8252488:8252499 | 8248150:8248176 |
| exon_skip_274816 | chr18 | 8248150:8248176:8252488:8252499:8253227:8253414 | 8252488:8252499 |
| exon_skip_69553 | chr18 | 8370933:8371006:8371760:8371810:8376046:8376200 | 8371760:8371810 |
| exon_skip_99932 | chr18 | 8247874:8247919:8253227:8253414:8296368:8296455 | 8253227:8253414 |
| 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 PTPRM |
| 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 |
| ENST00000332175 | 8253227 | 8253414 | Frame-shift |
| ENST00000332175 | 8380296 | 8380427 | 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 |
| ENST00000332175 | 8253227 | 8253414 | 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 |
| ENST00000332175 | 8253227 | 8253414 | Frame-shift |
| ENST00000332175 | 8370890 | 8371006 | In-frame |
| ENST00000332175 | 8380296 | 8380427 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTPRM |
p-ENSG00000173482_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 |
| ENST00000332175 | 6112 | 1452 | 8380296 | 8380427 | 4786 | 4916 | 1249 | 1293 |
| 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 |
| ENST00000332175 | 6112 | 1452 | 8370890 | 8371006 | 4054 | 4169 | 1005 | 1044 |
| ENST00000332175 | 6112 | 1452 | 8380296 | 8380427 | 4786 | 4916 | 1249 | 1293 |
| 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 |
| P28827 | 1249 | 1293 | 21 | 1452 | Chain | ID=PRO_0000025448;Note=Receptor-type tyrosine-protein phosphatase mu |
| P28827 | 1249 | 1293 | 1186 | 1448 | Domain | Note=Tyrosine-protein phosphatase 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
| P28827 | 1249 | 1293 | 765 | 1452 | Topological domain | Note=Cytoplasmic;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 |
| P28827 | 1005 | 1044 | 1014 | 1019 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1RPM |
| P28827 | 1005 | 1044 | 1022 | 1032 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1RPM |
| P28827 | 1005 | 1044 | 1035 | 1044 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1RPM |
| P28827 | 1005 | 1044 | 21 | 1452 | Chain | ID=PRO_0000025448;Note=Receptor-type tyrosine-protein phosphatase mu |
| P28827 | 1005 | 1044 | 900 | 1154 | Domain | Note=Tyrosine-protein phosphatase 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
| P28827 | 1005 | 1044 | 765 | 1452 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P28827 | 1249 | 1293 | 21 | 1452 | Chain | ID=PRO_0000025448;Note=Receptor-type tyrosine-protein phosphatase mu |
| P28827 | 1249 | 1293 | 1186 | 1448 | Domain | Note=Tyrosine-protein phosphatase 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00160 |
| P28827 | 1249 | 1293 | 765 | 1452 | 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 PTPRM |
| 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 PTPRM |
| - 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 PTPRM |
| 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 PTPRM |
| 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 PTPRM |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | KHDRBS2 | exon_skip_191987 | 6.419541e-01 | 3.704339e-17 |
| CB | EIF4G2 | exon_skip_191987 | 4.528675e-01 | 3.099813e-08 |
| CB | SRSF9 | exon_skip_191987 | 5.087971e-01 | 2.541387e-10 |
| CB | HNRNPK | exon_skip_71699 | 4.055206e-01 | 5.226494e-06 |
| CB | SRSF9 | exon_skip_69553 | 4.847494e-01 | 4.920863e-10 |
| CB | HNRNPH2 | exon_skip_69553 | 4.970398e-01 | 1.517526e-10 |
| HCC | RBM6 | exon_skip_191987 | -5.291099e-01 | 5.031055e-21 |
| HCC | TRNAU1AP | exon_skip_191987 | -4.618425e-01 | 8.912629e-16 |
| HCC | QKI | exon_skip_191987 | -5.369791e-01 | 1.019301e-21 |
| HCC | SF1 | exon_skip_191987 | -4.275475e-01 | 1.631395e-13 |
| HCC | RBM45 | exon_skip_191987 | -4.563205e-01 | 2.146350e-15 |
| HCC | EIF4G2 | exon_skip_191987 | -4.189555e-01 | 5.502186e-13 |
| HCC | PABPC1 | exon_skip_191987 | -4.142017e-01 | 1.062362e-12 |
| HCC | SRSF5 | exon_skip_191987 | -4.960915e-01 | 2.644597e-18 |
| HCC | TIA1 | exon_skip_71699 | -4.979878e-01 | 1.879187e-18 |
| HCC | TRNAU1AP | exon_skip_71699 | -4.432587e-01 | 1.612787e-14 |
| HCC | SFPQ | exon_skip_69553 | -5.758196e-01 | 2.018919e-25 |
| HCC | RBM6 | exon_skip_69553 | -5.740846e-01 | 3.027854e-25 |
| HCC | CNOT4 | exon_skip_69553 | -4.182097e-01 | 6.104726e-13 |
| HCC | HNRNPA2B1 | exon_skip_69553 | -4.571544e-01 | 1.881473e-15 |
| HCC | HNRNPF | exon_skip_69553 | -5.369819e-01 | 1.018705e-21 |
| PCC | RBM6 | exon_skip_191987 | -4.765595e-01 | 3.914411e-13 |
| PCC | TRNAU1AP | exon_skip_191987 | -4.952906e-01 | 3.277599e-14 |
| PCC | QKI | exon_skip_191987 | -5.313525e-01 | 1.765733e-16 |
| PCC | PABPC1 | exon_skip_191987 | -4.878221e-01 | 8.972412e-14 |
| PCC | TRNAU1AP | exon_skip_71699 | -4.556638e-01 | 3.670473e-12 |
| PCC | RBM6 | exon_skip_69553 | -4.313833e-01 | 4.588147e-11 |
| PCC | PUM1 | exon_skip_69553 | 4.558839e-01 | 2.502135e-12 |
| PCC | HNRNPF | exon_skip_69553 | -5.089971e-01 | 1.940517e-15 |
| TC | MBNL1 | exon_skip_191987 | 4.292097e-01 | 5.815887e-08 |
| TC | KHDRBS2 | exon_skip_191987 | 8.357041e-01 | 1.431581e-39 |
| TC | RBM45 | exon_skip_191987 | 4.254667e-01 | 7.787571e-08 |
| TC | EIF4G2 | exon_skip_191987 | 4.384467e-01 | 2.786718e-08 |
| TC | RBM25 | exon_skip_69553 | 4.187007e-01 | 7.199497e-08 |
| TC | ILF2 | exon_skip_69553 | 4.827910e-01 | 2.614610e-10 |
| TC | PUM1 | exon_skip_69553 | 5.267770e-01 | 2.663975e-12 |
| TC | NUP42 | exon_skip_69553 | 5.626249e-01 | 3.767895e-14 |
| TC | HNRNPH2 | exon_skip_69553 | 6.713023e-01 | 2.188876e-21 |
| TC | ESRP1 | exon_skip_69553 | 4.881244e-01 | 1.551422e-10 |
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RelatedDrugs for PTPRM |
| 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 PTPRM |
| 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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