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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 CTSL |
 Gene summary |
| Gene information | Gene symbol | CTSL | Gene ID | 1514 |
| Gene name | cathepsin L | |
| Synonyms | CATL|CTSL1|MEP | |
| Cytomap | 9q21.33 | |
| Type of gene | protein-coding | |
| Description | cathepsin L1major excreted protein | |
| Modification date | 20180523 | |
| UniProtAcc | P07711 | |
| Context | PubMed: CTSL [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 |
| CTSL | GO:0006508 | proteolysis | 8811434|21326229 |
| CTSL | GO:0030574 | collagen catabolic process | 22952693 |
| CTSL | GO:0051603 | proteolysis involved in cellular protein catabolic process | 22952693 |
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Exon skipping events across known transcript of Ensembl for CTSL 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 CTSL |
| 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 CTSL |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_496824 | 9 | 90341054:90341168:90342508:90342644:90342941:90343064 | 90342508:90342644 | ENSG00000135047.10 | ENST00000342020.5,ENST00000340342.6 |
| exon_skip_496828 | 9 | 90341054:90341223:90342508:90342644:90342941:90343064 | 90342508:90342644 | ENSG00000135047.10 | ENST00000482054.1 |
| exon_skip_496835 | 9 | 90342948:90343064:90343164:90343311:90343499:90343724 | 90343164:90343311 | ENSG00000135047.10 | ENST00000342020.5,ENST00000375894.5,ENST00000343150.5,ENST00000482054.1,ENST00000340342.6 |
| exon_skip_496839 | 9 | 90343164:90343311:90343499:90343724:90344487:90344595 | 90343499:90343724 | ENSG00000135047.10 | ENST00000375894.5,ENST00000343150.5,ENST00000482054.1,ENST00000340342.6 |
| exon_skip_496843 | 9 | 90344556:90344650:90345295:90345413:90345922:90345988 | 90345295:90345413 | ENSG00000135047.10 | ENST00000375894.5,ENST00000495822.1,ENST00000343150.5,ENST00000340342.6 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CTSL |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_496824 | 9 | 90341054:90341168:90342508:90342644:90342941:90343064 | 90342508:90342644 | ENSG00000135047.10 | ENST00000340342.6,ENST00000342020.5 |
| exon_skip_496828 | 9 | 90341054:90341223:90342508:90342644:90342941:90343064 | 90342508:90342644 | ENSG00000135047.10 | ENST00000482054.1 |
| exon_skip_496835 | 9 | 90342948:90343064:90343164:90343311:90343499:90343724 | 90343164:90343311 | ENSG00000135047.10 | ENST00000343150.5,ENST00000340342.6,ENST00000375894.5,ENST00000342020.5,ENST00000482054.1 |
| exon_skip_496839 | 9 | 90343164:90343311:90343499:90343724:90344487:90344595 | 90343499:90343724 | ENSG00000135047.10 | ENST00000343150.5,ENST00000340342.6,ENST00000375894.5,ENST00000482054.1 |
| exon_skip_496843 | 9 | 90344556:90344650:90345295:90345413:90345922:90345988 | 90345295:90345413 | ENSG00000135047.10 | ENST00000343150.5,ENST00000340342.6,ENST00000375894.5,ENST00000495822.1 |
| 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 CTSL |
| 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 |
| ENST00000340342 | 90342508 | 90342644 | 5CDS-5UTR |
| ENST00000340342 | 90345295 | 90345413 | Frame-shift |
| ENST00000343150 | 90345295 | 90345413 | Frame-shift |
| ENST00000340342 | 90343164 | 90343311 | In-frame |
| ENST00000343150 | 90343164 | 90343311 | In-frame |
| ENST00000340342 | 90343499 | 90343724 | In-frame |
| ENST00000343150 | 90343499 | 90343724 | 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 |
| ENST00000340342 | 90342508 | 90342644 | 5CDS-5UTR |
| ENST00000340342 | 90345295 | 90345413 | Frame-shift |
| ENST00000343150 | 90345295 | 90345413 | Frame-shift |
| ENST00000340342 | 90343164 | 90343311 | In-frame |
| ENST00000343150 | 90343164 | 90343311 | In-frame |
| ENST00000340342 | 90343499 | 90343724 | In-frame |
| ENST00000343150 | 90343499 | 90343724 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CTSL |
| 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 |
| ENST00000340342 | 1453 | 333 | 90343164 | 90343311 | 405 | 551 | 83 | 132 |
| ENST00000343150 | 2194 | 333 | 90343164 | 90343311 | 1140 | 1286 | 83 | 132 |
| ENST00000340342 | 1453 | 333 | 90343499 | 90343724 | 552 | 776 | 132 | 207 |
| ENST00000343150 | 2194 | 333 | 90343499 | 90343724 | 1287 | 1511 | 132 | 207 |
| 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 |
| ENST00000340342 | 1453 | 333 | 90343164 | 90343311 | 405 | 551 | 83 | 132 |
| ENST00000343150 | 2194 | 333 | 90343164 | 90343311 | 1140 | 1286 | 83 | 132 |
| ENST00000340342 | 1453 | 333 | 90343499 | 90343724 | 552 | 776 | 132 | 207 |
| ENST00000343150 | 2194 | 333 | 90343499 | 90343724 | 1287 | 1511 | 132 | 207 |
| 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 |
| P07711 | 83 | 132 | 103 | 105 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CJL |
| P07711 | 83 | 132 | 103 | 105 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CJL |
| P07711 | 83 | 132 | 116 | 119 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6EZX |
| P07711 | 83 | 132 | 116 | 119 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6EZX |
| P07711 | 83 | 132 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 83 | 132 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 83 | 132 | 85 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CS8 |
| P07711 | 83 | 132 | 85 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CS8 |
| P07711 | 83 | 132 | 120 | 123 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 83 | 132 | 120 | 123 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 83 | 132 | 18 | 113 | Propeptide | ID=PRO_0000026244;Note=Activation peptide |
| P07711 | 83 | 132 | 18 | 113 | Propeptide | ID=PRO_0000026244;Note=Activation peptide |
| P07711 | 132 | 207 | 138 | 138 | Active site | . |
| P07711 | 132 | 207 | 138 | 138 | Active site | . |
| P07711 | 132 | 207 | 134 | 136 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 134 | 136 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 196 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 196 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 132 | 207 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 132 | 207 | 135 | 178 | Disulfide bond | . |
| P07711 | 132 | 207 | 135 | 178 | Disulfide bond | . |
| P07711 | 132 | 207 | 169 | 211 | Disulfide bond | . |
| P07711 | 132 | 207 | 169 | 211 | Disulfide bond | . |
| P07711 | 132 | 207 | 138 | 155 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 138 | 155 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 163 | 169 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 163 | 169 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 177 | 179 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU4 |
| P07711 | 132 | 207 | 177 | 179 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU4 |
| P07711 | 132 | 207 | 183 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 183 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 171 | 174 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 171 | 174 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 199 | 201 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 199 | 201 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| 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 |
| P07711 | 83 | 132 | 103 | 105 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CJL |
| P07711 | 83 | 132 | 103 | 105 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CJL |
| P07711 | 83 | 132 | 116 | 119 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6EZX |
| P07711 | 83 | 132 | 116 | 119 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:6EZX |
| P07711 | 83 | 132 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 83 | 132 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 83 | 132 | 85 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CS8 |
| P07711 | 83 | 132 | 85 | 92 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1CS8 |
| P07711 | 83 | 132 | 120 | 123 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 83 | 132 | 120 | 123 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 83 | 132 | 18 | 113 | Propeptide | ID=PRO_0000026244;Note=Activation peptide |
| P07711 | 83 | 132 | 18 | 113 | Propeptide | ID=PRO_0000026244;Note=Activation peptide |
| P07711 | 132 | 207 | 138 | 138 | Active site | . |
| P07711 | 132 | 207 | 138 | 138 | Active site | . |
| P07711 | 132 | 207 | 134 | 136 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 134 | 136 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 196 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 196 | 198 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 132 | 207 | 114 | 288 | Chain | ID=PRO_0000026245;Note=Cathepsin L1 heavy chain |
| P07711 | 132 | 207 | 135 | 178 | Disulfide bond | . |
| P07711 | 132 | 207 | 135 | 178 | Disulfide bond | . |
| P07711 | 132 | 207 | 169 | 211 | Disulfide bond | . |
| P07711 | 132 | 207 | 169 | 211 | Disulfide bond | . |
| P07711 | 132 | 207 | 138 | 155 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 138 | 155 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 163 | 169 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 163 | 169 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 177 | 179 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU4 |
| P07711 | 132 | 207 | 177 | 179 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU4 |
| P07711 | 132 | 207 | 183 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 183 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 171 | 174 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 171 | 174 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 199 | 201 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
| P07711 | 132 | 207 | 199 | 201 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2XU3 |
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SNVs in the skipped exons for CTSL |
| - 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-G3-A3CJ-01 | exon_skip_496835 | 90343165 | 90343311 | 90343213 | 90343213 | Frame_Shift_Del | C | - | p.P100fs |
| LIHC | TCGA-DD-A39Y-01 | 90343500 | 90343724 | 90343523 | 90343523 | Frame_Shift_Del | T | - | p.A140fs |
| - 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 |
| SNUC4_LARGE_INTESTINE | 90343165 | 90343311 | 90343256 | 90343256 | Frame_Shift_Del | C | - | p.A114fs |
| SKMEL24_SKIN | 90342509 | 90342644 | 90342526 | 90342526 | Missense_Mutation | C | T | p.P3L |
| CORL88_LUNG | 90342509 | 90342644 | 90342594 | 90342594 | Missense_Mutation | G | C | p.E26Q |
| FEPD_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 90343165 | 90343311 | 90343208 | 90343208 | Missense_Mutation | G | A | p.R98H |
| KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 90343500 | 90343724 | 90343531 | 90343531 | Missense_Mutation | C | T | p.A143V |
| HEC6_ENDOMETRIUM | 90343500 | 90343724 | 90343543 | 90343543 | Missense_Mutation | T | C | p.L147P |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 90343500 | 90343724 | 90343545 | 90343545 | Missense_Mutation | G | C | p.E148Q |
| NCIH841_LUNG | 90343500 | 90343724 | 90343561 | 90343561 | Missense_Mutation | G | T | p.R153L |
| CW2_LARGE_INTESTINE | 90343500 | 90343724 | 90343570 | 90343570 | Missense_Mutation | G | T | p.G156V |
| HEC251_ENDOMETRIUM | 90343500 | 90343724 | 90343595 | 90343595 | Missense_Mutation | G | T | p.Q164H |
| LNCAPCLONEFGC_PROSTATE | 90343500 | 90343724 | 90343633 | 90343633 | Missense_Mutation | G | A | p.G177D |
| SNU81_LARGE_INTESTINE | 90345296 | 90345413 | 90345328 | 90345328 | Missense_Mutation | G | T | p.D273Y |
| SW48_LARGE_INTESTINE | 90345296 | 90345413 | 90345353 | 90345353 | Missense_Mutation | T | C | p.V281A |
| NB12_AUTONOMIC_GANGLIA | 90345296 | 90345413 | 90345383 | 90345383 | Missense_Mutation | A | T | p.D291V |
| MDAMB435S_SKIN | 90345296 | 90345413 | 90345389 | 90345389 | Missense_Mutation | A | G | p.N293S |
| HT115_LARGE_INTESTINE | 90342509 | 90342644 | 90342555 | 90342555 | Nonsense_Mutation | G | T | p.G13* |
| HEC1A_ENDOMETRIUM | 90343165 | 90343311 | 90343183 | 90343183 | Nonsense_Mutation | C | T | p.Q90* |
| BICR22_UPPER_AERODIGESTIVE_TRACT | 90345296 | 90345413 | 90345380 | 90345380 | Nonsense_Mutation | C | G | p.S290* |
| CW2_LARGE_INTESTINE | 90343165 | 90343311 | 90343166 | 90343166 | Splice_Site | C | T | p.T84I |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CTSL |
| 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 CTSL |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CTSL |
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RelatedDrugs for CTSL |
| 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 |
| P07711 | DB12010 | Fostamatinib | Cathepsin L1 | small molecule | approved|investigational |
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RelatedDiseases for CTSL |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CTSL | C0025286 | Meningioma | 1 | CTD_human |
| CTSL | C0033687 | Proteinuria | 1 | CTD_human |
| CTSL | C0038356 | Stomach Neoplasms | 1 | CTD_human |
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