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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 USP6 |
 Gene summary |
| Gene information | Gene symbol | USP6 | Gene ID | 9098 |
| Gene name | ubiquitin specific peptidase 6 | |
| Synonyms | HRP1|TRE17|TRE2|TRESMCR|Tre-2|USP6-short | |
| Cytomap | 17p13.2 | |
| Type of gene | protein-coding | |
| Description | ubiquitin carboxyl-terminal hydrolase 6TBC1D3 and USP32 fusiondeubiquitinating enzyme 6hyperpolymorphic gene 1proto-oncogene TRE-2ubiquitin specific peptidase 6 (Tre-2 oncogene)ubiquitin specific protease 6 (Tre-2 oncogene)ubiquitin thioesterase 6 | |
| Modification date | 20180523 | |
| UniProtAcc | P35125 | |
| Context | PubMed: USP6 [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 |
| USP6 | GO:0016579 | protein deubiquitination | 16127172 |
| USP6 | GO:0060627 | regulation of vesicle-mediated transport | 15509780 |
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Exon skipping events across known transcript of Ensembl for USP6 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 USP6 |
| 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 USP6 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_148251 | 17 | 5030798:5030934:5032246:5032428:5033230:5033384 | 5032246:5032428 | ENSG00000129204.12 | ENST00000332776.4,ENST00000574788.1 |
| exon_skip_148252 | 17 | 5039934:5040029:5040415:5040481:5040945:5041045 | 5040415:5040481 | ENSG00000129204.12 | ENST00000304328.5,ENST00000575709.1,ENST00000250066.6,ENST00000332776.4,ENST00000574788.1,ENST00000572949.1 |
| exon_skip_148253 | 17 | 5041415:5041568:5042265:5042476:5042549:5042969 | 5042265:5042476 | ENSG00000129204.12 | ENST00000304328.5,ENST00000575709.1 |
| exon_skip_148254 | 17 | 5045297:5045436:5045691:5045797:5047984:5048158 | 5045691:5045797 | ENSG00000129204.12 | ENST00000304328.5,ENST00000575709.1,ENST00000250066.6,ENST00000332776.4,ENST00000574788.1,ENST00000572949.1 |
| exon_skip_148255 | 17 | 5049317:5049469:5050377:5050489:5051850:5052062 | 5050377:5050489 | ENSG00000129204.12 | ENST00000304328.5,ENST00000575709.1,ENST00000250066.6,ENST00000574788.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for USP6 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_148251 | 17 | 5030798:5030934:5032246:5032428:5033230:5033384 | 5032246:5032428 | ENSG00000129204.12 | ENST00000574788.1,ENST00000332776.4 |
| exon_skip_148252 | 17 | 5039934:5040029:5040415:5040481:5040945:5041045 | 5040415:5040481 | ENSG00000129204.12 | ENST00000574788.1,ENST00000332776.4,ENST00000575709.1,ENST00000572949.1,ENST00000250066.6,ENST00000304328.5 |
| exon_skip_148254 | 17 | 5045297:5045436:5045691:5045797:5047984:5048158 | 5045691:5045797 | ENSG00000129204.12 | ENST00000574788.1,ENST00000332776.4,ENST00000575709.1,ENST00000572949.1,ENST00000250066.6,ENST00000304328.5 |
| exon_skip_148255 | 17 | 5049317:5049469:5050377:5050489:5051850:5052062 | 5050377:5050489 | ENSG00000129204.12 | ENST00000574788.1,ENST00000575709.1,ENST00000250066.6,ENST00000304328.5 |
| 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 USP6 |
| 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 |
| ENST00000574788 | 5032246 | 5032428 | 5UTR-5UTR |
| ENST00000250066 | 5045691 | 5045797 | Frame-shift |
| ENST00000574788 | 5045691 | 5045797 | Frame-shift |
| ENST00000250066 | 5050377 | 5050489 | Frame-shift |
| ENST00000574788 | 5050377 | 5050489 | Frame-shift |
| ENST00000250066 | 5040415 | 5040481 | In-frame |
| ENST00000574788 | 5040415 | 5040481 | 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 |
| ENST00000574788 | 5032246 | 5032428 | 5UTR-5UTR |
| ENST00000250066 | 5045691 | 5045797 | Frame-shift |
| ENST00000574788 | 5045691 | 5045797 | Frame-shift |
| ENST00000250066 | 5050377 | 5050489 | Frame-shift |
| ENST00000574788 | 5050377 | 5050489 | Frame-shift |
| ENST00000250066 | 5040415 | 5040481 | In-frame |
| ENST00000574788 | 5040415 | 5040481 | In-frame |
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Infer the effects of exon skipping event on protein functional features for USP6 |
| 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 |
| ENST00000250066 | 7993 | 1406 | 5040415 | 5040481 | 2459 | 2524 | 253 | 275 |
| ENST00000574788 | 8481 | 1406 | 5040415 | 5040481 | 2990 | 3055 | 253 | 275 |
| 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 |
| ENST00000250066 | 7993 | 1406 | 5040415 | 5040481 | 2459 | 2524 | 253 | 275 |
| ENST00000574788 | 8481 | 1406 | 5040415 | 5040481 | 2990 | 3055 | 253 | 275 |
| 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 |
| P35125 | 253 | 275 | 1 | 317 | Alternative sequence | ID=VSP_010878;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1565468;Dbxref=PMID:1565468 |
| P35125 | 253 | 275 | 1 | 317 | Alternative sequence | ID=VSP_010878;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1565468;Dbxref=PMID:1565468 |
| P35125 | 253 | 275 | 1 | 1406 | Chain | ID=PRO_0000080625;Note=Ubiquitin carboxyl-terminal hydrolase 6 |
| P35125 | 253 | 275 | 1 | 1406 | Chain | ID=PRO_0000080625;Note=Ubiquitin carboxyl-terminal hydrolase 6 |
| P35125 | 253 | 275 | 100 | 292 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| P35125 | 253 | 275 | 100 | 292 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| 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 |
| P35125 | 253 | 275 | 1 | 317 | Alternative sequence | ID=VSP_010878;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1565468;Dbxref=PMID:1565468 |
| P35125 | 253 | 275 | 1 | 317 | Alternative sequence | ID=VSP_010878;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:1565468;Dbxref=PMID:1565468 |
| P35125 | 253 | 275 | 1 | 1406 | Chain | ID=PRO_0000080625;Note=Ubiquitin carboxyl-terminal hydrolase 6 |
| P35125 | 253 | 275 | 1 | 1406 | Chain | ID=PRO_0000080625;Note=Ubiquitin carboxyl-terminal hydrolase 6 |
| P35125 | 253 | 275 | 100 | 292 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
| P35125 | 253 | 275 | 100 | 292 | Domain | Note=Rab-GAP TBC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00163 |
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SNVs in the skipped exons for USP6 |
| - 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-DD-A1EG-01 | exon_skip_148254 | 5045692 | 5045797 | 5045757 | 5045757 | Frame_Shift_Del | G | - | p.W593fs |
| GBM | TCGA-27-1831-01 | exon_skip_148255 | 5050378 | 5050489 | 5050405 | 5050405 | Nonsense_Mutation | C | T | p.Q783* |
| - 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 |
| LOUNH91_LUNG | 5050378 | 5050489 | 5050433 | 5050433 | Missense_Mutation | C | A | p.A792E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for USP6 |
| 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 USP6 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USP6 |
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RelatedDrugs for USP6 |
| 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 USP6 |
| 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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