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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 USP3 |
 Gene summary |
| Gene information | Gene symbol | USP3 | Gene ID | 9960 |
| Gene name | ubiquitin specific peptidase 3 | |
| Synonyms | SIH003|UBP | |
| Cytomap | 15q22.31 | |
| Type of gene | protein-coding | |
| Description | ubiquitin carboxyl-terminal hydrolase 3deubiquitinating enzyme 3ubiquitin thioesterase 3ubiquitin thiolesterase 3ubiquitin-specific-processing protease 3 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y6I4 | |
| Context | PubMed: USP3 [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 |
| USP3 | GO:0016578 | histone deubiquitination | 17980597 |
| USP3 | GO:0031647 | regulation of protein stability | 17980597 |
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Exon skipping events across known transcript of Ensembl for USP3 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 USP3 |
| 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 USP3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_122628 | 15 | 63796932:63797029:63821212:63821365:63824845:63824906 | 63821212:63821365 | ENSG00000140455.12 | ENST00000268049.7,ENST00000557884.1,ENST00000558157.1 |
| exon_skip_122631 | 15 | 63796932:63797029:63824845:63824906:63829223:63829255 | 63824845:63824906 | ENSG00000140455.12 | ENST00000380324.3,ENST00000536001.1 |
| exon_skip_122632 | 15 | 63796932:63797029:63824845:63824906:63845913:63845932 | 63824845:63824906 | ENSG00000140455.12 | ENST00000560070.1,ENST00000540797.1 |
| exon_skip_122639 | 15 | 63820031:63820339:63821212:63821365:63824845:63824906 | 63821212:63821365 | ENSG00000140455.12 | ENST00000559276.1 |
| exon_skip_122641 | 15 | 63824845:63824906:63826001:63826117:63829223:63829255 | 63826001:63826117 | ENSG00000140455.12 | ENST00000557884.1,ENST00000559192.1 |
| exon_skip_122642 | 15 | 63824845:63824906:63829223:63829355:63845913:63845932 | 63829223:63829355 | ENSG00000140455.12 | ENST00000380324.3,ENST00000536001.1,ENST00000558285.1,ENST00000268049.7,ENST00000558157.1,ENST00000561442.1,ENST00000559771.1 |
| exon_skip_122643 | 15 | 63829336:63829355:63834253:63834391:63845913:63845932 | 63834253:63834391 | ENSG00000140455.12 | ENST00000538686.2 |
| exon_skip_122644 | 15 | 63829336:63829355:63845913:63845997:63848865:63848900 | 63845913:63845997 | ENSG00000140455.12 | ENST00000380324.3,ENST00000536001.1,ENST00000559257.1,ENST00000558285.1,ENST00000268049.7,ENST00000557884.1,ENST00000558157.1,ENST00000559192.1,ENST00000559771.1 |
| exon_skip_122646 | 15 | 63848865:63848947:63850304:63850387:63852055:63852083 | 63850304:63850387 | ENSG00000140455.12 | ENST00000380324.3,ENST00000559711.1,ENST00000559257.1,ENST00000558285.1,ENST00000268049.7,ENST00000557884.1,ENST00000558157.1,ENST00000538686.2,ENST00000559192.1,ENST00000540797.1 |
| exon_skip_122649 | 15 | 63850304:63850387:63852055:63852169:63855093:63855207 | 63852055:63852169 | ENSG00000140455.12 | ENST00000380324.3,ENST00000559711.1,ENST00000559257.1,ENST00000558285.1,ENST00000268049.7,ENST00000558157.1,ENST00000538686.2,ENST00000559192.1,ENST00000540797.1 |
| exon_skip_122653 | 15 | 63855093:63855207:63862631:63862778:63866244:63866351 | 63862631:63862778 | ENSG00000140455.12 | ENST00000380324.3,ENST00000536001.1,ENST00000559711.1,ENST00000559257.1,ENST00000558285.1,ENST00000268049.7,ENST00000558157.1,ENST00000539772.1,ENST00000538686.2,ENST00000561326.1,ENST00000559192.1,ENST00000540797.1 |
| exon_skip_122655 | 15 | 63866521:63866602:63880503:63880622:63880900:63881014 | 63880503:63880622 | ENSG00000140455.12 | ENST00000380324.3,ENST00000559711.1,ENST00000559257.1,ENST00000558285.1,ENST00000268049.7,ENST00000558157.1,ENST00000539772.1,ENST00000538686.2,ENST00000559192.1,ENST00000540797.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for USP3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_122628 | 15 | 63796932:63797029:63821212:63821365:63824845:63824906 | 63821212:63821365 | ENSG00000140455.12 | ENST00000557884.1,ENST00000558157.1,ENST00000268049.7 |
| exon_skip_122631 | 15 | 63796932:63797029:63824845:63824906:63829223:63829255 | 63824845:63824906 | ENSG00000140455.12 | ENST00000380324.3,ENST00000536001.1 |
| exon_skip_122632 | 15 | 63796932:63797029:63824845:63824906:63845913:63845932 | 63824845:63824906 | ENSG00000140455.12 | ENST00000560070.1,ENST00000540797.1 |
| exon_skip_122634 | 15 | 63796932:63797029:63855093:63855207:63862631:63862778 | 63855093:63855207 | ENSG00000140455.12 | ENST00000561326.1,ENST00000539772.1 |
| exon_skip_122639 | 15 | 63820031:63820339:63821212:63821365:63824845:63824906 | 63821212:63821365 | ENSG00000140455.12 | ENST00000559276.1 |
| exon_skip_122641 | 15 | 63824845:63824906:63826001:63826117:63829223:63829255 | 63826001:63826117 | ENSG00000140455.12 | ENST00000557884.1,ENST00000559192.1 |
| exon_skip_122642 | 15 | 63824845:63824906:63829223:63829355:63845913:63845932 | 63829223:63829355 | ENSG00000140455.12 | ENST00000561442.1,ENST00000380324.3,ENST00000558157.1,ENST00000268049.7,ENST00000536001.1,ENST00000559771.1,ENST00000558285.1 |
| exon_skip_122643 | 15 | 63829336:63829355:63834253:63834391:63845913:63845932 | 63834253:63834391 | ENSG00000140455.12 | ENST00000538686.2 |
| exon_skip_122644 | 15 | 63829336:63829355:63845913:63845997:63848865:63848900 | 63845913:63845997 | ENSG00000140455.12 | ENST00000380324.3,ENST00000557884.1,ENST00000558157.1,ENST00000268049.7,ENST00000536001.1,ENST00000559192.1,ENST00000559771.1,ENST00000558285.1,ENST00000559257.1 |
| exon_skip_122646 | 15 | 63848865:63848947:63850304:63850387:63852055:63852083 | 63850304:63850387 | ENSG00000140455.12 | ENST00000540797.1,ENST00000380324.3,ENST00000557884.1,ENST00000558157.1,ENST00000268049.7,ENST00000559192.1,ENST00000558285.1,ENST00000559257.1,ENST00000538686.2,ENST00000559711.1 |
| exon_skip_122649 | 15 | 63850304:63850387:63852055:63852169:63855093:63855207 | 63852055:63852169 | ENSG00000140455.12 | ENST00000540797.1,ENST00000380324.3,ENST00000558157.1,ENST00000268049.7,ENST00000559192.1,ENST00000558285.1,ENST00000559257.1,ENST00000538686.2,ENST00000559711.1 |
| exon_skip_122653 | 15 | 63855093:63855207:63862631:63862778:63866244:63866351 | 63862631:63862778 | ENSG00000140455.12 | ENST00000540797.1,ENST00000380324.3,ENST00000558157.1,ENST00000268049.7,ENST00000561326.1,ENST00000536001.1,ENST00000539772.1,ENST00000559192.1,ENST00000558285.1,ENST00000559257.1,ENST00000538686.2,ENST00000559711.1 |
| exon_skip_122655 | 15 | 63866521:63866602:63880503:63880622:63880900:63881014 | 63880503:63880622 | ENSG00000140455.12 | ENST00000540797.1,ENST00000380324.3,ENST00000558157.1,ENST00000268049.7,ENST00000539772.1,ENST00000559192.1,ENST00000558285.1,ENST00000559257.1,ENST00000538686.2,ENST00000559711.1 |
| 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 USP3 |
| 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 |
| ENST00000380324 | 63824845 | 63824906 | Frame-shift |
| ENST00000380324 | 63850304 | 63850387 | Frame-shift |
| ENST00000380324 | 63880503 | 63880622 | Frame-shift |
| ENST00000380324 | 63829223 | 63829355 | In-frame |
| ENST00000380324 | 63845913 | 63845997 | In-frame |
| ENST00000380324 | 63852055 | 63852169 | In-frame |
| ENST00000380324 | 63862631 | 63862778 | 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 |
| ENST00000380324 | 63824845 | 63824906 | Frame-shift |
| ENST00000380324 | 63850304 | 63850387 | Frame-shift |
| ENST00000380324 | 63880503 | 63880622 | Frame-shift |
| ENST00000380324 | 63829223 | 63829355 | In-frame |
| ENST00000380324 | 63845913 | 63845997 | In-frame |
| ENST00000380324 | 63852055 | 63852169 | In-frame |
| ENST00000380324 | 63862631 | 63862778 | In-frame |
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Infer the effects of exon skipping event on protein functional features for USP3 |
| 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 |
| ENST00000380324 | 2350 | 520 | 63829223 | 63829355 | 282 | 413 | 51 | 94 |
| ENST00000380324 | 2350 | 520 | 63845913 | 63845997 | 414 | 497 | 95 | 122 |
| ENST00000380324 | 2350 | 520 | 63852055 | 63852169 | 663 | 776 | 178 | 215 |
| ENST00000380324 | 2350 | 520 | 63862631 | 63862778 | 891 | 1037 | 254 | 302 |
| 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 |
| ENST00000380324 | 2350 | 520 | 63829223 | 63829355 | 282 | 413 | 51 | 94 |
| ENST00000380324 | 2350 | 520 | 63845913 | 63845997 | 414 | 497 | 95 | 122 |
| ENST00000380324 | 2350 | 520 | 63852055 | 63852169 | 663 | 776 | 178 | 215 |
| ENST00000380324 | 2350 | 520 | 63862631 | 63862778 | 891 | 1037 | 254 | 302 |
| 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 |
| Q9Y6I4 | 51 | 94 | 51 | 95 | Alternative sequence | ID=VSP_044712;Note=In isoform 2. RYVNGHAKKHYEDAQVPLTNHKKSEKQDKVQHTVCMDCSSYSTYC->S;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9Y6I4 | 51 | 94 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 51 | 94 | 56 | 56 | Mutagenesis | Note=Does not reduce monoubiquitinated H2A and H2B stability. Interaction with monoubiquitinated H2A is strongly inhibited. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17980597;Dbxref=PMID:17980597 |
| Q9Y6I4 | 51 | 94 | 27 | 104 | Zinc finger | Note=UBP-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00502 |
| Q9Y6I4 | 95 | 122 | 51 | 95 | Alternative sequence | ID=VSP_044712;Note=In isoform 2. RYVNGHAKKHYEDAQVPLTNHKKSEKQDKVQHTVCMDCSSYSTYC->S;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9Y6I4 | 95 | 122 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 95 | 122 | 27 | 104 | Zinc finger | Note=UBP-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00502 |
| Q9Y6I4 | 178 | 215 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 178 | 215 | 159 | 511 | Domain | Note=USP |
| Q9Y6I4 | 254 | 302 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 254 | 302 | 159 | 511 | Domain | Note=USP |
| 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 |
| Q9Y6I4 | 51 | 94 | 51 | 95 | Alternative sequence | ID=VSP_044712;Note=In isoform 2. RYVNGHAKKHYEDAQVPLTNHKKSEKQDKVQHTVCMDCSSYSTYC->S;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9Y6I4 | 51 | 94 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 51 | 94 | 56 | 56 | Mutagenesis | Note=Does not reduce monoubiquitinated H2A and H2B stability. Interaction with monoubiquitinated H2A is strongly inhibited. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17980597;Dbxref=PMID:17980597 |
| Q9Y6I4 | 51 | 94 | 27 | 104 | Zinc finger | Note=UBP-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00502 |
| Q9Y6I4 | 95 | 122 | 51 | 95 | Alternative sequence | ID=VSP_044712;Note=In isoform 2. RYVNGHAKKHYEDAQVPLTNHKKSEKQDKVQHTVCMDCSSYSTYC->S;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9Y6I4 | 95 | 122 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 95 | 122 | 27 | 104 | Zinc finger | Note=UBP-type;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00502 |
| Q9Y6I4 | 178 | 215 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 178 | 215 | 159 | 511 | Domain | Note=USP |
| Q9Y6I4 | 254 | 302 | 1 | 520 | Chain | ID=PRO_0000080619;Note=Ubiquitin carboxyl-terminal hydrolase 3 |
| Q9Y6I4 | 254 | 302 | 159 | 511 | Domain | Note=USP |
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SNVs in the skipped exons for USP3 |
| - 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-A39Y-01 | exon_skip_122642 | 63829224 | 63829355 | 63829242 | 63829242 | Frame_Shift_Del | A | - | p.A35fs |
| UCS | TCGA-N7-A4Y0-01 | exon_skip_122642 | 63829224 | 63829355 | 63829242 | 63829242 | Frame_Shift_Del | A | - | p.A35fs |
| UCS | TCGA-N7-A4Y0-01 | exon_skip_122642 | 63829224 | 63829355 | 63829242 | 63829242 | Frame_Shift_Del | A | - | p.A57fs |
| STAD | TCGA-CG-5721-01 | exon_skip_122644 | 63845914 | 63845997 | 63845976 | 63845977 | Frame_Shift_Del | AA | - | p.116_116del |
| STAD | TCGA-CG-5721-01 | exon_skip_122644 | 63845914 | 63845997 | 63845976 | 63845977 | Frame_Shift_Del | AA | - | p.E116fs |
| LUAD | TCGA-78-7155-01 | exon_skip_122653 | 63862632 | 63862778 | 63862705 | 63862705 | Frame_Shift_Del | G | - | p.G257fs |
| LUAD | TCGA-78-7155-01 | exon_skip_122653 | 63862632 | 63862778 | 63862705 | 63862705 | Frame_Shift_Del | G | - | p.G279fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_122655 | 63880504 | 63880622 | 63880592 | 63880592 | Frame_Shift_Del | A | - | p.T373fs |
| UCEC | TCGA-BG-A0M9-01 | exon_skip_122642 | 63829224 | 63829355 | 63829241 | 63829242 | Frame_Shift_Ins | - | A | p.A57fs |
| THYM | TCGA-XH-A853-01 | exon_skip_122642 | 63829224 | 63829355 | 63829294 | 63829294 | Nonsense_Mutation | G | T | p.E75X |
| ESCA | TCGA-Z6-A8JD-01 | exon_skip_122653 | 63862632 | 63862778 | 63862741 | 63862741 | Nonsense_Mutation | G | T | p.E291* |
| ESCA | TCGA-Z6-A8JD-01 | exon_skip_122653 | 63862632 | 63862778 | 63862741 | 63862741 | Nonsense_Mutation | G | T | p.E291X |
| - 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 |
| HCC1833_LUNG | 63824846 | 63824906 | 63824885 | 63824885 | Missense_Mutation | G | C | p.C44S |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 63845914 | 63845997 | 63845927 | 63845927 | Missense_Mutation | G | A | p.D100N |
| CAL51_BREAST | 63845914 | 63845997 | 63845970 | 63845970 | Missense_Mutation | T | C | p.V114A |
| EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 63850305 | 63850387 | 63850309 | 63850309 | Missense_Mutation | G | C | p.S152T |
| CP67MEL_SKIN | 63852056 | 63852169 | 63852071 | 63852071 | Missense_Mutation | T | G | p.F183L |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 63852056 | 63852169 | 63852163 | 63852163 | Missense_Mutation | A | G | p.N214S |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 63852056 | 63852169 | 63852163 | 63852163 | Missense_Mutation | A | G | p.N214S |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 63862632 | 63862778 | 63862651 | 63862651 | Missense_Mutation | G | A | p.A261T |
| HCT15_LARGE_INTESTINE | 63862632 | 63862778 | 63862651 | 63862651 | Missense_Mutation | G | A | p.A261T |
| MDAMB415_BREAST | 63862632 | 63862778 | 63862666 | 63862666 | Missense_Mutation | C | T | p.R266C |
| SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 63862632 | 63862778 | 63862666 | 63862666 | Missense_Mutation | C | T | p.R266C |
| MERO84_LUNG | 63862632 | 63862778 | 63862667 | 63862667 | Missense_Mutation | G | A | p.R266H |
| NCIH1623_LUNG | 63829224 | 63829355 | 63829224 | 63829224 | Splice_Site | G | C | p.R51S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for USP3 |
| 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 |
| exon_skip_122643 | 15 | 63829336:63829355:63834253:63834391:63845913:63845932 | 63834253:63834391 | ENST00000538686.2 | COAD | rs1421151 | chr15:63834319 | A/T | 1.00e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USP3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USP3 |
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RelatedDrugs for USP3 |
| 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 USP3 |
| 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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