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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 USP28 |
 Gene summary |
| Gene information | Gene symbol | USP28 | Gene ID | 57646 |
| Gene name | ubiquitin specific peptidase 28 | |
| Synonyms | - | |
| Cytomap | 11q23.2 | |
| Type of gene | protein-coding | |
| Description | ubiquitin carboxyl-terminal hydrolase 28deubiquitinating enzyme 28ubiquitin carboxyl-terminal hydrolase 28 variant 1ubiquitin thioesterase 28ubiquitin thiolesterase 28ubiquitin-specific-processing protease 28 | |
| 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 |
| USP28 | GO:0006974 | cellular response to DNA damage stimulus | 17873522 |
| USP28 | GO:0010212 | response to ionizing radiation | 16901786 |
| USP28 | GO:0016579 | protein deubiquitination | 16901786|17558397|18662541 |
| USP28 | GO:0034644 | cellular response to UV | 17873522 |
| USP28 | GO:0042771 | intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator | 16901786 |
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Gene structures and expression levels for USP28 |
| 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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ENSG00000048028
| 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 |
| PG | DOWN | ENST00000538224.1 | USP28-206:protein_coding:USP28 | 2.474742e+00 | -9.052366e-01 | 6.641010e-04 | 1.083425e-02 |
| CB | UP | ENST00000545608.5 | USP28-215:nonsense_mediated_decay:USP28 | 3.538353e+00 | 1.800470e+00 | 3.474812e-11 | 2.657942e-09 |
| CB | UP | ENST00000542033.5 | USP28-210:lncRNA:USP28 | 1.167408e+01 | 2.278782e+00 | 3.610326e-06 | 4.454565e-05 |
| CB | UP | ENST00000535607.5 | USP28-202:nonsense_mediated_decay:USP28 | 1.407989e+00 | 1.852823e+00 | 3.843077e-06 | 4.690515e-05 |
| CB | UP | ENST00000545540.5 | USP28-214:protein_coding:USP28 | 4.179814e+01 | 1.283896e+00 | 5.036403e-06 | 5.892347e-05 |
| CB | UP | ENST00000540925.5 | USP28-209:protein_coding:USP28 | 3.308475e+00 | 1.082574e+00 | 1.326199e-05 | 1.337161e-04 |
| CB | UP | ENST00000538475.5 | USP28-207:protein_coding:USP28 | 2.203232e+00 | 1.247078e+00 | 9.222249e-05 | 6.915060e-04 |
| CB | DOWN | ENST00000497221.1 | DUSP28-205:lncRNA:DUSP28 | 4.808765e+00 | -8.308815e-01 | 1.641169e-03 | 7.819513e-03 |
| CB | UP | ENST00000537642.1 | USP28-204:protein_coding:USP28 | 4.450066e+00 | 9.679182e-01 | 3.032455e-03 | 1.302066e-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 USP28 |
| 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_106349 | chr11 | 113827233:113827360:113828844:113828920:113829197:113829345 | 113828844:113828920 |
| exon_skip_11337 | chr11 | 113815174:113815382:113817658:113817837:113823605:113823700 | 113817658:113817837 |
| exon_skip_129939 | chr11 | 113833424:113833557:113834249:113834335:113840598:113840757 | 113834249:113834335 |
| exon_skip_135909 | chr11 | 113833420:113833557:113834249:113834335:113840598:113840757 | 113834249:113834335 |
| exon_skip_14431 | chr11 | 113841663:113841768:113852501:113852633:113854258:113854335 | 113852501:113852633 |
| exon_skip_157199 | chr11 | 113830883:113830943:113831920:113831993:113833420:113833470 | 113831920:113831993 |
| exon_skip_164719 | chr11 | 113829221:113829345:113830867:113830943:113833420:113833552 | 113830867:113830943 |
| exon_skip_176479 | chr11 | 113830883:113830943:113831920:113831993:113833420:113833557 | 113831920:113831993 |
| exon_skip_176626 | chr11 | 113854258:113854335:113874517:113874879:113875445:113875496 | 113874517:113874879 |
| exon_skip_18335 | chr11 | 113830883:113830943:113831920:113831989:113833420:113833557 | 113831920:113831989 |
| exon_skip_187740 | chr11 | 113834249:113834335:113835207:113835327:113840598:113840757 | 113835207:113835327 |
| exon_skip_210185 | chr11 | 113806489:113806584:113808023:113808136:113808298:113808437 | 113808023:113808136 |
| exon_skip_217756 | chr11 | 113829221:113829345:113830867:113830943:113833420:113833470 | 113830867:113830943 |
| exon_skip_228188 | chr11 | 113829221:113829345:113830867:113830946:113833420:113833470 | 113830867:113830946 |
| exon_skip_234861 | chr11 | 113852622:113852633:113854258:113854335:113874517:113874800 | 113854258:113854335 |
| exon_skip_261893 | chr11 | 113854258:113854335:113874517:113874800:113875445:113875536 | 113874517:113874800 |
| exon_skip_264054 | chr11 | 113812279:113812504:113813885:113813955:113815174:113815382 | 113813885:113813955 |
| exon_skip_265084 | chr11 | 113852622:113852633:113854258:113854335:113875445:113875496 | 113854258:113854335 |
| exon_skip_269231 | chr11 | 113804928:113805046:113806489:113806584:113808298:113808437 | 113806489:113806584 |
| exon_skip_40976 | chr11 | 113815174:113815382:113817658:113817837:113823605:113823688 | 113817658:113817837 |
| exon_skip_45830 | chr11 | 113829221:113829345:113830867:113830946:113833420:113833517 | 113830867:113830946 |
| exon_skip_52122 | chr11 | 113804673:113804751:113804868:113805046:113808298:113808437 | 113804868:113805046 |
| exon_skip_53637 | chr11 | 113799062:113799415:113801483:113801678:113803158:113803281 | 113801483:113801678 |
| exon_skip_6769 | chr11 | 113803158:113803281:113803798:113803877:113804673:113804751 | 113803798:113803877 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_269231 | ROSMAP_PCC | 5.137864e-01 | 6.235294e-01 | -1.097430e-01 | 2.220841e-02 |
| exon_skip_269231 | Mayo_CB | 5.246341e-01 | 6.977941e-01 | -1.731600e-01 | 1.041919e-06 |
| exon_skip_71043 | Mayo_CB | 5.255000e-01 | 6.375758e-01 | -1.120758e-01 | 6.769730e-05 |
| exon_skip_106349 | Mayo_CB | 1.375309e-01 | 2.574603e-01 | -1.199295e-01 | 3.408191e-06 |
| exon_skip_273316 | Mayo_CB | 6.261842e-01 | 7.812500e-01 | -1.550658e-01 | 7.814067e-07 |
| exon_skip_269231 | Mayo_TC | 3.797500e-01 | 5.340984e-01 | -1.543484e-01 | 8.774119e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for USP28 |
| 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 |
| ENST00000003302 | 113801483 | 113801678 | Frame-shift |
| ENST00000003302 | 113803798 | 113803877 | Frame-shift |
| ENST00000003302 | 113831920 | 113831993 | Frame-shift |
| ENST00000003302 | 113852501 | 113852633 | Frame-shift |
| ENST00000003302 | 113806489 | 113806584 | In-frame |
| ENST00000003302 | 113817658 | 113817837 | In-frame |
| ENST00000003302 | 113834249 | 113834335 | 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 |
| ENST00000003302 | 113831920 | 113831993 | Frame-shift |
| ENST00000003302 | 113806489 | 113806584 | In-frame |
| ENST00000003302 | 113834249 | 113834335 | In-frame |
| 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 |
| ENST00000003302 | 113803798 | 113803877 | Frame-shift |
| ENST00000003302 | 113813885 | 113813955 | Frame-shift |
| ENST00000003302 | 113831920 | 113831993 | Frame-shift |
| ENST00000003302 | 113852501 | 113852633 | Frame-shift |
| ENST00000003302 | 113806489 | 113806584 | In-frame |
| ENST00000003302 | 113817658 | 113817837 | In-frame |
| ENST00000003302 | 113834249 | 113834335 | In-frame |
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Infer the effects of exon skipping event on protein functional features for USP28 |
p-ENSG00000048028_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 |
| ENST00000003302 | 4686 | 1077 | 113834249 | 113834335 | 604 | 689 | 178 | 206 |
| ENST00000003302 | 4686 | 1077 | 113817658 | 113817837 | 1353 | 1531 | 428 | 487 |
| ENST00000003302 | 4686 | 1077 | 113806489 | 113806584 | 2374 | 2468 | 768 | 799 |
| 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 |
| ENST00000003302 | 4686 | 1077 | 113834249 | 113834335 | 604 | 689 | 178 | 206 |
| ENST00000003302 | 4686 | 1077 | 113806489 | 113806584 | 2374 | 2468 | 768 | 799 |
| 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 |
| ENST00000003302 | 4686 | 1077 | 113834249 | 113834335 | 604 | 689 | 178 | 206 |
| ENST00000003302 | 4686 | 1077 | 113817658 | 113817837 | 1353 | 1531 | 428 | 487 |
| ENST00000003302 | 4686 | 1077 | 113806489 | 113806584 | 2374 | 2468 | 768 | 799 |
| 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 |
| Q96RU2 | 178 | 206 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| Q96RU2 | 178 | 206 | 162 | 650 | Domain | Note=USP |
| Q96RU2 | 428 | 487 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| Q96RU2 | 428 | 487 | 162 | 650 | Domain | Note=USP |
| Q96RU2 | 768 | 799 | 584 | 1077 | Alternative sequence | ID=VSP_057360;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96RU2 | 768 | 799 | 769 | 800 | Alternative sequence | ID=VSP_015580;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10819331;Dbxref=PMID:10819331 |
| Q96RU2 | 768 | 799 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| 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 |
| Q96RU2 | 178 | 206 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| Q96RU2 | 178 | 206 | 162 | 650 | Domain | Note=USP |
| Q96RU2 | 768 | 799 | 584 | 1077 | Alternative sequence | ID=VSP_057360;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96RU2 | 768 | 799 | 769 | 800 | Alternative sequence | ID=VSP_015580;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10819331;Dbxref=PMID:10819331 |
| Q96RU2 | 768 | 799 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| 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 |
| Q96RU2 | 178 | 206 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| Q96RU2 | 178 | 206 | 162 | 650 | Domain | Note=USP |
| Q96RU2 | 428 | 487 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
| Q96RU2 | 428 | 487 | 162 | 650 | Domain | Note=USP |
| Q96RU2 | 768 | 799 | 584 | 1077 | Alternative sequence | ID=VSP_057360;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96RU2 | 768 | 799 | 769 | 800 | Alternative sequence | ID=VSP_015580;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10819331;Dbxref=PMID:10819331 |
| Q96RU2 | 768 | 799 | 1 | 1077 | Chain | ID=PRO_0000080657;Note=Ubiquitin carboxyl-terminal hydrolase 28 |
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3'-UTR located exon skipping events that lost miRNA binding sites in USP28 |
| 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 USP28 |
| - 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 USP28 |
| 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 USP28 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_269231 | rs10789970 | chr11:113903224 | 8.924266e-05 | 1.583686e-02 |
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Correlation with RNA binding proteins (RBPs) for USP28 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | DAZAP1 | exon_skip_269231 | -4.394158e-01 | 1.849452e-08 |
| CB | PCBP4 | exon_skip_269231 | 4.974496e-01 | 9.424927e-11 |
| CB | TRA2A | exon_skip_269231 | -6.089639e-01 | 1.365125e-16 |
| CB | RBM6 | exon_skip_71043 | -4.954146e-01 | 2.053322e-10 |
| CB | RBM3 | exon_skip_71043 | 4.188403e-01 | 1.430305e-07 |
| CB | PCBP4 | exon_skip_71043 | 4.376971e-01 | 3.303558e-08 |
| CB | TRA2A | exon_skip_71043 | -5.444506e-01 | 1.217677e-12 |
| CB | NUP42 | exon_skip_71043 | 4.764137e-01 | 1.214926e-09 |
| CB | PABPC1 | exon_skip_71043 | 4.722487e-01 | 1.768379e-09 |
| CB | RBM3 | exon_skip_214857 | -4.436229e-01 | 2.870397e-08 |
| CB | TRA2A | exon_skip_214857 | 4.247130e-01 | 1.245232e-07 |
| CB | HNRNPA1 | exon_skip_106349 | 5.560269e-01 | 4.666285e-13 |
| CB | FUBP3 | exon_skip_106349 | 4.225598e-01 | 1.321988e-07 |
| CB | FUBP1 | exon_skip_106349 | -4.304881e-01 | 7.223807e-08 |
| CB | HNRNPA2B1 | exon_skip_106349 | -4.427920e-01 | 2.741122e-08 |
| CB | TARDBP | exon_skip_273316 | -4.390640e-01 | 1.391037e-07 |
| CB | ZNF638 | exon_skip_273316 | -5.146520e-01 | 2.739765e-10 |
| CB | RBM6 | exon_skip_273316 | -4.932665e-01 | 1.866187e-09 |
| CB | CNOT4 | exon_skip_273316 | -4.180555e-01 | 6.108028e-07 |
| CB | TRA2A | exon_skip_273316 | -4.671582e-01 | 1.634825e-08 |
| CB | NUP42 | exon_skip_273316 | 5.465053e-01 | 1.213836e-11 |
| CB | PTBP1 | exon_skip_273316 | -4.957681e-01 | 1.501166e-09 |
| CB | TARDBP | exon_skip_157199 | -4.709840e-01 | 7.347503e-08 |
| HCC | HNRNPF | exon_skip_269231 | -4.631785e-01 | 3.442123e-12 |
| TC | ILF2 | exon_skip_269231 | 4.594323e-01 | 1.001044e-08 |
| TC | HNRNPA0 | exon_skip_269231 | 6.413017e-01 | 1.065536e-17 |
| TC | HNRNPA1L2 | exon_skip_106349 | 4.168822e-01 | 4.451862e-07 |
| TC | HNRNPD | exon_skip_106349 | 5.483458e-01 | 4.836656e-12 |
| TC | RALYL | exon_skip_106349 | 5.046729e-01 | 3.733046e-10 |
| TC | HNRNPH2 | exon_skip_106349 | 5.127917e-01 | 1.742553e-10 |
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RelatedDrugs for USP28 |
| 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 USP28 |
| 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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