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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 USP16 |
 Gene summary |
| Gene information | Gene symbol | USP16 | Gene ID | 10600 |
| Gene name | ubiquitin specific peptidase 16 | |
| Synonyms | UBP-M|UBPM | |
| Cytomap | 21q21.3 | |
| Type of gene | protein-coding | |
| Description | ubiquitin carboxyl-terminal hydrolase 16deubiquitinating enzyme 16ubiquitin specific protease 16ubiquitin thioesterase 16ubiquitin thiolesterase 16ubiquitin-processing protease UBP-Mubiquitin-specific processing protease 16 | |
| Modification date | 20200313 | |
| UniProtAcc | H9KVB6, Q9Y5T5, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| USP16 | GO:0000278 | mitotic cell cycle | 17914355 |
| USP16 | GO:0006974 | cellular response to DNA damage stimulus | 20550933 |
| USP16 | GO:0016578 | histone deubiquitination | 17914355 |
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Gene structures and expression levels for USP16 |
| 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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ENSG00000156256
| 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 | UP | ENST00000399976.7 | USP16-204:protein_coding:USP16 | 1.060103e+02 | 9.514433e-01 | 5.130488e-03 | 4.648840e-02 |
| CB | UP | ENST00000228862.3 | DUSP16-201:protein_coding:DUSP16 | 9.541206e+01 | 1.219400e+00 | 3.221589e-05 | 2.831620e-04 |
| CB | UP | ENST00000541207.1 | DUSP16-205:protein_coding:DUSP16 | 1.624871e+00 | 1.097388e+00 | 4.116401e-04 | 2.444408e-03 |
| CB | DOWN | ENST00000399976.7 | USP16-204:protein_coding:USP16 | 2.470532e+02 | -1.425719e+00 | 1.345573e-02 | 4.418771e-02 |
| TC | UP | ENST00000541207.1 | DUSP16-205:protein_coding:DUSP16 | 7.566032e-01 | 1.684495e+00 | 2.764004e-05 | 5.777665e-04 |
| 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 USP16 |
| 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_103457 | chr21 | 29036271:29036374:29037276:29037463:29038335:29038430 | 29037276:29037463 |
| exon_skip_106738 | chr21 | 29024668:29024777:29026567:29026661:29027873:29027974 | 29026567:29026661 |
| exon_skip_110399 | chr21 | 29024668:29024777:29025709:29025771:29027873:29027974 | 29025709:29025771 |
| exon_skip_200426 | chr21 | 29048761:29048855:29050092:29050178:29053802:29053958 | 29050092:29050178 |
| exon_skip_225468 | chr21 | 29050092:29050178:29053802:29053958:29054066:29054488 | 29053802:29053958 |
| exon_skip_226627 | chr21 | 29036271:29036374:29037279:29037463:29038335:29038430 | 29037279:29037463 |
| exon_skip_266928 | chr21 | 29024668:29024777:29027873:29027974:29030595:29030773 | 29027873:29027974 |
| exon_skip_27132 | chr21 | 29039486:29039568:29040609:29040687:29042013:29042104 | 29040609:29040687 |
| exon_skip_60430 | chr21 | 29039481:29039568:29040609:29040687:29042013:29042104 | 29040609:29040687 |
| 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_110399 | Mayo_TC | 2.725610e-01 | 4.192208e-01 | -1.466598e-01 | 2.431632e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for USP16 |
| 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 |
| ENST00000399976 | 29027873 | 29027974 | 5CDS-5UTR |
| ENST00000334352 | 29025709 | 29025771 | 5UTR-5UTR |
| ENST00000334352 | 29040609 | 29040687 | Frame-shift |
| ENST00000399976 | 29040609 | 29040687 | Frame-shift |
| ENST00000334352 | 29053802 | 29053958 | Frame-shift |
| ENST00000399976 | 29053802 | 29053958 | Frame-shift |
| ENST00000334352 | 29050092 | 29050178 | In-frame |
| ENST00000399976 | 29050092 | 29050178 | 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 |
| ENST00000399976 | 29027873 | 29027974 | 5CDS-5UTR |
| ENST00000334352 | 29025709 | 29025771 | 5UTR-5UTR |
| ENST00000334352 | 29037276 | 29037463 | Frame-shift |
| ENST00000399976 | 29037276 | 29037463 | Frame-shift |
| ENST00000334352 | 29040609 | 29040687 | Frame-shift |
| ENST00000399976 | 29040609 | 29040687 | 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 |
| ENST00000399976 | 29027873 | 29027974 | 5CDS-5UTR |
| ENST00000334352 | 29025709 | 29025771 | 5UTR-5UTR |
| ENST00000334352 | 29037276 | 29037463 | Frame-shift |
| ENST00000399976 | 29037276 | 29037463 | Frame-shift |
| ENST00000334352 | 29040609 | 29040687 | Frame-shift |
| ENST00000399976 | 29040609 | 29040687 | Frame-shift |
| ENST00000334352 | 29053802 | 29053958 | Frame-shift |
| ENST00000399976 | 29053802 | 29053958 | Frame-shift |
| ENST00000334352 | 29050092 | 29050178 | In-frame |
| ENST00000399976 | 29050092 | 29050178 | In-frame |
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Infer the effects of exon skipping event on protein functional features for USP16 |
p-ENSG00000156256_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 |
| ENST00000334352 | 3021 | 823 | 29050092 | 29050178 | 2339 | 2424 | 702 | 731 |
| ENST00000399976 | 2980 | 823 | 29050092 | 29050178 | 2298 | 2383 | 702 | 731 |
| 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 |
| ENST00000334352 | 3021 | 823 | 29050092 | 29050178 | 2339 | 2424 | 702 | 731 |
| ENST00000399976 | 2980 | 823 | 29050092 | 29050178 | 2298 | 2383 | 702 | 731 |
| 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 |
| Q9Y5T5 | 702 | 731 | 394 | 823 | Alternative sequence | ID=VSP_036716;Note=In isoform 5. SGKKSVNDKNLKKTVEDEDQDSEEEKDNDSYIKERSDIPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQGKVLHLNDICTIDHPEDSEYEAEMSLQGEVNIKSNHISQEGVMHKEYCVNQKDLNGQAKMIESVTDNQKSTEEVDMKNINMDNDLEVLTSSPTRNLNGAYLTEGSNGEVDISNGFKNLNLNAALHPDEINIEILNDSHTPGTKVYEVVNEDPET |
| Q9Y5T5 | 702 | 731 | 394 | 823 | Alternative sequence | ID=VSP_036716;Note=In isoform 5. SGKKSVNDKNLKKTVEDEDQDSEEEKDNDSYIKERSDIPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQGKVLHLNDICTIDHPEDSEYEAEMSLQGEVNIKSNHISQEGVMHKEYCVNQKDLNGQAKMIESVTDNQKSTEEVDMKNINMDNDLEVLTSSPTRNLNGAYLTEGSNGEVDISNGFKNLNLNAALHPDEINIEILNDSHTPGTKVYEVVNEDPET |
| Q9Y5T5 | 702 | 731 | 1 | 823 | Chain | ID=PRO_0000080643;Note=Ubiquitin carboxyl-terminal hydrolase 16 |
| Q9Y5T5 | 702 | 731 | 1 | 823 | Chain | ID=PRO_0000080643;Note=Ubiquitin carboxyl-terminal hydrolase 16 |
| Q9Y5T5 | 702 | 731 | 196 | 822 | Domain | Note=USP |
| Q9Y5T5 | 702 | 731 | 196 | 822 | Domain | Note=USP |
| 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 |
| Q9Y5T5 | 702 | 731 | 394 | 823 | Alternative sequence | ID=VSP_036716;Note=In isoform 5. SGKKSVNDKNLKKTVEDEDQDSEEEKDNDSYIKERSDIPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQGKVLHLNDICTIDHPEDSEYEAEMSLQGEVNIKSNHISQEGVMHKEYCVNQKDLNGQAKMIESVTDNQKSTEEVDMKNINMDNDLEVLTSSPTRNLNGAYLTEGSNGEVDISNGFKNLNLNAALHPDEINIEILNDSHTPGTKVYEVVNEDPET |
| Q9Y5T5 | 702 | 731 | 394 | 823 | Alternative sequence | ID=VSP_036716;Note=In isoform 5. SGKKSVNDKNLKKTVEDEDQDSEEEKDNDSYIKERSDIPSGTSKHLQKKAKKQAKKQAKNQRRQQKIQGKVLHLNDICTIDHPEDSEYEAEMSLQGEVNIKSNHISQEGVMHKEYCVNQKDLNGQAKMIESVTDNQKSTEEVDMKNINMDNDLEVLTSSPTRNLNGAYLTEGSNGEVDISNGFKNLNLNAALHPDEINIEILNDSHTPGTKVYEVVNEDPET |
| Q9Y5T5 | 702 | 731 | 1 | 823 | Chain | ID=PRO_0000080643;Note=Ubiquitin carboxyl-terminal hydrolase 16 |
| Q9Y5T5 | 702 | 731 | 1 | 823 | Chain | ID=PRO_0000080643;Note=Ubiquitin carboxyl-terminal hydrolase 16 |
| Q9Y5T5 | 702 | 731 | 196 | 822 | Domain | Note=USP |
| Q9Y5T5 | 702 | 731 | 196 | 822 | Domain | Note=USP |
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3'-UTR located exon skipping events that lost miRNA binding sites in USP16 |
| 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 USP16 |
| - Differential PSIs between mutated versus non-mutated samples. |
ENSG00000156256.exon_skip_200426.ROSMAP_DLPFC.WGS.boxplot.svg |
| - Depth of Coverage in the skipped exon of the mutated samples. |
ENSG00000156256.exon_skip_200426.ROSMAP_DLPFC.427_120507.WGS.svg |
| - Sashimi plot in the skipped exon of the mutated samples. |
ENSG00000156256.exon_skip_200426.ROSMAP_DLPFC.427_120507.WGS.png |
| - 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 USP16 |
| 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 USP16 |
| 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 USP16 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RALYL | exon_skip_110399 | 5.284256e-01 | 6.029835e-12 |
| CB | ELAVL1 | exon_skip_266928 | -4.522837e-01 | 3.651175e-08 |
| CB | TRA2A | exon_skip_266928 | -4.581343e-01 | 2.307607e-08 |
| CB | RC3H1 | exon_skip_266928 | -4.302954e-01 | 1.900115e-07 |
| CB | FUBP1 | exon_skip_266928 | -5.037113e-01 | 4.740123e-10 |
| CB | TARDBP | exon_skip_27132 | -5.279538e-01 | 1.199304e-12 |
| CB | TRA2A | exon_skip_27132 | -4.907633e-01 | 6.797127e-11 |
| DLPFC | RC3H1 | exon_skip_110399 | 4.475363e-01 | 9.341755e-18 |
| DLPFC | EIF4B | exon_skip_110399 | 4.276883e-01 | 3.384211e-16 |
| FL | RALYL | exon_skip_110399 | 4.506366e-01 | 1.945653e-10 |
| HCC | SFPQ | exon_skip_110399 | -5.579453e-01 | 1.417060e-23 |
| HCC | RBM47 | exon_skip_110399 | -5.110561e-01 | 1.960423e-19 |
| HCC | FUBP1 | exon_skip_110399 | -4.427956e-01 | 1.932483e-14 |
| IFG | RBM47 | exon_skip_110399 | -4.809380e-01 | 9.576076e-03 |
| PCC | RALYL | exon_skip_110399 | 4.385348e-01 | 2.500356e-11 |
| PG | RBM47 | exon_skip_110399 | -4.177583e-01 | 7.754333e-08 |
| PG | RALYL | exon_skip_110399 | 6.428613e-01 | 3.286462e-19 |
| PG | EIF4B | exon_skip_110399 | 4.354828e-01 | 1.846495e-08 |
| STG | RBM47 | exon_skip_110399 | -5.081694e-01 | 2.382179e-06 |
| STG | RALYL | exon_skip_110399 | 4.554020e-01 | 3.161254e-05 |
| TC | RALYL | exon_skip_110399 | 5.100134e-01 | 6.572271e-12 |
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RelatedDrugs for USP16 |
| 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 USP16 |
| 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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