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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 OTUD4 |
 Gene summary |
| Gene information | Gene symbol | OTUD4 | Gene ID | 54726 |
| Gene name | OTU deubiquitinase 4 | |
| Synonyms | DUBA6|HIN1|HSHIN1 | |
| Cytomap | 4q31.21 | |
| Type of gene | protein-coding | |
| Description | OTU domain-containing protein 4HIV-1 induced protein HIN-1 | |
| 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 |
| OTUD4 | GO:0034122 | negative regulation of toll-like receptor signaling pathway | 29395066 |
| OTUD4 | GO:0070536 | protein K63-linked deubiquitination | 29395066 |
| OTUD4 | GO:0071108 | protein K48-linked deubiquitination | 23827681 |
| OTUD4 | GO:1901537 | positive regulation of DNA demethylation | 25944111 |
| OTUD4 | GO:1903093 | regulation of protein K48-linked deubiquitination | 25944111 |
| OTUD4 | GO:2000660 | negative regulation of interleukin-1-mediated signaling pathway | 29395066 |
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Gene structures and expression levels for OTUD4 |
| 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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ENSG00000164164
| 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 |
| CB | UP | ENST00000509517.1 | OTUD4-207:retained_intron:OTUD4 | 1.438557e+01 | 8.514740e-01 | 3.006400e-07 | 5.393745e-06 |
| 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 OTUD4 |
| 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_165254 | chr4 | 145159520:145159635:145162640:145162721:145164154:145164226 | 145162640:145162721 |
| exon_skip_172660 | chr4 | 145155569:145155686:145155936:145155996:145159503:145159635 | 145155936:145155996 |
| exon_skip_177013 | chr4 | 145171670:145171720:145174661:145174744:145179815:145179928 | 145174661:145174744 |
| exon_skip_192914 | chr4 | 145164154:145164226:145165151:145165197:145171670:145171711 | 145165151:145165197 |
| exon_skip_245415 | chr4 | 145150802:145150905:145152541:145152635:145155411:145155475 | 145152541:145152635 |
| exon_skip_260424 | chr4 | 145155936:145155996:145159503:145159635:145162640:145162721 | 145159503:145159635 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for OTUD4 |
| 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 |
| ENST00000447906 | 145152541 | 145152635 | Frame-shift |
| ENST00000447906 | 145162640 | 145162721 | Frame-shift |
| ENST00000447906 | 145174661 | 145174744 | 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 |
| ENST00000447906 | 145152541 | 145152635 | Frame-shift |
| ENST00000447906 | 145155936 | 145155996 | Frame-shift |
| ENST00000447906 | 145159503 | 145159635 | Frame-shift |
| ENST00000447906 | 145174661 | 145174744 | 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 |
| ENST00000447906 | 145152541 | 145152635 | Frame-shift |
| ENST00000447906 | 145159503 | 145159635 | Frame-shift |
| ENST00000447906 | 145165151 | 145165197 | Frame-shift |
| ENST00000447906 | 145174661 | 145174744 | In-frame |
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Infer the effects of exon skipping event on protein functional features for OTUD4 |
p-ENSG00000164164_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 |
| ENST00000447906 | 7290 | 1114 | 145174661 | 145174744 | 348 | 430 | 53 | 80 |
| 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 |
| ENST00000447906 | 7290 | 1114 | 145174661 | 145174744 | 348 | 430 | 53 | 80 |
| 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 |
| ENST00000447906 | 7290 | 1114 | 145174661 | 145174744 | 348 | 430 | 53 | 80 |
| 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 |
| Q01804 | 53 | 80 | 1 | 65 | Alternative sequence | ID=VSP_038830;Note=In isoform 2%2C isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:1475186,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:1475186,PMID:154893 |
| Q01804 | 53 | 80 | 1 | 1114 | Chain | ID=PRO_0000083979;Note=OTU domain-containing protein 4 |
| Q01804 | 53 | 80 | 34 | 155 | Domain | Note=OTU;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00139,ECO:0000269|PubMed:29395066;Dbxref=PMID:29395066 |
| 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 |
| Q01804 | 53 | 80 | 1 | 65 | Alternative sequence | ID=VSP_038830;Note=In isoform 2%2C isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:1475186,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:1475186,PMID:154893 |
| Q01804 | 53 | 80 | 1 | 1114 | Chain | ID=PRO_0000083979;Note=OTU domain-containing protein 4 |
| Q01804 | 53 | 80 | 34 | 155 | Domain | Note=OTU;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00139,ECO:0000269|PubMed:29395066;Dbxref=PMID:29395066 |
| 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 |
| Q01804 | 53 | 80 | 1 | 65 | Alternative sequence | ID=VSP_038830;Note=In isoform 2%2C isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:1475186,ECO:0000303|PubMed:15489334;Dbxref=PMID:14702039,PMID:1475186,PMID:154893 |
| Q01804 | 53 | 80 | 1 | 1114 | Chain | ID=PRO_0000083979;Note=OTU domain-containing protein 4 |
| Q01804 | 53 | 80 | 34 | 155 | Domain | Note=OTU;Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00139,ECO:0000269|PubMed:29395066;Dbxref=PMID:29395066 |
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3'-UTR located exon skipping events that lost miRNA binding sites in OTUD4 |
| 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 OTUD4 |
| - 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 OTUD4 |
| 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 OTUD4 |
| 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 OTUD4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for OTUD4 |
| 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 OTUD4 |
| 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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