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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 BAP1 |
 Gene summary |
| Gene information | Gene symbol | BAP1 | Gene ID | 8314 |
| Gene name | BRCA1 associated protein 1 | |
| Synonyms | HUCEP-13|UCHL2|hucep-6 | |
| Cytomap | 3p21.1 | |
| Type of gene | protein-coding | |
| Description | ubiquitin carboxyl-terminal hydrolase BAP1BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)cerebral protein 6cerebral protein-13 | |
| Modification date | 20200315 | |
| 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 |
| BAP1 | GO:0016579 | protein deubiquitination | 18757409|19815555 |
| BAP1 | GO:0035520 | monoubiquitinated protein deubiquitination | 24703950 |
| BAP1 | GO:0035522 | monoubiquitinated histone H2A deubiquitination | 20436459|25451922 |
| BAP1 | GO:0045892 | negative regulation of transcription, DNA-templated | 25451922 |
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Gene structures and expression levels for BAP1 |
| 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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ENSG00000163930
| 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 |
| PCC | UP | ENST00000469613.5 | BAP1-204:protein_coding:BAP1 | 2.776897e+02 | 8.238082e-01 | 2.482045e-03 | 4.445073e-02 |
| CB | DOWN | ENST00000471534.1 | HSPBAP1-205:lncRNA:HSPBAP1 | 1.408373e+02 | -1.038925e+00 | 1.358642e-17 | 1.900338e-14 |
| CB | DOWN | ENST00000469613.5 | BAP1-204:protein_coding:BAP1 | 8.281736e+02 | -1.257746e+00 | 2.790528e-11 | 2.233395e-09 |
| CB | UP | ENST00000625521.2 | UBAP1-204:protein_coding:UBAP1 | 9.896323e+01 | 8.433021e-01 | 9.918275e-07 | 1.485758e-05 |
| CB | DOWN | ENST00000379186.8 | UBAP1-203:protein_coding:UBAP1 | 2.894234e+01 | -1.558487e+00 | 1.051776e-02 | 3.623629e-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 BAP1 |
| 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_105801 | chr3 | 52408064:52408077:52408474:52408606:52409554:52409608 | 52408474:52408606 |
| exon_skip_121283 | chr3 | 52407179:52407316:52407399:52407460:52407958:52407992 | 52407399:52407460 |
| exon_skip_14596 | chr3 | 52402602:52402674:52402779:52402940:52403138:52403298 | 52402779:52402940 |
| exon_skip_150026 | chr3 | 52406829:52406907:52407399:52407460:52407958:52408047 | 52407399:52407460 |
| exon_skip_157853 | chr3 | 52406253:52406376:52406829:52406907:52407174:52407316 | 52406829:52406907 |
| exon_skip_189686 | chr3 | 52403138:52403298:52403416:52403894:52404453:52404477 | 52403416:52403894 |
| exon_skip_195769 | chr3 | 52404453:52404586:52405110:52405294:52405765:52405912 | 52405110:52405294 |
| exon_skip_199169 | chr3 | 52406646:52406907:52407174:52407316:52407399:52407460 | 52407174:52407316 |
| exon_skip_200048 | chr3 | 52407179:52407316:52407399:52407460:52407958:52408039 | 52407399:52407460 |
| exon_skip_230242 | chr3 | 52406829:52406907:52407174:52407316:52407399:52407460 | 52407174:52407316 |
| exon_skip_266714 | chr3 | 52407179:52407316:52407399:52407460:52407958:52408047 | 52407399:52407460 |
| exon_skip_45015 | chr3 | 52406756:52406907:52407174:52407316:52407399:52407460 | 52407174:52407316 |
| exon_skip_70611 | chr3 | 52407958:52408077:52408474:52408606:52409554:52409608 | 52408474:52408606 |
| exon_skip_75382 | chr3 | 52402602:52402674:52402779:52402871:52403138:52403298 | 52402779:52402871 |
| 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 BAP1 |
| 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 |
| ENST00000460680 | 52403416 | 52403894 | Frame-shift |
| ENST00000460680 | 52405110 | 52405294 | Frame-shift |
| ENST00000460680 | 52407174 | 52407316 | Frame-shift |
| ENST00000460680 | 52407399 | 52407460 | Frame-shift |
| ENST00000460680 | 52408474 | 52408606 | Frame-shift |
| 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 |
| ENST00000460680 | 52407399 | 52407460 | 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 |
| ENST00000460680 | 52405110 | 52405294 | Frame-shift |
| ENST00000460680 | 52406829 | 52406907 | Frame-shift |
| ENST00000460680 | 52407174 | 52407316 | Frame-shift |
| ENST00000460680 | 52407399 | 52407460 | Frame-shift |
| ENST00000460680 | 52408474 | 52408606 | Frame-shift |
| ENST00000460680 | 52402779 | 52402871 | In-frame |
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Infer the effects of exon skipping event on protein functional features for BAP1 |
p-ENSG00000163930_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 |
| 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 |
| ENST00000460680 | 3954 | 729 | 52402779 | 52402871 | 2363 | 2454 | 630 | 660 |
| 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 |
| 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 |
| Q92560 | 630 | 660 | 1 | 729 | Chain | ID=PRO_0000211069;Note=Ubiquitin carboxyl-terminal hydrolase BAP1 |
| Q92560 | 630 | 660 | 630 | 661 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q92560 | 630 | 660 | 656 | 661 | Mutagenesis | Note=Does not affect nuclear localization. KRKKFK->AAAAAA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18757409;Dbxref=PMID:18757409 |
| Q92560 | 630 | 660 | 596 | 721 | Region | Note=Interaction with BRCA1 |
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3'-UTR located exon skipping events that lost miRNA binding sites in BAP1 |
| 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 BAP1 |
| - 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 BAP1 |
| 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 BAP1 |
| 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 BAP1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for BAP1 |
| 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 BAP1 |
| 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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