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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 VPS13B |
 Gene summary |
| Gene information | Gene symbol | VPS13B | Gene ID | 157680 |
| Gene name | vacuolar protein sorting 13 homolog B | |
| Synonyms | CHS1|COH1 | |
| Cytomap | 8q22.2 | |
| Type of gene | protein-coding | |
| Description | vacuolar protein sorting-associated protein 13B | |
| 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 |
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Gene structures and expression levels for VPS13B |
| 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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ENSG00000132549
| 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. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| 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 VPS13B |
| 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_158788 | chr8 | 99868289:99868465:99870785:99870887:99871448:99871697 | 99870785:99870887 |
| exon_skip_172636 | chr8 | 99501687:99501858:99502836:99502950:99507137:99507203 | 99502836:99502950 |
| exon_skip_18163 | chr8 | 99501687:99501858:99502836:99502950:99507770:99507911 | 99502836:99502950 |
| exon_skip_204359 | chr8 | 99502836:99502950:99507137:99507203:99511104:99511512 | 99507137:99507203 |
| exon_skip_25236 | chr8 | 99766774:99766970:99776775:99776956:99778682:99778835 | 99776775:99776956 |
| exon_skip_262487 | chr8 | 99391557:99391704:99429570:99429647:99431521:99431664 | 99429570:99429647 |
| exon_skip_275998 | chr8 | 99502836:99502950:99507137:99507203:99507770:99507911 | 99507137:99507203 |
| exon_skip_289234 | chr8 | 99853451:99854256:99859304:99859480:99861776:99861946 | 99859304:99859480 |
| exon_skip_33775 | chr8 | 99818713:99818888:99819412:99819582:99819921:99820122 | 99819412:99819582 |
| exon_skip_42471 | chr8 | 99103059:99103120:99111098:99111279:99115700:99115874 | 99111098:99111279 |
| exon_skip_62222 | chr8 | 99147841:99148010:99156549:99156743:99170039:99170163 | 99156549:99156743 |
| exon_skip_63120 | chr8 | 99507137:99507203:99507770:99507911:99511104:99511512 | 99507770:99507911 |
| exon_skip_65178 | chr8 | 99502836:99502950:99507770:99507911:99511104:99511512 | 99507770:99507911 |
| exon_skip_85011 | chr8 | 99136665:99136752:99142974:99143165:99147841:99148010 | 99142974:99143165 |
| exon_skip_95092 | chr8 | 99391557:99391704:99431537:99431664:99442401:99442411 | 99431537:99431664 |
| exon_skip_95205 | chr8 | 99817540:99817803:99818451:99818534:99818713:99818888 | 99818451:99818534 |
| 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 VPS13B |
| 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 |
| ENST00000358544 | 99111098 | 99111279 | Frame-shift |
| ENST00000358544 | 99502836 | 99502950 | Frame-shift |
| ENST00000358544 | 99507770 | 99507911 | Frame-shift |
| ENST00000358544 | 99776775 | 99776956 | Frame-shift |
| ENST00000358544 | 99870785 | 99870887 | Frame-shift |
| ENST00000358544 | 99142974 | 99143165 | In-frame |
| ENST00000358544 | 99156549 | 99156743 | In-frame |
| ENST00000358544 | 99859304 | 99859480 | 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 |
| ENST00000358544 | 99111098 | 99111279 | Frame-shift |
| ENST00000358544 | 99502836 | 99502950 | Frame-shift |
| ENST00000358544 | 99507770 | 99507911 | Frame-shift |
| ENST00000358544 | 99142974 | 99143165 | In-frame |
| ENST00000358544 | 99156549 | 99156743 | 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 |
| ENST00000358544 | 99111098 | 99111279 | Frame-shift |
| ENST00000358544 | 99431537 | 99431664 | Frame-shift |
| ENST00000358544 | 99502836 | 99502950 | Frame-shift |
| ENST00000358544 | 99507770 | 99507911 | Frame-shift |
| ENST00000358544 | 99776775 | 99776956 | Frame-shift |
| ENST00000358544 | 99870785 | 99870887 | Frame-shift |
| ENST00000358544 | 99156549 | 99156743 | In-frame |
| ENST00000358544 | 99818451 | 99818534 | In-frame |
| ENST00000358544 | 99819412 | 99819582 | In-frame |
| ENST00000358544 | 99859304 | 99859480 | In-frame |
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Infer the effects of exon skipping event on protein functional features for VPS13B |
p-ENSG00000132549_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 |
| ENST00000358544 | 14111 | 4022 | 99142974 | 99143165 | 1764 | 1954 | 551 | 614 |
| ENST00000358544 | 14111 | 4022 | 99156549 | 99156743 | 2126 | 2319 | 671 | 736 |
| ENST00000358544 | 14111 | 4022 | 99859304 | 99859480 | 11055 | 11230 | 3648 | 3706 |
| 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 |
| ENST00000358544 | 14111 | 4022 | 99142974 | 99143165 | 1764 | 1954 | 551 | 614 |
| ENST00000358544 | 14111 | 4022 | 99156549 | 99156743 | 2126 | 2319 | 671 | 736 |
| 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 |
| ENST00000358544 | 14111 | 4022 | 99156549 | 99156743 | 2126 | 2319 | 671 | 736 |
| ENST00000358544 | 14111 | 4022 | 99818451 | 99818534 | 8549 | 8631 | 2812 | 2840 |
| ENST00000358544 | 14111 | 4022 | 99819412 | 99819582 | 8809 | 8978 | 2899 | 2955 |
| ENST00000358544 | 14111 | 4022 | 99859304 | 99859480 | 11055 | 11230 | 3648 | 3706 |
| 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 |
| Q7Z7G8 | 551 | 614 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 551 | 614 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| Q7Z7G8 | 671 | 736 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 671 | 736 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| Q7Z7G8 | 3648 | 3706 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 3648 | 3706 | 864 | 4022 | Alternative sequence | ID=VSP_009407;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 3648 | 3706 | 1428 | 4022 | Alternative sequence | ID=VSP_009410;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 3648 | 3706 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| 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 |
| Q7Z7G8 | 551 | 614 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 551 | 614 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| Q7Z7G8 | 671 | 736 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 671 | 736 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| 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 |
| Q7Z7G8 | 671 | 736 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 671 | 736 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| Q7Z7G8 | 2812 | 2840 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 2812 | 2840 | 864 | 4022 | Alternative sequence | ID=VSP_009407;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 2812 | 2840 | 1428 | 4022 | Alternative sequence | ID=VSP_009410;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 2812 | 2840 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| Q7Z7G8 | 2812 | 2840 | 2820 | 2820 | Natural variant | ID=VAR_058755;Note=In COH1. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15211651;Dbxref=dbSNP:rs120074155,PMID:15211651 |
| Q7Z7G8 | 2812 | 2840 | 2822 | 2822 | Natural variant | ID=VAR_058756;Note=Y->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16648375;Dbxref=dbSNP:rs371325199,PMID:16648375 |
| Q7Z7G8 | 2899 | 2955 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 2899 | 2955 | 864 | 4022 | Alternative sequence | ID=VSP_009407;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 2899 | 2955 | 1428 | 4022 | Alternative sequence | ID=VSP_009410;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 2899 | 2955 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
| Q7Z7G8 | 3648 | 3706 | 416 | 4022 | Alternative sequence | ID=VSP_009405;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12730828,ECO:0000303|PubMed:14702039;Dbxref=PMID:12730828,PMID:14702039 |
| Q7Z7G8 | 3648 | 3706 | 864 | 4022 | Alternative sequence | ID=VSP_009407;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 3648 | 3706 | 1428 | 4022 | Alternative sequence | ID=VSP_009410;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:12730828;Dbxref=PMID:12730828 |
| Q7Z7G8 | 3648 | 3706 | 1 | 4022 | Chain | ID=PRO_0000065880;Note=Vacuolar protein sorting-associated protein 13B |
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3'-UTR located exon skipping events that lost miRNA binding sites in VPS13B |
| 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 VPS13B |
| - 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 VPS13B |
| 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 VPS13B |
| 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 VPS13B |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for VPS13B |
| 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 VPS13B |
| 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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