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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for VPS36 |
Gene summary |
Gene information | Gene symbol | VPS36 | Gene ID | 51028 |
Gene name | vacuolar protein sorting 36 homolog | |
Synonyms | C13orf9|CGI-145|EAP45 | |
Cytomap | 13q14.3 | |
Type of gene | protein-coding | |
Description | vacuolar protein-sorting-associated protein 36ELL-associated protein of 45 kDaESCRT-II complex subunit VPS36 | |
Modification date | 20200313 | |
UniProtAcc | A0A3B3ISW7, Q86VN1, | |
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 VPS36 |
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. |
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 VPS36 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_128721 | chr13 | 52417057:52417141:52417437:52417679:52417992:52418056 | 52417437:52417679 |
exon_skip_150013 | chr13 | 52417992:52418056:52423574:52423639:52425932:52426066 | 52423574:52423639 |
exon_skip_170434 | chr13 | 52426989:52427066:52427187:52427219:52433662:52433748 | 52427187:52427219 |
exon_skip_173181 | chr13 | 52427187:52427219:52433662:52433748:52434793:52434882 | 52433662:52433748 |
exon_skip_32936 | chr13 | 52425932:52426066:52426989:52427066:52427187:52427219 | 52426989:52427066 |
exon_skip_59553 | chr13 | 52417057:52417141:52417992:52418056:52423574:52423639 | 52417992:52418056 |
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 VPS36 |
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 |
ENST00000378060 | 52417992 | 52418056 | Frame-shift |
ENST00000378060 | 52423574 | 52423639 | In-frame |
ENST00000378060 | 52426989 | 52427066 | In-frame |
ENST00000378060 | 52427187 | 52427219 | In-frame |
ENST00000378060 | 52433662 | 52433748 | 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 |
ENST00000378060 | 52417992 | 52418056 | Frame-shift |
ENST00000378060 | 52423574 | 52423639 | 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 |
ENST00000378060 | 52417992 | 52418056 | Frame-shift |
ENST00000378060 | 52423574 | 52423639 | In-frame |
ENST00000378060 | 52426989 | 52427066 | In-frame |
ENST00000378060 | 52433662 | 52433748 | In-frame |
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Infer the effects of exon skipping event on protein functional features for VPS36 |
p-ENSG00000136100_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 |
ENST00000378060 | 4434 | 386 | 52433662 | 52433748 | 470 | 555 | 147 | 175 |
ENST00000378060 | 4434 | 386 | 52427187 | 52427219 | 557 | 588 | 176 | 186 |
ENST00000378060 | 4434 | 386 | 52426989 | 52427066 | 590 | 666 | 187 | 212 |
ENST00000378060 | 4434 | 386 | 52423574 | 52423639 | 803 | 867 | 258 | 279 |
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 |
ENST00000378060 | 4434 | 386 | 52423574 | 52423639 | 803 | 867 | 258 | 279 |
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 |
ENST00000378060 | 4434 | 386 | 52433662 | 52433748 | 470 | 555 | 147 | 175 |
ENST00000378060 | 4434 | 386 | 52426989 | 52427066 | 590 | 666 | 187 | 212 |
ENST00000378060 | 4434 | 386 | 52423574 | 52423639 | 803 | 867 | 258 | 279 |
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 |
Q86VN1 | 147 | 175 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 147 | 175 | 160 | 185 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q86VN1 | 147 | 175 | 175 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 176 | 186 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 176 | 186 | 160 | 185 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q86VN1 | 176 | 186 | 175 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 176 | 186 | 185 | 185 | Sequence conflict | Note=M->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q86VN1 | 187 | 212 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 187 | 212 | 175 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 187 | 212 | 197 | 199 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 262 | 265 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 278 | 280 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 258 | 279 | 240 | 259 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 266 | 275 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
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 |
Q86VN1 | 258 | 279 | 262 | 265 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 278 | 280 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 258 | 279 | 240 | 259 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 266 | 275 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
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 |
Q86VN1 | 147 | 175 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 147 | 175 | 160 | 185 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Q86VN1 | 147 | 175 | 175 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 187 | 212 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 187 | 212 | 175 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 187 | 212 | 197 | 199 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 262 | 265 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 278 | 280 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 1 | 386 | Chain | ID=PRO_0000215222;Note=Vacuolar protein-sorting-associated protein 36 |
Q86VN1 | 258 | 279 | 240 | 259 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
Q86VN1 | 258 | 279 | 266 | 275 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3CUQ |
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3'-UTR located exon skipping events that lost miRNA binding sites in VPS36 |
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 VPS36 |
- 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 VPS36 |
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 VPS36 |
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 VPS36 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | RBM45 | exon_skip_59553 | 4.744969e-01 | 1.112258e-09 |
CB | RBM4 | exon_skip_59553 | -4.423481e-01 | 1.813651e-08 |
CB | MBNL1 | exon_skip_150013 | -4.150206e-01 | 1.168080e-07 |
CB | HNRNPA2B1 | exon_skip_150013 | -4.600559e-01 | 2.800203e-09 |
CB | HNRNPF | exon_skip_150013 | -4.493098e-01 | 7.169106e-09 |
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RelatedDrugs for VPS36 |
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 VPS36 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |