|
||||||
|
 | |
| |
| |
| 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 VPS8 |
 Gene summary |
| Gene information | Gene symbol | VPS8 | Gene ID | 23355 |
| Gene name | VPS8 subunit of CORVET complex | |
| Synonyms | KIAA0804 | |
| Cytomap | 3q27.2 | |
| Type of gene | protein-coding | |
| Description | vacuolar protein sorting-associated protein 8 homologVPS8, CORVET complex subunitvacuolar protein sorting 8 homolog | |
| 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 |
Top |
Gene structures and expression levels for VPS8 |
| 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. |
 |
ENSG00000156931
| 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 |
| CB | DOWN | ENST00000446204.6 | VPS8-210:protein_coding:VPS8 | 3.253278e+02 | -1.553785e+00 | 5.000531e-05 | 4.112892e-04 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for VPS8 |
| 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_107484 | chr3 | 184824633:184824785:184824931:184825048:184826163:184826231 | 184824931:184825048 |
| exon_skip_11457 | chr3 | 184839698:184839752:184843240:184843245:184849071:184849195 | 184843240:184843245 |
| exon_skip_122912 | chr3 | 184870744:184870805:184886110:184886156:184893234:184893412 | 184886110:184886156 |
| exon_skip_127662 | chr3 | 184869523:184869528:184870716:184870805:184886110:184886156 | 184870716:184870805 |
| exon_skip_147111 | chr3 | 184870744:184870805:184882349:184882433:184886110:184886156 | 184882349:184882433 |
| exon_skip_15737 | chr3 | 184868024:184868059:184868946:184869036:184869482:184869528 | 184868946:184869036 |
| exon_skip_162200 | chr3 | 184886110:184886156:184893234:184893412:184894703:184894925 | 184893234:184893412 |
| exon_skip_163116 | chr3 | 184834675:184834742:184836247:184836330:184838714:184838746 | 184836247:184836330 |
| exon_skip_165461 | chr3 | 184838714:184838746:184839698:184839752:184849071:184849195 | 184839698:184839752 |
| exon_skip_173659 | chr3 | 184849936:184850022:184852500:184852567:184853857:184853886 | 184852500:184852567 |
| exon_skip_20161 | chr3 | 184898565:184898654:184900921:184900972:184913519:184913561 | 184900921:184900972 |
| exon_skip_213869 | chr3 | 184886110:184886156:184894703:184894925:184898565:184898654 | 184894703:184894925 |
| exon_skip_22579 | chr3 | 184870716:184870805:184886110:184886156:184894703:184894925 | 184886110:184886156 |
| exon_skip_242811 | chr3 | 184870744:184870805:184886110:184886156:184894703:184894925 | 184886110:184886156 |
| exon_skip_244743 | chr3 | 184999696:184999861:185024336:185024389:185048479:185048559 | 185024336:185024389 |
| exon_skip_26253 | chr3 | 184826163:184826231:184832689:184832819:184834649:184834660 | 184832689:184832819 |
| exon_skip_270985 | chr3 | 184812207:184812225:184824147:184824232:184824545:184824785 | 184824147:184824232 |
| exon_skip_33899 | chr3 | 184920127:184920198:184922429:184922483:184924862:184924981 | 184922429:184922483 |
| exon_skip_57319 | chr3 | 184983012:184983094:184993983:184994063:184996332:184996501 | 184993983:184994063 |
| exon_skip_58945 | chr3 | 184850000:184850022:184852500:184852567:184853857:184853886 | 184852500:184852567 |
| exon_skip_81143 | chr3 | 184812195:184812225:184824147:184824232:184824545:184824785 | 184824147:184824232 |
| exon_skip_85328 | chr3 | 184839698:184839752:184843240:184843245:184849071:184849141 | 184843240:184843245 |
| exon_skip_91329 | chr3 | 184898569:184898654:184900921:184900972:184913519:184913561 | 184900921:184900972 |
| 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 |
| exon_skip_85328 | Mayo_TC | 2.158228e-01 | 3.727273e-01 | -1.569045e-01 | 1.022211e-07 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for VPS8 |
| 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 |
| ENST00000625842 | 184832689 | 184832819 | Frame-shift |
| ENST00000625842 | 184852500 | 184852567 | Frame-shift |
| ENST00000625842 | 184886110 | 184886156 | Frame-shift |
| ENST00000625842 | 184894703 | 184894925 | Frame-shift |
| ENST00000625842 | 184900921 | 184900972 | Frame-shift |
| ENST00000625842 | 184843240 | 184843245 | In-frame |
| ENST00000625842 | 184993983 | 184994063 | In-frame |
| ENST00000625842 | 185024336 | 185024389 | 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 |
| ENST00000625842 | 184832689 | 184832819 | Frame-shift |
| ENST00000625842 | 184852500 | 184852567 | Frame-shift |
| ENST00000625842 | 184886110 | 184886156 | Frame-shift |
| ENST00000625842 | 184894703 | 184894925 | Frame-shift |
| ENST00000625842 | 184900921 | 184900972 | Frame-shift |
| ENST00000625842 | 184843240 | 184843245 | In-frame |
| ENST00000625842 | 184870716 | 184870805 | 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 |
| ENST00000625842 | 184832689 | 184832819 | Frame-shift |
| ENST00000625842 | 184852500 | 184852567 | Frame-shift |
| ENST00000625842 | 184868946 | 184869036 | Frame-shift |
| ENST00000625842 | 184886110 | 184886156 | Frame-shift |
| ENST00000625842 | 184894703 | 184894925 | Frame-shift |
| ENST00000625842 | 184900921 | 184900972 | Frame-shift |
| ENST00000625842 | 184843240 | 184843245 | In-frame |
| ENST00000625842 | 184993983 | 184994063 | In-frame |
| ENST00000625842 | 185024336 | 185024389 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for VPS8 |
p-ENSG00000156931_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 |
| ENST00000625842 | 4986 | 1428 | 184993983 | 184994063 | 3694 | 3773 | 1195 | 1222 |
| ENST00000625842 | 4986 | 1428 | 185024336 | 185024389 | 4111 | 4163 | 1334 | 1352 |
| 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 |
| ENST00000625842 | 4986 | 1428 | 184870716 | 184870805 | 1753 | 1841 | 548 | 578 |
| 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 |
| ENST00000625842 | 4986 | 1428 | 184993983 | 184994063 | 3694 | 3773 | 1195 | 1222 |
| ENST00000625842 | 4986 | 1428 | 185024336 | 185024389 | 4111 | 4163 | 1334 | 1352 |
| 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 |
| Q8N3P4 | 1195 | 1222 | 1 | 1428 | Chain | ID=PRO_0000278267;Note=Vacuolar protein sorting-associated protein 8 homolog |
| Q8N3P4 | 1334 | 1352 | 1 | 1428 | Chain | ID=PRO_0000278267;Note=Vacuolar protein sorting-associated protein 8 homolog |
| 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 |
| Q8N3P4 | 548 | 578 | 578 | 667 | Alternative sequence | ID=VSP_023250;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005 |
| Q8N3P4 | 548 | 578 | 1 | 1428 | Chain | ID=PRO_0000278267;Note=Vacuolar protein sorting-associated protein 8 homolog |
| 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 |
| Q8N3P4 | 1195 | 1222 | 1 | 1428 | Chain | ID=PRO_0000278267;Note=Vacuolar protein sorting-associated protein 8 homolog |
| Q8N3P4 | 1334 | 1352 | 1 | 1428 | Chain | ID=PRO_0000278267;Note=Vacuolar protein sorting-associated protein 8 homolog |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in VPS8 |
| 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 |
Top |
SNVs in the skipped exons for VPS8 |
| - 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 |
Top |
AD stage-associated exon skippint events for VPS8 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VPS8 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for VPS8 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | ELAVL1 | exon_skip_58945 | -4.373115e-01 | 4.731354e-08 |
| CB | FUBP1 | exon_skip_58945 | -5.620624e-01 | 2.790772e-13 |
| CB | KHSRP | exon_skip_58945 | -4.365855e-01 | 5.008051e-08 |
| CB | RBM45 | exon_skip_162200 | 4.814544e-01 | 4.462363e-10 |
| FL | EIF4B | exon_skip_85328 | 4.149813e-01 | 4.868685e-08 |
| HCC | PABPN1 | exon_skip_11457 | -5.116854e-01 | 6.941050e-19 |
| STG | EIF4B | exon_skip_85328 | 4.601265e-01 | 7.887436e-05 |
| TC | RBM3 | exon_skip_85328 | 4.434574e-01 | 8.038367e-08 |
| TC | NOVA1 | exon_skip_162200 | 4.157649e-01 | 1.480321e-07 |
Top |
RelatedDrugs for VPS8 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for VPS8 |
| 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)
|