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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 VAC14 |
Gene summary |
Gene information | Gene symbol | VAC14 | Gene ID | 55697 |
Gene name | VAC14 component of PIKFYVE complex | |
Synonyms | ArPIKfyve|TAX1BP2|TRX | |
Cytomap | 16q22.1-q22.2 | |
Type of gene | protein-coding | |
Description | protein VAC14 homologTax1 (human T-cell leukemia virus type I) binding proteinVac14, PIKFYVE complex component | |
Modification date | 20200327 | |
UniProtAcc | ||
Context | - 26862204(The amyloid precursor protein APP) binds the PIKfyve complex and modulates its function) |
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 VAC14 |
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 |
CB | DOWN | ENST00000567648.1 | VAC14-209:protein_coding:VAC14 | 2.708126e+01 | -3.250928e+00 | 4.647188e-05 | 3.867758e-04 |
TC | UP | ENST00000666405.1 | VAC14-AS1-204:lncRNA:VAC14 | 3.586679e+01 | 8.024760e-01 | 2.684132e-09 | 2.967994e-07 |
TC | DOWN | ENST00000568886.5 | VAC14-211:nonsense_mediated_decay:VAC14 | 9.290161e+00 | -5.810050e+00 | 1.091774e-04 | 1.731981e-03 |
TC | DOWN | ENST00000567648.1 | VAC14-209:protein_coding:VAC14 | 5.124519e+01 | -1.643694e+00 | 7.003238e-04 | 7.493874e-03 |
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 VAC14 |
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_133720 | chr16 | 70688043:70688090:70692821:70692971:70695544:70695593 | 70692821:70692971 |
exon_skip_240358 | chr16 | 70731495:70731627:70744423:70744579:70762540:70762605 | 70744423:70744579 |
exon_skip_276196 | chr16 | 70785702:70785869:70786215:70786365:70800797:70800982 | 70786215:70786365 |
exon_skip_277157 | chr16 | 70784113:70784220:70784776:70784838:70785702:70785869 | 70784776:70784838 |
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 VAC14 |
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 |
ENST00000261776 | 70786215 | 70786365 | Frame-shift |
ENST00000261776 | 70784776 | 70784838 | 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 |
ENST00000261776 | 70786215 | 70786365 | 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 |
ENST00000261776 | 70692821 | 70692971 | Frame-shift |
ENST00000261776 | 70744423 | 70744579 | Frame-shift |
ENST00000261776 | 70786215 | 70786365 | Frame-shift |
ENST00000261776 | 70784776 | 70784838 | In-frame |
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Infer the effects of exon skipping event on protein functional features for VAC14 |
p-ENSG00000103043_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 |
ENST00000261776 | 3116 | 782 | 70784776 | 70784838 | 685 | 746 | 141 | 161 |
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 |
ENST00000261776 | 3116 | 782 | 70784776 | 70784838 | 685 | 746 | 141 | 161 |
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 |
Q08AM6 | 141 | 161 | 1 | 568 | Alternative sequence | ID=VSP_056097;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q08AM6 | 141 | 161 | 1 | 782 | Chain | ID=PRO_0000300485;Note=Protein VAC14 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 |
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 |
Q08AM6 | 141 | 161 | 1 | 568 | Alternative sequence | ID=VSP_056097;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q08AM6 | 141 | 161 | 1 | 782 | Chain | ID=PRO_0000300485;Note=Protein VAC14 homolog |
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3'-UTR located exon skipping events that lost miRNA binding sites in VAC14 |
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 VAC14 |
- 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 VAC14 |
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 VAC14 |
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 VAC14 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for VAC14 |
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 VAC14 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |