|
||||||
|
 | |
| |
| |
| 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 VTI1A |
 Gene summary |
| Gene information | Gene symbol | VTI1A | Gene ID | 143187 |
| Gene name | vesicle transport through interaction with t-SNAREs 1A | |
| Synonyms | MMDS3|MVti1|VTI1RP2|Vti1-rp2 | |
| Cytomap | 10q25.2 | |
| Type of gene | protein-coding | |
| Description | vesicle transport through interaction with t-SNAREs homolog 1ASNARE Vti1a-beta proteinvesicle transport v-SNARE protein Vti1-like 2 | |
| Modification date | 20200313 | |
| UniProtAcc | Q96AJ9, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| VTI1A | GO:0042147 | retrograde transport, endosome to Golgi | 15215310|18195106 |
Top |
Gene structures and expression levels for VTI1A |
| 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. |
 |
ENSG00000151532
| 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. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for VTI1A |
| 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_134339 | chr10 | 112527087:112527164:112533530:112533550:112538246:112538301 | 112533530:112533550 |
| exon_skip_207599 | chr10 | 112460524:112460582:112464547:112464657:112527087:112527164 | 112464547:112464657 |
| exon_skip_60421 | chr10 | 112464547:112464657:112527087:112527164:112538246:112538301 | 112527087:112527164 |
| exon_skip_98923 | chr10 | 112447359:112447467:112460524:112460582:112464547:112464657 | 112460524:112460582 |
| 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_134339 | MSBB_PG | 5.564706e-01 | 6.905660e-01 | -1.340954e-01 | 2.909178e-04 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for VTI1A |
| 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 |
| ENST00000432306 | 112460524 | 112460582 | Frame-shift |
| ENST00000432306 | 112464547 | 112464657 | 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 |
| ENST00000432306 | 112460524 | 112460582 | 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 |
| ENST00000432306 | 112460524 | 112460582 | Frame-shift |
| ENST00000432306 | 112527087 | 112527164 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for VTI1A |
p-ENSG00000151532_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 |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in VTI1A |
| 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 VTI1A |
| - 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 VTI1A |
| 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 VTI1A |
| 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 VTI1A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| FL | ILF2 | exon_skip_134339 | 4.568366e-01 | 2.424043e-11 |
| HCC | TRNAU1AP | exon_skip_134339 | -4.397700e-01 | 5.247954e-14 |
| HCC | RBM47 | exon_skip_134339 | -4.635603e-01 | 1.411916e-15 |
| HCC | KHDRBS2 | exon_skip_134339 | 4.460337e-01 | 2.081454e-14 |
| HCC | RBM45 | exon_skip_134339 | -4.256208e-01 | 3.957050e-13 |
| HCC | HNRNPF | exon_skip_134339 | -5.233971e-01 | 4.127501e-20 |
| IFG | RBM47 | exon_skip_134339 | -5.957429e-01 | 8.230901e-04 |
| IFG | KHDRBS2 | exon_skip_134339 | 4.454527e-01 | 1.752297e-02 |
| IFG | HNRNPF | exon_skip_134339 | -4.424336e-01 | 1.839630e-02 |
| PCC | RBM47 | exon_skip_134339 | -4.196300e-01 | 5.087305e-10 |
| PCC | HNRNPF | exon_skip_134339 | -5.040907e-01 | 2.041293e-14 |
| PG | ILF2 | exon_skip_134339 | 4.082133e-01 | 5.516660e-09 |
| PG | KHDRBS2 | exon_skip_134339 | 5.055508e-01 | 1.175215e-13 |
| PG | HNRNPD | exon_skip_134339 | 4.025779e-01 | 9.319579e-09 |
| TC | ILF2 | exon_skip_134339 | 4.444015e-01 | 1.530432e-08 |
| TC | KHDRBS2 | exon_skip_134339 | 7.840768e-01 | 4.784946e-32 |
| TC | RBM45 | exon_skip_134339 | 4.282760e-01 | 5.636086e-08 |
| TC | HNRNPD | exon_skip_134339 | 5.251602e-01 | 7.266089e-12 |
Top |
RelatedDrugs for VTI1A |
| 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 VTI1A |
| 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)
|