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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 VCP |
 Gene summary |
| Gene information | Gene symbol | VCP | Gene ID | 7415 |
| Gene name | valosin containing protein | |
| Synonyms | CDC48|TERA|p97 | |
| Cytomap | 9p13.3 | |
| Type of gene | protein-coding | |
| Description | transitional endoplasmic reticulum ATPase15S Mg(2+)-ATPase p97 subunitTER ATPase | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context | - 30954774(Mutation and association analyses of dementia-causal genes in Han Chinese patients with early-onset and familial Alzheimer's disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| VCP | GO:0006302 | double-strand break repair | 10855792|22120668 |
| VCP | GO:0006974 | cellular response to DNA damage stimulus | 16140914|22120668|23042605 |
| VCP | GO:0016567 | protein ubiquitination | 22120668 |
| VCP | GO:0030433 | ubiquitin-dependent ERAD pathway | 17872946 |
| VCP | GO:0030970 | retrograde protein transport, ER to cytosol | 15215856 |
| VCP | GO:0031334 | positive regulation of protein complex assembly | 18775313 |
| VCP | GO:0032436 | positive regulation of proteasomal ubiquitin-dependent protein catabolic process | 9452483 |
| VCP | GO:0036503 | ERAD pathway | 25088257 |
| VCP | GO:0045732 | positive regulation of protein catabolic process | 11483959|18775313 |
| VCP | GO:0090263 | positive regulation of canonical Wnt signaling pathway | 28689657 |
| VCP | GO:1903006 | positive regulation of protein K63-linked deubiquitination | 22970133 |
| VCP | GO:1903007 | positive regulation of Lys63-specific deubiquitinase activity | 22970133 |
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Gene structures and expression levels for VCP |
| 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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ENSG00000165280
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| PG | UP | ENST00000448530.5 | VCP-203:protein_coding:VCP | 8.358159e+00 | 2.100959e+00 | 5.006920e-07 | 5.240517e-05 |
| PG | UP | ENST00000417448.1 | VCP-202:protein_coding:VCP | 9.803235e+00 | 8.050057e-01 | 4.210657e-05 | 1.442703e-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 VCP |
| 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_118346 | chr9 | 35060313:35060525:35060801:35060923:35061015:35061179 | 35060801:35060923 |
| exon_skip_127703 | chr9 | 35057376:35057530:35059064:35059219:35059493:35059801 | 35059064:35059219 |
| exon_skip_232866 | chr9 | 35062978:35063080:35064154:35064285:35065251:35065381 | 35064154:35064285 |
| 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 VCP |
| 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 |
| ENST00000358901 | 35059064 | 35059219 | In-frame |
| ENST00000358901 | 35060801 | 35060923 | In-frame |
| ENST00000358901 | 35064154 | 35064285 | 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 |
| ENST00000358901 | 35059064 | 35059219 | 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 |
| ENST00000358901 | 35059064 | 35059219 | In-frame |
| ENST00000358901 | 35064154 | 35064285 | In-frame |
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Infer the effects of exon skipping event on protein functional features for VCP |
p-ENSG00000165280_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 |
| ENST00000358901 | 4387 | 806 | 35064154 | 35064285 | 1473 | 1603 | 192 | 235 |
| ENST00000358901 | 4387 | 806 | 35060801 | 35060923 | 2256 | 2377 | 453 | 493 |
| ENST00000358901 | 4387 | 806 | 35059064 | 35059219 | 2901 | 3055 | 668 | 719 |
| 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 |
| ENST00000358901 | 4387 | 806 | 35059064 | 35059219 | 2901 | 3055 | 668 | 719 |
| 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 |
| ENST00000358901 | 4387 | 806 | 35064154 | 35064285 | 1473 | 1603 | 192 | 235 |
| ENST00000358901 | 4387 | 806 | 35059064 | 35059219 | 2901 | 3055 | 668 | 719 |
| 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 |
| P55072 | 192 | 235 | 198 | 200 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 192 | 235 | 2 | 806 | Chain | ID=PRO_0000084572;Note=Transitional endoplasmic reticulum ATPase |
| P55072 | 192 | 235 | 191 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KDL |
| P55072 | 192 | 235 | 203 | 205 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 210 | 219 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 221 | 225 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 227 | 233 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 198 | 198 | Natural variant | ID=VAR_076468;Note=In IBMPFD1%3B increased ATPase activity%3B impaired autophagic function. L->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17935506,ECO:0000269|PubMed:20335036,ECO:0000269|PubMed:25878907,ECO |
| P55072 | 192 | 235 | 232 | 232 | Natural variant | ID=VAR_033022;Note=In IBMPFD1%3B increased ATPase activity%3B no defect in ubiquitin-dependent protein degradation by the proteasome%3B impaired autophagic function%3B defect in maturation of ubiquitin-containing autophagosomes%3B decreased interaction wi |
| P55072 | 453 | 493 | 458 | 461 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 453 | 493 | 2 | 806 | Chain | ID=PRO_0000084572;Note=Transitional endoplasmic reticulum ATPase |
| P55072 | 453 | 493 | 449 | 457 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 453 | 493 | 476 | 478 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTK |
| P55072 | 453 | 493 | 483 | 498 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 453 | 493 | 462 | 462 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P55072 | 453 | 493 | 462 | 468 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 668 | 719 | 2 | 806 | Chain | ID=PRO_0000084572;Note=Transitional endoplasmic reticulum ATPase |
| P55072 | 668 | 719 | 672 | 678 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 668 | 719 | 684 | 706 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 668 | 719 | 668 | 668 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q01853 |
| P55072 | 668 | 719 | 668 | 668 | Modified residue | Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q01853 |
| P55072 | 668 | 719 | 702 | 702 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| 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 |
| P55072 | 668 | 719 | 2 | 806 | Chain | ID=PRO_0000084572;Note=Transitional endoplasmic reticulum ATPase |
| P55072 | 668 | 719 | 672 | 678 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 668 | 719 | 684 | 706 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 668 | 719 | 668 | 668 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q01853 |
| P55072 | 668 | 719 | 668 | 668 | Modified residue | Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q01853 |
| P55072 | 668 | 719 | 702 | 702 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| 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 |
| P55072 | 192 | 235 | 198 | 200 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 192 | 235 | 2 | 806 | Chain | ID=PRO_0000084572;Note=Transitional endoplasmic reticulum ATPase |
| P55072 | 192 | 235 | 191 | 193 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KDL |
| P55072 | 192 | 235 | 203 | 205 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 210 | 219 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 221 | 225 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 227 | 233 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4KO8 |
| P55072 | 192 | 235 | 198 | 198 | Natural variant | ID=VAR_076468;Note=In IBMPFD1%3B increased ATPase activity%3B impaired autophagic function. L->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17935506,ECO:0000269|PubMed:20335036,ECO:0000269|PubMed:25878907,ECO |
| P55072 | 192 | 235 | 232 | 232 | Natural variant | ID=VAR_033022;Note=In IBMPFD1%3B increased ATPase activity%3B no defect in ubiquitin-dependent protein degradation by the proteasome%3B impaired autophagic function%3B defect in maturation of ubiquitin-containing autophagosomes%3B decreased interaction wi |
| P55072 | 668 | 719 | 2 | 806 | Chain | ID=PRO_0000084572;Note=Transitional endoplasmic reticulum ATPase |
| P55072 | 668 | 719 | 672 | 678 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 668 | 719 | 684 | 706 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5FTJ |
| P55072 | 668 | 719 | 668 | 668 | Modified residue | Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q01853 |
| P55072 | 668 | 719 | 668 | 668 | Modified residue | Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q01853 |
| P55072 | 668 | 719 | 702 | 702 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
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3'-UTR located exon skipping events that lost miRNA binding sites in VCP |
| 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 VCP |
| - 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 VCP |
| 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 VCP |
| 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 VCP |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for VCP |
| 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 VCP |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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