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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for VPS41 |
 Gene summary |
| Gene information | Gene symbol | VPS41 | Gene ID | 27072 |
| Gene name | VPS41, HOPS complex subunit | |
| Synonyms | HVPS41|HVSP41|hVps41p | |
| Cytomap | 7p14.1 | |
| Type of gene | protein-coding | |
| Description | vacuolar protein sorting-associated protein 41 homologS53vacuolar assembly protein 41vacuolar protein sorting 41 homolog | |
| Modification date | 20180523 | |
| UniProtAcc | P49754 | |
| Context | PubMed: VPS41 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| 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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Exon skipping events across known transcript of Ensembl for VPS41 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for VPS41 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for VPS41 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_474774 | 7 | 38766508:38766588:38767940:38768034:38768141:38768186 | 38767940:38768034 | ENSG00000006715.11 | ENST00000448833.1 |
| exon_skip_474775 | 7 | 38766508:38766588:38768141:38768186:38768291:38768391 | 38768141:38768186 | ENSG00000006715.11 | ENST00000395969.2,ENST00000482217.1,ENST00000310301.4 |
| exon_skip_474778 | 7 | 38768141:38768186:38768291:38768391:38781584:38781721 | 38768291:38768391 | ENSG00000006715.11 | ENST00000395969.2,ENST00000482217.1,ENST00000310301.4,ENST00000448833.1 |
| exon_skip_474782 | 7 | 38807136:38807198:38810797:38810854:38812121:38812237 | 38810797:38810854 | ENSG00000006715.11 | ENST00000395969.2,ENST00000310301.4 |
| exon_skip_474783 | 7 | 38813757:38813844:38816278:38816376:38829400:38829467 | 38816278:38816376 | ENSG00000006715.11 | ENST00000466017.1,ENST00000395969.2,ENST00000310301.4 |
| exon_skip_474784 | 7 | 38835141:38835211:38836014:38836126:38836344:38836464 | 38836014:38836126 | ENSG00000006715.11 | ENST00000265745.9 |
| exon_skip_474788 | 7 | 38857416:38857482:38860802:38860865:38869853:38869928 | 38860802:38860865 | ENSG00000006715.11 | ENST00000413141.1,ENST00000418457.2,ENST00000414632.1,ENST00000310301.4,ENST00000265745.9 |
| exon_skip_474791 | 7 | 38860817:38860865:38869853:38869928:38902144:38902222 | 38869853:38869928 | ENSG00000006715.11 | ENST00000457055.1,ENST00000418457.2,ENST00000414632.1,ENST00000310301.4,ENST00000265745.9 |
| exon_skip_474794 | 7 | 38908745:38908853:38937690:38937729:38948753:38948774 | 38937690:38937729 | ENSG00000006715.11 | ENST00000395969.2,ENST00000265745.9 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for VPS41 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_474774 | 7 | 38766508:38766588:38767940:38768034:38768141:38768186 | 38767940:38768034 | ENSG00000006715.11 | ENST00000448833.1 |
| exon_skip_474775 | 7 | 38766508:38766588:38768141:38768186:38768291:38768391 | 38768141:38768186 | ENSG00000006715.11 | ENST00000310301.4,ENST00000395969.2,ENST00000482217.1 |
| exon_skip_474778 | 7 | 38768141:38768186:38768291:38768391:38781584:38781721 | 38768291:38768391 | ENSG00000006715.11 | ENST00000310301.4,ENST00000395969.2,ENST00000448833.1,ENST00000482217.1 |
| exon_skip_474782 | 7 | 38807136:38807198:38810797:38810854:38812121:38812237 | 38810797:38810854 | ENSG00000006715.11 | ENST00000310301.4,ENST00000395969.2 |
| exon_skip_474783 | 7 | 38813757:38813844:38816278:38816376:38829400:38829467 | 38816278:38816376 | ENSG00000006715.11 | ENST00000310301.4,ENST00000395969.2,ENST00000466017.1 |
| exon_skip_474784 | 7 | 38835141:38835211:38836014:38836126:38836344:38836464 | 38836014:38836126 | ENSG00000006715.11 | ENST00000265745.9 |
| exon_skip_474791 | 7 | 38860817:38860865:38869853:38869928:38902144:38902222 | 38869853:38869928 | ENSG00000006715.11 | ENST00000310301.4,ENST00000265745.9,ENST00000414632.1,ENST00000418457.2,ENST00000457055.1 |
| exon_skip_474794 | 7 | 38908745:38908853:38937690:38937729:38948753:38948774 | 38937690:38937729 | ENSG00000006715.11 | ENST00000395969.2,ENST00000265745.9 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for VPS41 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000310301 | 38768291 | 38768391 | Frame-shift |
| ENST00000310301 | 38816278 | 38816376 | Frame-shift |
| ENST00000310301 | 38768141 | 38768186 | In-frame |
| ENST00000310301 | 38810797 | 38810854 | In-frame |
| ENST00000310301 | 38860802 | 38860865 | In-frame |
| ENST00000310301 | 38869853 | 38869928 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000310301 | 38768291 | 38768391 | Frame-shift |
| ENST00000310301 | 38816278 | 38816376 | Frame-shift |
| ENST00000310301 | 38768141 | 38768186 | In-frame |
| ENST00000310301 | 38810797 | 38810854 | In-frame |
| ENST00000310301 | 38869853 | 38869928 | In-frame |
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Infer the effects of exon skipping event on protein functional features for VPS41 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000310301 | 5920 | 854 | 38869853 | 38869928 | 302 | 376 | 82 | 107 |
| ENST00000310301 | 5920 | 854 | 38860802 | 38860865 | 377 | 439 | 107 | 128 |
| ENST00000310301 | 5920 | 854 | 38810797 | 38810854 | 1184 | 1240 | 376 | 395 |
| ENST00000310301 | 5920 | 854 | 38768141 | 38768186 | 2415 | 2459 | 786 | 801 |
| Loci of skipped exons in GTEx 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 |
| ENST00000310301 | 5920 | 854 | 38869853 | 38869928 | 302 | 376 | 82 | 107 |
| ENST00000310301 | 5920 | 854 | 38810797 | 38810854 | 1184 | 1240 | 376 | 395 |
| ENST00000310301 | 5920 | 854 | 38768141 | 38768186 | 2415 | 2459 | 786 | 801 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| P49754 | 82 | 107 | 83 | 107 | Alternative sequence | ID=VSP_054169;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P49754 | 82 | 107 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 82 | 107 | 1 | 540 | Region | Note=Interaction with ARL8B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25908847;Dbxref=PMID:25908847 |
| P49754 | 107 | 128 | 83 | 107 | Alternative sequence | ID=VSP_054169;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P49754 | 107 | 128 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 107 | 128 | 1 | 540 | Region | Note=Interaction with ARL8B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25908847;Dbxref=PMID:25908847 |
| P49754 | 376 | 395 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 376 | 395 | 1 | 540 | Region | Note=Interaction with ARL8B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25908847;Dbxref=PMID:25908847 |
| P49754 | 786 | 801 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 786 | 801 | 791 | 839 | Zinc finger | Note=RING-type%3B atypical;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00175 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| P49754 | 82 | 107 | 83 | 107 | Alternative sequence | ID=VSP_054169;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P49754 | 82 | 107 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 82 | 107 | 1 | 540 | Region | Note=Interaction with ARL8B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25908847;Dbxref=PMID:25908847 |
| P49754 | 376 | 395 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 376 | 395 | 1 | 540 | Region | Note=Interaction with ARL8B;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25908847;Dbxref=PMID:25908847 |
| P49754 | 786 | 801 | 1 | 854 | Chain | ID=PRO_0000212823;Note=Vacuolar protein sorting-associated protein 41 homolog |
| P49754 | 786 | 801 | 791 | 839 | Zinc finger | Note=RING-type%3B atypical;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00175 |
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SNVs in the skipped exons for VPS41 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| COAD | TCGA-AA-3713-01 | exon_skip_474782 | 38810798 | 38810854 | 38810820 | 38810820 | Frame_Shift_Del | T | - | p.N363fs |
| STAD | TCGA-BR-4280-01 | exon_skip_474782 | 38810798 | 38810854 | 38810820 | 38810820 | Frame_Shift_Del | T | - | p.N388fs |
| STAD | TCGA-BR-6566-01 | exon_skip_474782 | 38810798 | 38810854 | 38810820 | 38810820 | Frame_Shift_Del | T | - | p.N388fs |
| UCEC | TCGA-B5-A0JZ-01 | exon_skip_474782 | 38810798 | 38810854 | 38810820 | 38810820 | Frame_Shift_Del | T | - | p.N388fs |
| CHOL | TCGA-W5-AA39-01 | exon_skip_474788 | 38860803 | 38860865 | 38860830 | 38860830 | Frame_Shift_Del | A | - | p.F119fs |
| CHOL | TCGA-W5-AA39-01 | exon_skip_474788 | 38860803 | 38860865 | 38860830 | 38860830 | Frame_Shift_Del | A | - | p.H120fs |
| COAD | TCGA-AZ-6598-01 | exon_skip_474782 | 38810798 | 38810854 | 38810819 | 38810820 | Frame_Shift_Ins | - | T | p.N363fs |
| COAD | TCGA-AD-6889-01 | exon_skip_474783 | 38816279 | 38816376 | 38816280 | 38816281 | Frame_Shift_Ins | - | T | p.T269fs |
| BLCA | TCGA-DK-A6AW-01 | exon_skip_474788 | 38860803 | 38860865 | 38860835 | 38860835 | Nonsense_Mutation | C | A | p.E118* |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_474794 | 38937691 | 38937729 | 38937711 | 38937711 | Nonsense_Mutation | C | A | p.E14* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| RKO_LARGE_INTESTINE | 38810798 | 38810854 | 38810820 | 38810820 | Frame_Shift_Del | T | - | p.N388fs |
| WM2664_SKIN | 38810798 | 38810854 | 38810819 | 38810820 | Frame_Shift_Ins | - | T | p.N388fs |
| ESS1_ENDOMETRIUM | 38768142 | 38768186 | 38768168 | 38768168 | Missense_Mutation | G | A | p.S793L |
| JHUEM7_ENDOMETRIUM | 38768292 | 38768391 | 38768321 | 38768321 | Missense_Mutation | C | T | p.R777Q |
| NCIH226_LUNG | 38768292 | 38768391 | 38768321 | 38768321 | Missense_Mutation | C | T | p.R777Q |
| MG63_BONE | 38768292 | 38768391 | 38768328 | 38768328 | Missense_Mutation | T | C | p.M775V |
| KYSE150_OESOPHAGUS | 38768292 | 38768391 | 38768350 | 38768350 | Missense_Mutation | G | C | p.D767E |
| 22RV1_PROSTATE | 38768292 | 38768391 | 38768358 | 38768358 | Missense_Mutation | C | T | p.V765I |
| LS180_LARGE_INTESTINE | 38768292 | 38768391 | 38768358 | 38768358 | Missense_Mutation | C | T | p.V765I |
| ONCODG1_OVARY | 38768292 | 38768391 | 38768367 | 38768367 | Missense_Mutation | T | C | p.K762E |
| NIHOVCAR3_OVARY | 38768292 | 38768391 | 38768367 | 38768367 | Missense_Mutation | T | C | p.K762E |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 38816279 | 38816376 | 38816293 | 38816293 | Missense_Mutation | T | C | p.I290V |
| HCC2998_LARGE_INTESTINE | 38816279 | 38816376 | 38816310 | 38816310 | Missense_Mutation | A | C | p.L284R |
| GP2D_LARGE_INTESTINE | 38869854 | 38869928 | 38869873 | 38869873 | Missense_Mutation | A | G | p.V101A |
| GP5D_LARGE_INTESTINE | 38869854 | 38869928 | 38869873 | 38869873 | Missense_Mutation | A | G | p.V101A |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 38869854 | 38869928 | 38869893 | 38869893 | Missense_Mutation | T | G | p.E94D |
| NCIH345_LUNG | 38768142 | 38768186 | 38768184 | 38768184 | Nonsense_Mutation | C | A | p.E788* |
| SKMG1_CENTRAL_NERVOUS_SYSTEM | 38768292 | 38768391 | 38768292 | 38768292 | Splice_Site | C | T | p.E787K |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 38860803 | 38860865 | 38860865 | 38860865 | Splice_Site | C | G | p.V108L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VPS41 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS41 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS41 |
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RelatedDrugs for VPS41 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for VPS41 |
| 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)
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