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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:STUM-VTI1A (FusionGDB2 ID:HG375057TG143187)

Fusion Gene Summary for STUM-VTI1A

check button Fusion gene summary
Fusion gene informationFusion gene name: STUM-VTI1A
Fusion gene ID: hg375057tg143187
HgeneTgene
Gene symbol

STUM

VTI1A

Gene ID

375057

143187

Gene namestum, mechanosensory transduction mediator homologvesicle transport through interaction with t-SNAREs 1A
SynonymsC1orf95MMDS3|MVti1|VTI1RP2|Vti1-rp2
Cytomap('C1orf95','STUM')('VTI1A','VTI1A')

1q42.12

10q25.2

Type of geneprotein-codingprotein-coding
Descriptionprotein stum homologstumble homologvesicle transport through interaction with t-SNAREs homolog 1ASNARE Vti1a-beta proteinvesicle transport v-SNARE protein Vti1-like 2
Modification date2020031320200313
UniProtAcc.

Q96AJ9

Ensembl transtripts involved in fusion geneENST00000366788, ENST00000366789, 
Fusion gene scores* DoF score2 X 1 X 1=217 X 15 X 10=2550
# samples 224
** MAII scorelog2(2/2*10)=3.32192809488736log2(24/2550*10)=-3.4093909361377
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STUM [Title/Abstract] AND VTI1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC1orf95(226736807)-VTI1A(114286846), # samples:2
STUM(226736807)-VTI1A(114286846), # samples:1
Anticipated loss of major functional domain due to fusion event.C1orf95-VTI1A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
C1orf95-VTI1A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneVTI1A

GO:0042147

retrograde transport, endosome to Golgi

15215310|18195106



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LUADTCGA-55-6969-01AC1orf95chr1

226736807

-VTI1Achr10

114286846

+
ChimerDB4LUADTCGA-55-6969-01AC1orf95chr1

226736807

+VTI1Achr10

114286846

+
ChimerDB4LUADTCGA-55-6969-01ASTUMchr1

226736807

+VTI1Achr10

114286846

+


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Fusion Gene ORF analysis for STUM-VTI1A

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-intronENST00000366788ENST00000483122C1orf95chr1

226736807

+VTI1Achr10

114286846

+
5CDS-intronENST00000366789ENST00000483122C1orf95chr1

226736807

+VTI1Achr10

114286846

+
Frame-shiftENST00000366788ENST00000393077C1orf95chr1

226736807

+VTI1Achr10

114286846

+
Frame-shiftENST00000366788ENST00000432306C1orf95chr1

226736807

+VTI1Achr10

114286846

+
Frame-shiftENST00000366789ENST00000393077C1orf95chr1

226736807

+VTI1Achr10

114286846

+
Frame-shiftENST00000366789ENST00000432306C1orf95chr1

226736807

+VTI1Achr10

114286846

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for STUM-VTI1A


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
C1orf95chr1226736807+VTI1Achr10114286845+2.72E-060.99999726
C1orf95chr1226736807+VTI1Achr10114286845+2.72E-060.99999726


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for STUM-VTI1A


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:226736807/:114286846)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.VTI1A

Q96AJ9

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non-conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence. {ECO:0000269|PubMed:18195106, ECO:0000269|PubMed:19138172}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for STUM-VTI1A


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for STUM-VTI1A


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for STUM-VTI1A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for STUM-VTI1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0001418Adenocarcinoma1CTD_human
TgeneC0009402Colorectal Carcinoma1CTD_human
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneC0205643Carcinoma, Cribriform1CTD_human
TgeneC0205644Carcinoma, Granular Cell1CTD_human
TgeneC0205645Adenocarcinoma, Tubular1CTD_human