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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:VCL-VCL (FusionGDB2 ID:97985)

Fusion Gene Summary for VCL-VCL

check button Fusion gene summary
Fusion gene informationFusion gene name: VCL-VCL
Fusion gene ID: 97985
HgeneTgene
Gene symbol

VCL

VCL

Gene ID

7414

7414

Gene namevinculinvinculin
SynonymsCMD1W|CMH15|HEL114|MV|MVCLCMD1W|CMH15|HEL114|MV|MVCL
Cytomap

10q22.2

10q22.2

Type of geneprotein-codingprotein-coding
Descriptionvinculinepididymis luminal protein 114epididymis secretory sperm binding proteinmeta-vinculinmetavinculinvinculinepididymis luminal protein 114epididymis secretory sperm binding proteinmeta-vinculinmetavinculin
Modification date2020032920200329
UniProtAcc.

P18206

Ensembl transtripts involved in fusion geneENST00000211998, ENST00000372755, 
ENST00000417648, ENST00000478896, 
ENST00000211998, ENST00000372755, 
ENST00000417648, ENST00000478896, 
Fusion gene scores* DoF score16 X 16 X 13=332810 X 13 X 5=650
# samples 3812
** MAII scorelog2(38/3328*10)=-3.13058410981014
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/650*10)=-2.4374053123073
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VCL [Title/Abstract] AND VCL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVCL(75879672)-VCL(75879238), # samples:1
VCL(75879672)-VCL(75879237), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneVCL

GO:1903140

regulation of establishment of endothelial barrier

26923917

TgeneVCL

GO:1903140

regulation of establishment of endothelial barrier

26923917


check buttonFusion gene breakpoints across VCL (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across VCL (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChiTaRS5.0N/ABU608049VCLchr10

75879672

-VCLchr10

75879238

+
ChiTaRS5.0N/ACA310524VCLchr10

75879672

-VCLchr10

75879237

+


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Fusion Gene ORF analysis for VCL-VCL

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
3UTR-3UTRENST00000211998ENST00000211998VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-3UTRENST00000211998ENST00000211998VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-3UTRENST00000211998ENST00000372755VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-3UTRENST00000211998ENST00000372755VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-3UTRENST00000372755ENST00000211998VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-3UTRENST00000372755ENST00000211998VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-3UTRENST00000372755ENST00000372755VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-3UTRENST00000372755ENST00000372755VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-intronENST00000211998ENST00000417648VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-intronENST00000211998ENST00000417648VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-intronENST00000211998ENST00000478896VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-intronENST00000211998ENST00000478896VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-intronENST00000372755ENST00000417648VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-intronENST00000372755ENST00000417648VCLchr10

75879672

-VCLchr10

75879237

+
3UTR-intronENST00000372755ENST00000478896VCLchr10

75879672

-VCLchr10

75879238

+
3UTR-intronENST00000372755ENST00000478896VCLchr10

75879672

-VCLchr10

75879237

+
intron-3UTRENST00000417648ENST00000211998VCLchr10

75879672

-VCLchr10

75879238

+
intron-3UTRENST00000417648ENST00000211998VCLchr10

75879672

-VCLchr10

75879237

+
intron-3UTRENST00000417648ENST00000372755VCLchr10

75879672

-VCLchr10

75879238

+
intron-3UTRENST00000417648ENST00000372755VCLchr10

75879672

-VCLchr10

75879237

+
intron-3UTRENST00000478896ENST00000211998VCLchr10

75879672

-VCLchr10

75879238

+
intron-3UTRENST00000478896ENST00000211998VCLchr10

75879672

-VCLchr10

75879237

+
intron-3UTRENST00000478896ENST00000372755VCLchr10

75879672

-VCLchr10

75879238

+
intron-3UTRENST00000478896ENST00000372755VCLchr10

75879672

-VCLchr10

75879237

+
intron-intronENST00000417648ENST00000417648VCLchr10

75879672

-VCLchr10

75879238

+
intron-intronENST00000417648ENST00000417648VCLchr10

75879672

-VCLchr10

75879237

+
intron-intronENST00000417648ENST00000478896VCLchr10

75879672

-VCLchr10

75879238

+
intron-intronENST00000417648ENST00000478896VCLchr10

75879672

-VCLchr10

75879237

+
intron-intronENST00000478896ENST00000417648VCLchr10

75879672

-VCLchr10

75879238

+
intron-intronENST00000478896ENST00000417648VCLchr10

75879672

-VCLchr10

75879237

+
intron-intronENST00000478896ENST00000478896VCLchr10

75879672

-VCLchr10

75879238

+
intron-intronENST00000478896ENST00000478896VCLchr10

75879672

-VCLchr10

75879237

+

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 VCL-VCL


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for VCL-VCL


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/:75879672/:75879238)
- 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
.VCL

P18206

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: Actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion. {ECO:0000269|PubMed:20484056}.

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 VCL-VCL


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 VCL-VCL


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 VCL-VCL


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 VCL-VCL


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource