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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:RBFOX1-EPHA6 (FusionGDB2 ID:72645)

Fusion Gene Summary for RBFOX1-EPHA6

check button Fusion gene summary
Fusion gene informationFusion gene name: RBFOX1-EPHA6
Fusion gene ID: 72645
HgeneTgene
Gene symbol

RBFOX1

EPHA6

Gene ID

54715

285220

Gene nameRNA binding fox-1 homolog 1EPH receptor A6
Synonyms2BP1|A2BP1|FOX-1|FOX1|HRNBP1EHK-2|EHK2|EK12|EPA6|HEK12|PRO57066
Cytomap

16p13.3

3q11.2

Type of geneprotein-codingprotein-coding
DescriptionRNA binding protein fox-1 homolog 1RNA binding protein, fox-1 homolog 1ataxin 2-binding protein 1fox-1 homolog Afox-1-like RNA-binding protein 1hexaribonucleotide binding protein 1 isoform alphahexaribonucleotide binding protein 1 isoform betahexarephrin type-A receptor 6EPH homology kinase 2EPH-like kinase 12ephrin receptor EphA6
Modification date2020031320200313
UniProtAcc.

Q9UF33

Ensembl transtripts involved in fusion geneENST00000311745, ENST00000340209, 
ENST00000355637, ENST00000547372, 
ENST00000422070, ENST00000436368, 
ENST00000535565, ENST00000547338, 
ENST00000547427, ENST00000550418, 
ENST00000552089, ENST00000553186, 
ENST00000389672, ENST00000442602, 
ENST00000470610, ENST00000502694, 
ENST00000514100, ENST00000542517, 
Fusion gene scores* DoF score19 X 19 X 1=36110 X 11 X 4=440
# samples 1911
** MAII scorelog2(19/361*10)=-0.925999418556223
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/440*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBFOX1 [Title/Abstract] AND EPHA6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBFOX1(7760885)-EPHA6(97187269), # 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

check buttonFusion gene breakpoints across RBFOX1 (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 EPHA6 (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/AAI141205RBFOX1chr16

7760885

-EPHA6chr3

97187269

-


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Fusion Gene ORF analysis for RBFOX1-EPHA6

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-intronENST00000311745ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000311745ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000311745ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000311745ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000311745ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000311745ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000340209ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000340209ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000340209ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000340209ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000340209ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000340209ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000355637ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000355637ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000355637ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000355637ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000355637ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000355637ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000547372ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000547372ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000547372ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000547372ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000547372ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
3UTR-intronENST00000547372ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000422070ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000422070ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000422070ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000422070ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000422070ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000422070ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000436368ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000436368ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000436368ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000436368ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000436368ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000436368ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000535565ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000535565ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000535565ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000535565ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000535565ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000535565ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547338ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547338ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547338ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547338ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547338ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547338ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547427ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547427ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547427ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547427ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547427ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000547427ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000550418ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000550418ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000550418ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000550418ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000550418ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000550418ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000552089ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000552089ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000552089ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000552089ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000552089ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000552089ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000553186ENST00000389672RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000553186ENST00000442602RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000553186ENST00000470610RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000553186ENST00000502694RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000553186ENST00000514100RBFOX1chr16

7760885

-EPHA6chr3

97187269

-
intron-intronENST00000553186ENST00000542517RBFOX1chr16

7760885

-EPHA6chr3

97187269

-

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 RBFOX1-EPHA6


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 RBFOX1-EPHA6


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/:7760885/:97187269)
- 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
.EPHA6

Q9UF33

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: Receptor tyrosine kinase which binds promiscuously GPI-anchored ephrin-A family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling (By similarity). {ECO:0000250}.

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 RBFOX1-EPHA6


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 RBFOX1-EPHA6


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 RBFOX1-EPHA6


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 RBFOX1-EPHA6


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