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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:EPHA4-FBXL13 (FusionGDB2 ID:26961)

Fusion Gene Summary for EPHA4-FBXL13

check button Fusion gene summary
Fusion gene informationFusion gene name: EPHA4-FBXL13
Fusion gene ID: 26961
HgeneTgene
Gene symbol

EPHA4

FBXL13

Gene ID

2043

222235

Gene nameEPH receptor A4F-box and leucine rich repeat protein 13
SynonymsEK8|HEK8|SEK|TYRO1CFAP169|DRC6|Fbl13
Cytomap

2q36.1

7q22.1

Type of geneprotein-codingprotein-coding
Descriptionephrin type-A receptor 4EPH-like kinase 8TYRO1 protein tyrosine kinasereceptor protein-tyrosine kinase HEK8tyrosine-protein kinase TYRO1tyrosine-protein kinase receptor SEKdynein regulatory complex subunit 6F-box/LRR-repeat protein 13cilia and flagella associated protein 169
Modification date2020031320200313
UniProtAcc

P54764

Q8NEE6

Ensembl transtripts involved in fusion geneENST00000281821, ENST00000392071, 
ENST00000409854, ENST00000409938, 
ENST00000469354, 		ENST00000313221, 
ENST00000379305, ENST00000379306, 
ENST00000379308, ENST00000393772, 
ENST00000436908, ENST00000455112, 
ENST00000456695, ENST00000471074, 
Fusion gene scores* DoF score4 X 3 X 3=367 X 7 X 4=196
# samples 47
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(7/196*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EPHA4 [Title/Abstract] AND FBXL13 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEPHA4(222291271)-FBXL13(102584839), # 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
HgeneEPHA4

GO:0018108

peptidyl-tyrosine phosphorylation

12775584

HgeneEPHA4

GO:0046777

protein autophosphorylation

12775584

HgeneEPHA4

GO:2001108

positive regulation of Rho guanyl-nucleotide exchange factor activity

12775584


check buttonFusion gene breakpoints across EPHA4 (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 FBXL13 (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/ABI494738EPHA4chr2

222291271

+FBXL13chr7

102584839

+


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Fusion Gene ORF analysis for EPHA4-FBXL13

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
intron-intronENST00000281821ENST00000313221EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000379305EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000379306EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000379308EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000393772EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000436908EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000455112EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000456695EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000281821ENST00000471074EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000313221EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000379305EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000379306EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000379308EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000393772EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000436908EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000455112EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000456695EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000392071ENST00000471074EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000313221EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000379305EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000379306EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000379308EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000393772EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000436908EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000455112EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000456695EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409854ENST00000471074EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000313221EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000379305EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000379306EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000379308EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000393772EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000436908EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000455112EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000456695EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000409938ENST00000471074EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000313221EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000379305EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000379306EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000379308EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000393772EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000436908EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000455112EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000456695EPHA4chr2

222291271

+FBXL13chr7

102584839

+
intron-intronENST00000469354ENST00000471074EPHA4chr2

222291271

+FBXL13chr7

102584839

+

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 EPHA4-FBXL13


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 EPHA4-FBXL13


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/:222291271/:102584839)
- 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
EPHA4

P54764

FBXL13

Q8NEE6

FUNCTION: Receptor tyrosine kinase which binds membrane-bound ephrin 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. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. May also control the segregation of motor and sensory axons during neuromuscular circuit development. In addition to its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium. During development of the cochlear organ of Corti, regulates pillar cell separation by forming a ternary complex with ADAM10 and CADH1 which facilitates the cleavage of CADH1 by ADAM10 and disruption of adherens junctions (By similarity). {ECO:0000250|UniProtKB:Q03137, ECO:0000269|PubMed:17143272}.FUNCTION: Component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. {ECO:0000250, ECO:0000250|UniProtKB:A8JHD7}.

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 EPHA4-FBXL13


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 EPHA4-FBXL13


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 EPHA4-FBXL13


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 EPHA4-FBXL13


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