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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:EPHA6-CPEB1 (FusionGDB2 ID:26971)

Fusion Gene Summary for EPHA6-CPEB1

check button Fusion gene summary
Fusion gene informationFusion gene name: EPHA6-CPEB1
Fusion gene ID: 26971
HgeneTgene
Gene symbol

EPHA6

CPEB1

Gene ID

285220

64506

Gene nameEPH receptor A6cytoplasmic polyadenylation element binding protein 1
SynonymsEHK-2|EHK2|EK12|EPA6|HEK12|PRO57066CPE-BP1|CPEB|CPEB-1|h-CPEB|hCPEB-1
Cytomap

3q11.2

15q25.2

Type of geneprotein-codingprotein-coding
Descriptionephrin type-A receptor 6EPH homology kinase 2EPH-like kinase 12ephrin receptor EphA6cytoplasmic polyadenylation element-binding protein 1CPE-binding protein 1
Modification date2020031320200320
UniProtAcc

Q9UF33

Q9BZB8

Ensembl transtripts involved in fusion geneENST00000389672, ENST00000442602, 
ENST00000470610, ENST00000502694, 
ENST00000514100, ENST00000542517, 
ENST00000261723, ENST00000398591, 
ENST00000398592, ENST00000423133, 
ENST00000450751, ENST00000562019, 
ENST00000563519, ENST00000563800, 
ENST00000564522, ENST00000568128, 
ENST00000568757, 
Fusion gene scores* DoF score6 X 5 X 4=1203 X 3 X 2=18
# samples 74
** MAII scorelog2(7/120*10)=-0.777607578663552
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: EPHA6 [Title/Abstract] AND CPEB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEPHA6(96960626)-CPEB1(83281271), # 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
TgeneCPEB1

GO:0032869

cellular response to insulin stimulus

18752464

TgeneCPEB1

GO:0071456

cellular response to hypoxia

18752464

TgeneCPEB1

GO:1900365

positive regulation of mRNA polyadenylation

28383716


check buttonFusion gene breakpoints across EPHA6 (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 CPEB1 (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/AAX187048EPHA6chr3

96960626

+CPEB1chr15

83281271

-


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Fusion Gene ORF analysis for EPHA6-CPEB1

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-intronENST00000389672ENST00000261723EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000398591EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000398592EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000423133EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000450751EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000562019EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000563519EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000563800EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000564522EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000568128EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000389672ENST00000568757EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000261723EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000398591EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000398592EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000423133EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000450751EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000562019EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000563519EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000563800EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000564522EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000568128EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000442602ENST00000568757EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000261723EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000398591EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000398592EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000423133EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000450751EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000562019EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000563519EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000563800EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000564522EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000568128EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000470610ENST00000568757EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000261723EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000398591EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000398592EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000423133EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000450751EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000562019EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000563519EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000563800EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000564522EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000568128EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000502694ENST00000568757EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000261723EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000398591EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000398592EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000423133EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000450751EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000562019EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000563519EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000563800EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000564522EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000568128EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000514100ENST00000568757EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000261723EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000398591EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000398592EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000423133EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000450751EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000562019EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000563519EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000563800EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000564522EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000568128EPHA6chr3

96960626

+CPEB1chr15

83281271

-
intron-intronENST00000542517ENST00000568757EPHA6chr3

96960626

+CPEB1chr15

83281271

-

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 EPHA6-CPEB1


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 EPHA6-CPEB1


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/:96960626/:83281271)
- 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

CPEB1

Q9BZB8

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}.FUNCTION: Sequence-specific RNA-binding protein that regulates mRNA cytoplasmic polyadenylation and translation initiation during oocyte maturation, early development and at postsynapse sites of neurons. Binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU-3') within the mRNA 3'-UTR. RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). In absence of phosphorylation and in association with TACC3 is also involved as a repressor of translation of CPE-containing mRNA; a repression that is relieved by phosphorylation or degradation (By similarity). Involved in the transport of CPE-containing mRNA to dendrites; those mRNAs may be transported to dendrites in a translationally dormant form and translationally activated at synapses (By similarity). Its interaction with APLP1 promotes local CPE-containing mRNA polyadenylation and translation activation (By similarity). Induces the assembly of stress granules in the absence of stress. Required for cell cycle progression, specifically for prophase entry (PubMed:26398195). {ECO:0000250|UniProtKB:P70166, ECO:0000269|PubMed:15731006, ECO:0000269|PubMed:15966895, ECO:0000269|PubMed:24990967, ECO:0000269|PubMed:26398195}.

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 EPHA6-CPEB1


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 EPHA6-CPEB1


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 EPHA6-CPEB1


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 EPHA6-CPEB1


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