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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:LRRFIP2-EPHA3 (FusionGDB2 ID:49842)

Fusion Gene Summary for LRRFIP2-EPHA3

check button Fusion gene summary
Fusion gene informationFusion gene name: LRRFIP2-EPHA3
Fusion gene ID: 49842
HgeneTgene
Gene symbol

LRRFIP2

EPHA3

Gene ID

9209

2042

Gene nameLRR binding FLII interacting protein 2EPH receptor A3
SynonymsHUFI-2EK4|ETK|ETK1|HEK|HEK4|TYRO4
Cytomap

3p22.2

3p11.1

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat flightless-interacting protein 2LRR FLII-interacting protein 2leucine rich repeat (in FLII) interacting protein 2ephrin type-A receptor 3EPH-like kinase 4TYRO4 protein tyrosine kinaseeph-like tyrosine kinase 1human embryo kinase 1testicular tissue protein Li 64tyrosine-protein kinase receptor ETK1
Modification date2020031320200313
UniProtAcc.

P29320

Ensembl transtripts involved in fusion geneENST00000421307, ENST00000354379, 
ENST00000336686, ENST00000421276, 
ENST00000396428, ENST00000440230, 
ENST00000490597, 		ENST00000336596, 
ENST00000452448, ENST00000494014, 
Fusion gene scores* DoF score15 X 15 X 8=18008 X 9 X 5=360
# samples 179
** MAII scorelog2(17/1800*10)=-3.40439025507934
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/360*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LRRFIP2 [Title/Abstract] AND EPHA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLRRFIP2(37190385)-EPHA3(89521614), # samples:1
Anticipated loss of major functional domain due to fusion event.LRRFIP2-EPHA3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
LRRFIP2-EPHA3 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
LRRFIP2-EPHA3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
LRRFIP2-EPHA3 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
LRRFIP2-EPHA3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
TgeneEPHA3

GO:0018108

peptidyl-tyrosine phosphorylation

11877430

TgeneEPHA3

GO:0032956

regulation of actin cytoskeleton organization

11870224

TgeneEPHA3

GO:0043087

regulation of GTPase activity

11870224

TgeneEPHA3

GO:0045806

negative regulation of endocytosis

11877430

TgeneEPHA3

GO:0048013

ephrin receptor signaling pathway

11870224

TgeneEPHA3

GO:0051893

regulation of focal adhesion assembly

11870224

TgeneEPHA3

GO:0070507

regulation of microtubule cytoskeleton organization

11870224

TgeneEPHA3

GO:1903078

positive regulation of protein localization to plasma membrane

11877430


check buttonFusion gene breakpoints across LRRFIP2 (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 EPHA3 (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
ChimerDB4STADTCGA-BR-4363-01ALRRFIP2chr3

37190385

-EPHA3chr3

89521614

+


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Fusion Gene ORF analysis for LRRFIP2-EPHA3

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
Frame-shiftENST00000421307ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000421307ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000421307ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
Frame-shiftENST00000354379ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000354379ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000354379ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
Frame-shiftENST00000336686ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000336686ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000336686ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
Frame-shiftENST00000421276ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000421276ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000421276ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
Frame-shiftENST00000396428ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000396428ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000396428ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
Frame-shiftENST00000440230ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000440230ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
5CDS-intronENST00000440230ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
intron-3CDSENST00000490597ENST00000336596LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
intron-intronENST00000490597ENST00000452448LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+
intron-intronENST00000490597ENST00000494014LRRFIP2chr3

37190385

-EPHA3chr3

89521614

+

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 LRRFIP2-EPHA3


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)
LRRFIP2chr337190384-EPHA3chr389521613+7.23E-091
LRRFIP2chr337190384-EPHA3chr389521613+7.23E-091

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 LRRFIP2-EPHA3


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.EPHA3

P29320

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Receptor tyrosine kinase which binds promiscuously 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 for ephrin-A ligands it binds preferentially EFNA5. Upon activation by EFNA5 regulates cell-cell adhesion, cytoskeletal organization and cell migration. Plays a role in cardiac cells migration and differentiation and regulates the formation of the atrioventricular canal and septum during development probably through activation by EFNA1. Involved in the retinotectal mapping of neurons. May also control the segregation but not the guidance of motor and sensory axons during neuromuscular circuit development. {ECO:0000269|PubMed:11870224}.

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 LRRFIP2-EPHA3


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 LRRFIP2-EPHA3


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 LRRFIP2-EPHA3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneEPHA3P29320DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneEPHA3P29320DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneEPHA3P29320DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneEPHA3P29320DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgeneEPHA3P29320DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

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Related Diseases for LRRFIP2-EPHA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneEPHA3C0004238Atrial Fibrillation2CTD_human
TgeneEPHA3C0235480Paroxysmal atrial fibrillation2CTD_human
TgeneEPHA3C2585653Persistent atrial fibrillation2CTD_human
TgeneEPHA3C3468561familial atrial fibrillation2CTD_human