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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:LY6E-KCNQ1 (FusionGDB2 ID:50414)

Fusion Gene Summary for LY6E-KCNQ1

check button Fusion gene summary
Fusion gene informationFusion gene name: LY6E-KCNQ1
Fusion gene ID: 50414
HgeneTgene
Gene symbol

LY6E

KCNQ1

Gene ID

4061

3784

Gene namelymphocyte antigen 6 family member Epotassium voltage-gated channel subfamily Q member 1
SynonymsRIG-E|RIGE|SCA-2|SCA2|TSA-1ATFB1|ATFB3|JLNS1|KCNA8|KCNA9|KVLQT1|Kv1.9|Kv7.1|LQT|LQT1|RWS|SQT2|WRS
Cytomap

8q24.3

11p15.5-p15.4

Type of geneprotein-codingprotein-coding
Descriptionlymphocyte antigen 6Ely-6Elymphocyte antigen 6 complex, locus Eretinoic acid induced gene Eretinoic acid-induced gene E proteinstem cell antigen 2thymic shared antigen 1potassium voltage-gated channel subfamily KQT member 1IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1kidney and cardiac voltage dependend K+ channelpotassium channel, voltage gated KQT-like subfamily Q, member 1potassium voltag
Modification date2020031320200313
UniProtAcc

Q16553

P51787

Ensembl transtripts involved in fusion geneENST00000292494, ENST00000429120, 
ENST00000517503, ENST00000519546, 
ENST00000520466, ENST00000521182, 
ENST00000521699, ENST00000522971, 
ENST00000519611, ENST00000519615, 
ENST00000520531, ENST00000521003, 
ENST00000522024, ENST00000522528, 
ENST00000523847, 		ENST00000155840, 
ENST00000335475, ENST00000526095, 
Fusion gene scores* DoF score9 X 8 X 4=28810 X 10 X 5=500
# samples 1012
** MAII scorelog2(10/288*10)=-1.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/500*10)=-2.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LY6E [Title/Abstract] AND KCNQ1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLY6E(144103385)-KCNQ1(2532796), # 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
TgeneKCNQ1

GO:0035690

cellular response to drug

9108097

TgeneKCNQ1

GO:0060306

regulation of membrane repolarization

11299204

TgeneKCNQ1

GO:0071320

cellular response to cAMP

11299204|16002409

TgeneKCNQ1

GO:0071805

potassium ion transmembrane transport

9354802|11299204|16002409

TgeneKCNQ1

GO:0086011

membrane repolarization during action potential

8900283|11299204|19646991

TgeneKCNQ1

GO:0097623

potassium ion export across plasma membrane

8900283|10400998|17289006

TgeneKCNQ1

GO:1901381

positive regulation of potassium ion transmembrane transport

8900283


check buttonFusion gene breakpoints across LY6E (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 KCNQ1 (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/ACA488052LY6Echr8

144103385

+KCNQ1chr11

2532796

+


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Fusion Gene ORF analysis for LY6E-KCNQ1

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-intronENST00000292494ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000292494ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000292494ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000429120ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000429120ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000429120ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000517503ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000517503ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000517503ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000519546ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000519546ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000519546ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000520466ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000520466ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000520466ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000521182ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000521182ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000521182ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000521699ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000521699ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000521699ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000522971ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000522971ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
3UTR-intronENST00000522971ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000519611ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000519611ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000519611ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000519615ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000519615ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000519615ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000520531ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000520531ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000520531ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000521003ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000521003ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000521003ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000522024ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000522024ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000522024ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000522528ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000522528ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000522528ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000523847ENST00000155840LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000523847ENST00000335475LY6Echr8

144103385

+KCNQ1chr11

2532796

+
intron-intronENST00000523847ENST00000526095LY6Echr8

144103385

+KCNQ1chr11

2532796

+

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 LY6E-KCNQ1


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 LY6E-KCNQ1


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/:144103385/:2532796)
- 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
LY6E

Q16553

KCNQ1

P51787

FUNCTION: GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation. Regulates the T-cell receptor (TCR) signaling by interacting with component CD3Z/CD247 at the plasma membrane, leading to CD3Z/CD247 phosphorylation modulation (By similarity). Restricts the entry of human coronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2, by interfering with spike protein-mediated membrane fusion (PubMed:32641482). Plays also an essential role in placenta formation by acting as the main receptor for syncytin-A (SynA). Therefore, participates in the normal fusion of syncytiotrophoblast layer I (SynT-I) and in the proper morphogenesis of both fetal and maternal vasculatures within the placenta. May also act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity (By similarity). {ECO:0000250|UniProtKB:Q64253, ECO:0000269|PubMed:32641482}.; FUNCTION: (Microbial infection) Promotes entry, likely through an enhanced virus-cell fusion process, of various viruses including HIV-1, West Nile virus, dengue virus and Zika virus (PubMed:28130445). In contrast, the paramyxovirus PIV5, which enters at the plasma membrane, does not require LY6E (PubMed:28130445, PubMed:29610346). Mechanistically, adopts a microtubule-like organization upon viral infection and enhances viral uncoating after endosomal escape (PubMed:28130445, PubMed:30190477). {ECO:0000269|PubMed:28130445, ECO:0000269|PubMed:29610346, ECO:0000269|PubMed:30190477}.FUNCTION: Potassium channel that plays an important role in a number of tissues, including heart, inner ear, stomach and colon (PubMed:10646604, PubMed:25441029). Associates with KCNE beta subunits that modulates current kinetics (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505, PubMed:19687231). Induces a voltage-dependent current by rapidly activating and slowly deactivating potassium-selective outward current (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505, PubMed:25441029). Promotes also a delayed voltage activated potassium current showing outward rectification characteristic (By similarity). During beta-adrenergic receptor stimulation participates in cardiac repolarization by associating with KCNE1 to form the I(Ks) cardiac potassium current that increases the amplitude and slows down the activation kinetics of outward potassium current I(Ks) (By similarity) (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505). Muscarinic agonist oxotremorine-M strongly suppresses KCNQ1/KCNE1 current (PubMed:10713961). When associated with KCNE3, forms the potassium channel that is important for cyclic AMP-stimulated intestinal secretion of chloride ions (PubMed:10646604). This interaction with KCNE3 is reduced by 17beta-estradiol, resulting in the reduction of currents (By similarity). During conditions of increased substrate load, maintains the driving force for proximal tubular and intestinal sodium ions absorption, gastric acid secretion, and cAMP-induced jejunal chloride ions secretion (By similarity). Allows the provision of potassium ions to the luminal membrane of the secretory canaliculus in the resting state as well as during stimulated acid secretion (By similarity). When associated with KCNE2, forms a heterooligomer complex leading to currents with an apparently instantaneous activation, a rapid deactivation process and a linear current-voltage relationship and decreases the amplitude of the outward current (PubMed:11101505). When associated with KCNE4, inhibits voltage-gated potassium channel activity (PubMed:19687231). When associated with KCNE5, this complex only conducts current upon strong and continued depolarization (PubMed:12324418). Also forms a heterotetramer with KCNQ5; has a voltage-gated potassium channel activity (PubMed:24855057). Binds with phosphatidylinositol 4,5-bisphosphate (PubMed:25037568). {ECO:0000250|UniProtKB:P97414, ECO:0000250|UniProtKB:Q9Z0N7, ECO:0000269|PubMed:10646604, ECO:0000269|PubMed:10713961, ECO:0000269|PubMed:11101505, ECO:0000269|PubMed:12324418, ECO:0000269|PubMed:19687231, ECO:0000269|PubMed:24855057, ECO:0000269|PubMed:25037568, ECO:0000269|PubMed:8900283, ECO:0000269|PubMed:9108097, ECO:0000269|PubMed:9312006}.; FUNCTION: [Isoform 2]: Non-functional alone but modulatory when coexpressed with the full-length isoform 1. {ECO:0000269|PubMed:9305853}.

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 LY6E-KCNQ1


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 LY6E-KCNQ1


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 LY6E-KCNQ1


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 LY6E-KCNQ1


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