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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:FOXN3-KCNQ1 (FusionGDB2 ID:31143)

Fusion Gene Summary for FOXN3-KCNQ1

check button Fusion gene summary
Fusion gene informationFusion gene name: FOXN3-KCNQ1
Fusion gene ID: 31143
HgeneTgene
Gene symbol

FOXN3

KCNQ1

Gene ID

1112

3784

Gene nameforkhead box N3potassium voltage-gated channel subfamily Q member 1
SynonymsC14orf116|CHES1|PRO1635ATFB1|ATFB3|JLNS1|KCNA8|KCNA9|KVLQT1|Kv1.9|Kv7.1|LQT|LQT1|RWS|SQT2|WRS
Cytomap

14q31.3-q32.11

11p15.5-p15.4

Type of geneprotein-codingprotein-coding
Descriptionforkhead box protein N3checkpoint suppressor 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

O00409

P51787

Ensembl transtripts involved in fusion geneENST00000261302, ENST00000345097, 
ENST00000555353, ENST00000557258, 
ENST00000555658, 
ENST00000526095, 
ENST00000155840, ENST00000335475, 
Fusion gene scores* DoF score21 X 18 X 8=302410 X 10 X 5=500
# samples 2212
** MAII scorelog2(22/3024*10)=-3.78088271069641
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: FOXN3 [Title/Abstract] AND KCNQ1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFOXN3(89747294)-KCNQ1(2790074), # samples:2
Anticipated loss of major functional domain due to fusion event.FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
FOXN3-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
FOXN3-KCNQ1 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
HgeneFOXN3

GO:0045892

negative regulation of transcription, DNA-templated

16102918

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 FOXN3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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.
all structure

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
ChimerDB4PRADTCGA-V1-A8MG-01AFOXN3chr14

89747294

-KCNQ1chr11

2790074

+


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Fusion Gene ORF analysis for FOXN3-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
5CDS-intronENST00000261302ENST00000526095FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
5CDS-intronENST00000345097ENST00000526095FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
5CDS-intronENST00000555353ENST00000526095FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
5CDS-intronENST00000557258ENST00000526095FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
5UTR-3CDSENST00000555658ENST00000155840FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
5UTR-3CDSENST00000555658ENST00000335475FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
5UTR-intronENST00000555658ENST00000526095FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
Frame-shiftENST00000261302ENST00000155840FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
Frame-shiftENST00000261302ENST00000335475FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
Frame-shiftENST00000557258ENST00000155840FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
Frame-shiftENST00000557258ENST00000335475FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
In-frameENST00000345097ENST00000155840FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
In-frameENST00000345097ENST00000335475FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
In-frameENST00000555353ENST00000155840FOXN3chr14

89747294

-KCNQ1chr11

2790074

+
In-frameENST00000555353ENST00000335475FOXN3chr14

89747294

-KCNQ1chr11

2790074

+

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)
ENST00000345097FOXN3chr1489747294-ENST00000155840KCNQ1chr112790074+24858621171124335
ENST00000345097FOXN3chr1489747294-ENST00000335475KCNQ1chr112790074+16148621171124335
ENST00000555353FOXN3chr1489747294-ENST00000155840KCNQ1chr112790074+25048811361143335
ENST00000555353FOXN3chr1489747294-ENST00000335475KCNQ1chr112790074+16338811361143335

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
ENST00000345097ENST00000155840FOXN3chr1489747294-KCNQ1chr112790074+0.275261580.7247384
ENST00000345097ENST00000335475FOXN3chr1489747294-KCNQ1chr112790074+0.23137710.76862293
ENST00000555353ENST00000155840FOXN3chr1489747294-KCNQ1chr112790074+0.27225260.72774744
ENST00000555353ENST00000335475FOXN3chr1489747294-KCNQ1chr112790074+0.213026580.7869734

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Fusion Genomic Features for FOXN3-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)
FOXN3chr1489747293-KCNQ1chr112790073+1.42E-060.99999857
FOXN3chr1489747293-KCNQ1chr112790073+1.42E-060.99999857

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for FOXN3-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/chr14:89747294/chr11:2790074)
- 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
FOXN3

O00409

KCNQ1

P51787

FUNCTION: Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints). {ECO:0000269|PubMed:16102918}.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
HgeneFOXN3chr14:89747294chr11:2790074ENST00000261302-36113_204248491.0DNA bindingFork-head
HgeneFOXN3chr14:89747294chr11:2790074ENST00000345097-47113_204248491.0DNA bindingFork-head
HgeneFOXN3chr14:89747294chr11:2790074ENST00000555353-46113_204248469.0DNA bindingFork-head
HgeneFOXN3chr14:89747294chr11:2790074ENST00000557258-46113_204248469.0DNA bindingFork-head
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016585_621504677.0Coiled coilOntology_term=ECO:0000269
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016585_621377550.0Coiled coilOntology_term=ECO:0000269
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016589_620504677.0RegionC-terminal assembly domain
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016589_620377550.0RegionC-terminal assembly domain

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016300_320504677.0IntramembranePore-forming%3B Name%3DSegment H5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016300_320377550.0IntramembranePore-forming%3B Name%3DSegment H5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016312_317504677.0MotifSelectivity filter
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016312_317377550.0MotifSelectivity filter
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016143_147504677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016169_196504677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST0000015584010161_121504677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016218_225504677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016249_261504677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016283_299504677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016321_327504677.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016349_676504677.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016143_147377550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016169_196377550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST0000033547510161_121377550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016218_225377550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016249_261377550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016283_299377550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016321_327377550.0Topological domainExtracellular
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016349_676377550.0Topological domainCytoplasmic
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016122_142504677.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016148_168504677.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016197_217504677.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016226_248504677.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016262_282504677.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016328_348504677.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016122_142377550.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016148_168377550.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016197_217377550.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016226_248377550.0TransmembraneHelical%3B Voltage-sensor%3B Name%3DSegment S4
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016262_282377550.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016328_348377550.0TransmembraneHelical%3B Name%3DSegment S6


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Fusion Gene Sequence for FOXN3-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.
>31143_31143_1_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000345097_KCNQ1_chr11_2790074_ENST00000155840_length(transcript)=2485nt_BP=862nt
CCGGGAGACGGCGCGACCCGGCGGCGGGGCCACCCGCGAGTCCAGCGTCGCCGCAGCCCCCCAATGCGGCCGCGAGAAGCAGCGGGGGGG
CAGGCGATCGAAGGAGCCTTCACGTAAATGGGTCCAGTCATGCCTCCCAGTAAGAAGCCAGAAAGCTCAGGAATTAGTGTCTCCAGTGGA
CTGAGTCAGTGTTACGGGGGCAGCGGTTTCTCCAAGGCCCTTCAGGAAGACGATGACCTCGACTTTTCTCTGCCTGACATCCGATTAGAA
GAGGGGGCCATGGAAGATGAAGAGCTGACCAACCTGAACTGGCTGCACGAGAGCAAGAACTTGCTGAAGAGCTTTGGGGAGTCGGTCCTC
AGGAGTGTCAGCCCCGTCCAGGACCTGGACGATGACACCCCCCCATCCCCTGCCCACTCTGACATGCCCTACGATGCCAGGCAGAACCCC
AACTGCAAACCCCCCTACTCCTTCAGCTGCCTCATATTTATGGCCATCGAGGACTCTCCAACCAAGCGCCTGCCAGTGAAGGATATCTAC
AACTGGATCTTGGAACATTTTCCGTATTTTGCAAATGCACCTACTGGGTGGAAAAACTCAGTGAGACACAATTTATCATTGAATAAGTGT
TTTAAGAAAGTGGACAAAGAGAGGAGTCAGAGTATTGGGAAAGGGTCGTTGTGGTGCATAGACCCAGAGTATAGACAAAATCTAATTCAG
GCTTTGAAAAAGACACCTTATCACCCACACCCACACGTGTTCAATACACCTCCCACCTGTCCTCAGGCATATCAAAGCACATCAGGTCCA
CCCATCTGGCCGGGCAGTACCTTCTTCAAGAGAAATGGAGCCCTTCTCCAAGGCTGCGGGAACACCATCGGGCCACCATTAAGGTCATTC
GACGCATGCAGTACTTTGTGGCCAAGAAGAAATTCCAGCAAGCGCGGAAGCCTTACGATGTGCGGGACGTCATTGAGCAGTACTCGCAGG
GCCACCTCAACCTCATGGTGCGCATCAAGGAGCTGCAGAGGAGGCTGGACCAGTCCATTGGGAAGCCCTCACTGTTCATCTCCGTCTCAG
AAAAGAGCAAGGATCGCGGCAGCAACACGATCGGCGCCCGCCTGAACCGAGTAGAAGACAAGGTGACGCAGCTGGACCAGAGGCTGGCAC
TCATCACCGACATGCTTCACCAGCTGCTCTCCTTGCACGGTGGCAGCACCCCCGGCAGCGGCGGCCCCCCCAGAGAGGGCGGGGCCCACA
TCACCCAGCCCTGCGGCAGTGGCGGCTCCGTCGACCCTGAGCTCTTCCTGCCCAGCAACACCCTGCCCACCTACGAGCAGCTGACCGTGC
CCAGGAGGGGCCCCGATGAGGGGTCCTGAGGAGGGGATGGGGCTGGGGGATGGGCCTGAGTGAGAGGGGAGGCCAAGAGTGGCCCCACCT
GGCCCTCTCTGAAGGAGGCCACCTCCTAAAAGGCCCAGAGAGAAGAGCCCCACTCTCAGAGGCCCCAATACCCCATGGACCATGCTGTCT
GGCACAGCCTGCACTTGGGGGCTCAGCAAGGCCACCTCTTCCTGGCCGGTGTGGGGGCCCCGTCTCAGGTCTGAGTTGTTACCCCAAGCG
CCCTGGCCCCCACATGGTGATGTTGACATCACTGGCATGGTGGTTGGGACCCAGTGGCAGGGCACAGGGCCTGGCCCATGTATGGCCAGG
AAGTAGCACAGGCTGAGTGCAGGCCCACCCTGCTTGGCCCAGGGGGCTTCCTGAGGGGAGACAGAGCAACCCCTGGACCCCAGCCTCAAA
TCCAGGACCCTGCCAGGCACAGGCAGGGCAGGACCAGCCCACGCTGACTACAGGGCCGCCGGCAATAAAAGCCCAGGAGCCCATTTGGAG
GGCCTGGGCCTGGCTCCCTCACTCTCAGGAAATGCTGACCCATGGGCAGGAGACTGTGGAGACTGCTCCTGAGCCCCCAGCTTCCAGCAG
GAGGGACAGTCTCACCATTTCCCCAGGGCACGTGGTTGAGTGGGGGGAACGCCCACTTCCCTGGGTTAGACTGCCAGCTCTTCCTAGCTG
GAGAGGAGCCCTGCCTCTCCGCCCCTGAGCCCACTGTGCGTGGGGCTCCCGCCTCCAACCCCTCGCCCAGTCCCAGCAGCCAGCCAAACA
CACAGAAGGGGACTGCCACCTCCCCTTGCCAGCTGCTGAGCCGCAGAGAAGTGACGGTTCCTACACAGGACAGGGGTTCCTTCTGGGCAT
TACATCGCATAGAAATCAATAATTTGTGGTGATTTGGATCTGTGTTTTAATGAGTTTCACAGTGTGATTTTGATTATTAATTGTGCAAGC
TTTTCCTAATAAACGTGGAGAATCACAGGCTGGGCTGGGCACTGCTCTCACCTTGGTTCCTGGGGCATCCATGGGGTCTCTCACAGACAG

>31143_31143_1_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000345097_KCNQ1_chr11_2790074_ENST00000155840_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------
>31143_31143_2_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000345097_KCNQ1_chr11_2790074_ENST00000335475_length(transcript)=1614nt_BP=862nt
CCGGGAGACGGCGCGACCCGGCGGCGGGGCCACCCGCGAGTCCAGCGTCGCCGCAGCCCCCCAATGCGGCCGCGAGAAGCAGCGGGGGGG
CAGGCGATCGAAGGAGCCTTCACGTAAATGGGTCCAGTCATGCCTCCCAGTAAGAAGCCAGAAAGCTCAGGAATTAGTGTCTCCAGTGGA
CTGAGTCAGTGTTACGGGGGCAGCGGTTTCTCCAAGGCCCTTCAGGAAGACGATGACCTCGACTTTTCTCTGCCTGACATCCGATTAGAA
GAGGGGGCCATGGAAGATGAAGAGCTGACCAACCTGAACTGGCTGCACGAGAGCAAGAACTTGCTGAAGAGCTTTGGGGAGTCGGTCCTC
AGGAGTGTCAGCCCCGTCCAGGACCTGGACGATGACACCCCCCCATCCCCTGCCCACTCTGACATGCCCTACGATGCCAGGCAGAACCCC
AACTGCAAACCCCCCTACTCCTTCAGCTGCCTCATATTTATGGCCATCGAGGACTCTCCAACCAAGCGCCTGCCAGTGAAGGATATCTAC
AACTGGATCTTGGAACATTTTCCGTATTTTGCAAATGCACCTACTGGGTGGAAAAACTCAGTGAGACACAATTTATCATTGAATAAGTGT
TTTAAGAAAGTGGACAAAGAGAGGAGTCAGAGTATTGGGAAAGGGTCGTTGTGGTGCATAGACCCAGAGTATAGACAAAATCTAATTCAG
GCTTTGAAAAAGACACCTTATCACCCACACCCACACGTGTTCAATACACCTCCCACCTGTCCTCAGGCATATCAAAGCACATCAGGTCCA
CCCATCTGGCCGGGCAGTACCTTCTTCAAGAGAAATGGAGCCCTTCTCCAAGGCTGCGGGAACACCATCGGGCCACCATTAAGGTCATTC
GACGCATGCAGTACTTTGTGGCCAAGAAGAAATTCCAGCAAGCGCGGAAGCCTTACGATGTGCGGGACGTCATTGAGCAGTACTCGCAGG
GCCACCTCAACCTCATGGTGCGCATCAAGGAGCTGCAGAGGAGGCTGGACCAGTCCATTGGGAAGCCCTCACTGTTCATCTCCGTCTCAG
AAAAGAGCAAGGATCGCGGCAGCAACACGATCGGCGCCCGCCTGAACCGAGTAGAAGACAAGGTGACGCAGCTGGACCAGAGGCTGGCAC
TCATCACCGACATGCTTCACCAGCTGCTCTCCTTGCACGGTGGCAGCACCCCCGGCAGCGGCGGCCCCCCCAGAGAGGGCGGGGCCCACA
TCACCCAGCCCTGCGGCAGTGGCGGCTCCGTCGACCCTGAGCTCTTCCTGCCCAGCAACACCCTGCCCACCTACGAGCAGCTGACCGTGC
CCAGGAGGGGCCCCGATGAGGGGTCCTGAGGAGGGGATGGGGCTGGGGGATGGGCCTGAGTGAGAGGGGAGGCCAAGAGTGGCCCCACCT
GGCCCTCTCTGAAGGAGGCCACCTCCTAAAAGGCCCAGAGAGAAGAGCCCCACTCTCAGAGGCCCCAATACCCCATGGACCATGCTGTCT

>31143_31143_2_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000345097_KCNQ1_chr11_2790074_ENST00000335475_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------
>31143_31143_3_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000555353_KCNQ1_chr11_2790074_ENST00000155840_length(transcript)=2504nt_BP=881nt
GCGATCTGCTGCAGCTCGGCCGGGAGACGGCGCGACCCGGCGGCGGGGCCACCCGCGAGTCCAGCGTCGCCGCAGCCCCCCAATGCGGCC
GCGAGAAGCAGCGGGGGGGCAGGCGATCGAAGGAGCCTTCACGTAAATGGGTCCAGTCATGCCTCCCAGTAAGAAGCCAGAAAGCTCAGG
AATTAGTGTCTCCAGTGGACTGAGTCAGTGTTACGGGGGCAGCGGTTTCTCCAAGGCCCTTCAGGAAGACGATGACCTCGACTTTTCTCT
GCCTGACATCCGATTAGAAGAGGGGGCCATGGAAGATGAAGAGCTGACCAACCTGAACTGGCTGCACGAGAGCAAGAACTTGCTGAAGAG
CTTTGGGGAGTCGGTCCTCAGGAGTGTCAGCCCCGTCCAGGACCTGGACGATGACACCCCCCCATCCCCTGCCCACTCTGACATGCCCTA
CGATGCCAGGCAGAACCCCAACTGCAAACCCCCCTACTCCTTCAGCTGCCTCATATTTATGGCCATCGAGGACTCTCCAACCAAGCGCCT
GCCAGTGAAGGATATCTACAACTGGATCTTGGAACATTTTCCGTATTTTGCAAATGCACCTACTGGGTGGAAAAACTCAGTGAGACACAA
TTTATCATTGAATAAGTGTTTTAAGAAAGTGGACAAAGAGAGGAGTCAGAGTATTGGGAAAGGGTCGTTGTGGTGCATAGACCCAGAGTA
TAGACAAAATCTAATTCAGGCTTTGAAAAAGACACCTTATCACCCACACCCACACGTGTTCAATACACCTCCCACCTGTCCTCAGGCATA
TCAAAGCACATCAGGTCCACCCATCTGGCCGGGCAGTACCTTCTTCAAGAGAAATGGAGCCCTTCTCCAAGGCTGCGGGAACACCATCGG
GCCACCATTAAGGTCATTCGACGCATGCAGTACTTTGTGGCCAAGAAGAAATTCCAGCAAGCGCGGAAGCCTTACGATGTGCGGGACGTC
ATTGAGCAGTACTCGCAGGGCCACCTCAACCTCATGGTGCGCATCAAGGAGCTGCAGAGGAGGCTGGACCAGTCCATTGGGAAGCCCTCA
CTGTTCATCTCCGTCTCAGAAAAGAGCAAGGATCGCGGCAGCAACACGATCGGCGCCCGCCTGAACCGAGTAGAAGACAAGGTGACGCAG
CTGGACCAGAGGCTGGCACTCATCACCGACATGCTTCACCAGCTGCTCTCCTTGCACGGTGGCAGCACCCCCGGCAGCGGCGGCCCCCCC
AGAGAGGGCGGGGCCCACATCACCCAGCCCTGCGGCAGTGGCGGCTCCGTCGACCCTGAGCTCTTCCTGCCCAGCAACACCCTGCCCACC
TACGAGCAGCTGACCGTGCCCAGGAGGGGCCCCGATGAGGGGTCCTGAGGAGGGGATGGGGCTGGGGGATGGGCCTGAGTGAGAGGGGAG
GCCAAGAGTGGCCCCACCTGGCCCTCTCTGAAGGAGGCCACCTCCTAAAAGGCCCAGAGAGAAGAGCCCCACTCTCAGAGGCCCCAATAC
CCCATGGACCATGCTGTCTGGCACAGCCTGCACTTGGGGGCTCAGCAAGGCCACCTCTTCCTGGCCGGTGTGGGGGCCCCGTCTCAGGTC
TGAGTTGTTACCCCAAGCGCCCTGGCCCCCACATGGTGATGTTGACATCACTGGCATGGTGGTTGGGACCCAGTGGCAGGGCACAGGGCC
TGGCCCATGTATGGCCAGGAAGTAGCACAGGCTGAGTGCAGGCCCACCCTGCTTGGCCCAGGGGGCTTCCTGAGGGGAGACAGAGCAACC
CCTGGACCCCAGCCTCAAATCCAGGACCCTGCCAGGCACAGGCAGGGCAGGACCAGCCCACGCTGACTACAGGGCCGCCGGCAATAAAAG
CCCAGGAGCCCATTTGGAGGGCCTGGGCCTGGCTCCCTCACTCTCAGGAAATGCTGACCCATGGGCAGGAGACTGTGGAGACTGCTCCTG
AGCCCCCAGCTTCCAGCAGGAGGGACAGTCTCACCATTTCCCCAGGGCACGTGGTTGAGTGGGGGGAACGCCCACTTCCCTGGGTTAGAC
TGCCAGCTCTTCCTAGCTGGAGAGGAGCCCTGCCTCTCCGCCCCTGAGCCCACTGTGCGTGGGGCTCCCGCCTCCAACCCCTCGCCCAGT
CCCAGCAGCCAGCCAAACACACAGAAGGGGACTGCCACCTCCCCTTGCCAGCTGCTGAGCCGCAGAGAAGTGACGGTTCCTACACAGGAC
AGGGGTTCCTTCTGGGCATTACATCGCATAGAAATCAATAATTTGTGGTGATTTGGATCTGTGTTTTAATGAGTTTCACAGTGTGATTTT
GATTATTAATTGTGCAAGCTTTTCCTAATAAACGTGGAGAATCACAGGCTGGGCTGGGCACTGCTCTCACCTTGGTTCCTGGGGCATCCA

>31143_31143_3_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000555353_KCNQ1_chr11_2790074_ENST00000155840_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------
>31143_31143_4_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000555353_KCNQ1_chr11_2790074_ENST00000335475_length(transcript)=1633nt_BP=881nt
GCGATCTGCTGCAGCTCGGCCGGGAGACGGCGCGACCCGGCGGCGGGGCCACCCGCGAGTCCAGCGTCGCCGCAGCCCCCCAATGCGGCC
GCGAGAAGCAGCGGGGGGGCAGGCGATCGAAGGAGCCTTCACGTAAATGGGTCCAGTCATGCCTCCCAGTAAGAAGCCAGAAAGCTCAGG
AATTAGTGTCTCCAGTGGACTGAGTCAGTGTTACGGGGGCAGCGGTTTCTCCAAGGCCCTTCAGGAAGACGATGACCTCGACTTTTCTCT
GCCTGACATCCGATTAGAAGAGGGGGCCATGGAAGATGAAGAGCTGACCAACCTGAACTGGCTGCACGAGAGCAAGAACTTGCTGAAGAG
CTTTGGGGAGTCGGTCCTCAGGAGTGTCAGCCCCGTCCAGGACCTGGACGATGACACCCCCCCATCCCCTGCCCACTCTGACATGCCCTA
CGATGCCAGGCAGAACCCCAACTGCAAACCCCCCTACTCCTTCAGCTGCCTCATATTTATGGCCATCGAGGACTCTCCAACCAAGCGCCT
GCCAGTGAAGGATATCTACAACTGGATCTTGGAACATTTTCCGTATTTTGCAAATGCACCTACTGGGTGGAAAAACTCAGTGAGACACAA
TTTATCATTGAATAAGTGTTTTAAGAAAGTGGACAAAGAGAGGAGTCAGAGTATTGGGAAAGGGTCGTTGTGGTGCATAGACCCAGAGTA
TAGACAAAATCTAATTCAGGCTTTGAAAAAGACACCTTATCACCCACACCCACACGTGTTCAATACACCTCCCACCTGTCCTCAGGCATA
TCAAAGCACATCAGGTCCACCCATCTGGCCGGGCAGTACCTTCTTCAAGAGAAATGGAGCCCTTCTCCAAGGCTGCGGGAACACCATCGG
GCCACCATTAAGGTCATTCGACGCATGCAGTACTTTGTGGCCAAGAAGAAATTCCAGCAAGCGCGGAAGCCTTACGATGTGCGGGACGTC
ATTGAGCAGTACTCGCAGGGCCACCTCAACCTCATGGTGCGCATCAAGGAGCTGCAGAGGAGGCTGGACCAGTCCATTGGGAAGCCCTCA
CTGTTCATCTCCGTCTCAGAAAAGAGCAAGGATCGCGGCAGCAACACGATCGGCGCCCGCCTGAACCGAGTAGAAGACAAGGTGACGCAG
CTGGACCAGAGGCTGGCACTCATCACCGACATGCTTCACCAGCTGCTCTCCTTGCACGGTGGCAGCACCCCCGGCAGCGGCGGCCCCCCC
AGAGAGGGCGGGGCCCACATCACCCAGCCCTGCGGCAGTGGCGGCTCCGTCGACCCTGAGCTCTTCCTGCCCAGCAACACCCTGCCCACC
TACGAGCAGCTGACCGTGCCCAGGAGGGGCCCCGATGAGGGGTCCTGAGGAGGGGATGGGGCTGGGGGATGGGCCTGAGTGAGAGGGGAG
GCCAAGAGTGGCCCCACCTGGCCCTCTCTGAAGGAGGCCACCTCCTAAAAGGCCCAGAGAGAAGAGCCCCACTCTCAGAGGCCCCAATAC
CCCATGGACCATGCTGTCTGGCACAGCCTGCACTTGGGGGCTCAGCAAGGCCACCTCTTCCTGGCCGGTGTGGGGGCCCCGTCTCAGGTC

>31143_31143_4_FOXN3-KCNQ1_FOXN3_chr14_89747294_ENST00000555353_KCNQ1_chr11_2790074_ENST00000335475_length(amino acids)=335AA_BP=248
MGPVMPPSKKPESSGISVSSGLSQCYGGSGFSKALQEDDDLDFSLPDIRLEEGAMEDEELTNLNWLHESKNLLKSFGESVLRSVSPVQDL
DDDTPPSPAHSDMPYDARQNPNCKPPYSFSCLIFMAIEDSPTKRLPVKDIYNWILEHFPYFANAPTGWKNSVRHNLSLNKCFKKVDKERS
QSIGKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKRNGALLQGCGNTIGPPLRSFDACSTLWPR

--------------------------------------------------------------

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Fusion Gene PPI Analysis for FOXN3-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
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016588_616504.6666666666667677.0AKAP9
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016588_616377.6666666666667550.0AKAP9
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016515_529504.6666666666667677.0CALM%3B calcium-dependent
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016515_529377.6666666666667550.0CALM%3B calcium-dependent
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016535_572504.6666666666667677.0KCNE1 C-terminus
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016535_572377.6666666666667550.0KCNE1 C-terminus


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgeneKCNQ1chr14:89747294chr11:2790074ENST000001558401016370_382504.6666666666667677.0CALM
TgeneKCNQ1chr14:89747294chr11:2790074ENST000003354751016370_382377.6666666666667550.0CALM


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 FOXN3-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 FOXN3-KCNQ1


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