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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:MTA3-KCNMA1 (FusionGDB2 ID:55495)

Fusion Gene Summary for MTA3-KCNMA1

check button Fusion gene summary
Fusion gene informationFusion gene name: MTA3-KCNMA1
Fusion gene ID: 55495
HgeneTgene
Gene symbol

MTA3

KCNMA1

Gene ID

57504

3778

Gene namemetastasis associated 1 family member 3potassium calcium-activated channel subfamily M alpha 1
Synonyms-BKTM|CADEDS|IEG16|KCa1.1|LIWAS|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1
Cytomap

2p21

10q22.3

Type of geneprotein-codingprotein-coding
Descriptionmetastasis-associated protein MTA3metastasis associated gene family, member 3calcium-activated potassium channel subunit alpha-1uncharacterized proteinBK channel alpha subunitBKCA alpha subunitbig potassium channel alpha subunitcalcium-activated potassium channel, subfamily M subunit alpha-1k(VCA)alphamaxi-K channel HSLOpo
Modification date2020031320200315
UniProtAcc

Q9BTC8

Q12791

Ensembl transtripts involved in fusion geneENST00000405094, ENST00000405592, 
ENST00000406652, ENST00000406911, 
ENST00000407270, ENST00000472767, 
ENST00000286627, ENST00000286628, 
ENST00000354353, ENST00000372440, 
ENST00000372443, ENST00000404771, 
ENST00000404857, ENST00000406533, 
ENST00000480683, ENST00000481070, 
ENST00000484507, 
Fusion gene scores* DoF score10 X 10 X 3=30018 X 17 X 8=2448
# samples 1121
** MAII scorelog2(11/300*10)=-1.44745897697122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/2448*10)=-3.54314232502653
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MTA3 [Title/Abstract] AND KCNMA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMTA3(42952029)-KCNMA1(78762955), # 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
TgeneKCNMA1

GO:0001666

response to hypoxia

15528406

TgeneKCNMA1

GO:0006813

potassium ion transport

7573516|7877450|11245614|12388065|17706472|18458941

TgeneKCNMA1

GO:0006970

response to osmotic stress

10840032|12388065

TgeneKCNMA1

GO:0030007

cellular potassium ion homeostasis

11245614

TgeneKCNMA1

GO:0034465

response to carbon monoxide

15528406

TgeneKCNMA1

GO:0042391

regulation of membrane potential

7877450|7993625

TgeneKCNMA1

GO:0045794

negative regulation of cell volume

12388065

TgeneKCNMA1

GO:0051592

response to calcium ion

12388065|18458941

TgeneKCNMA1

GO:0060073

micturition

11641143

TgeneKCNMA1

GO:0060083

smooth muscle contraction involved in micturition

11641143


check buttonFusion gene breakpoints across MTA3 (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 KCNMA1 (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/AM85843MTA3chr2

42952029

+KCNMA1chr10

78762955

-


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Fusion Gene ORF analysis for MTA3-KCNMA1

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-intronENST00000405094ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-

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 MTA3-KCNMA1


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 MTA3-KCNMA1


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/:42952029/:78762955)
- 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
MTA3

Q9BTC8

KCNMA1

Q12791

FUNCTION: Plays a role in maintenance of the normal epithelial architecture through the repression of SNAI1 transcription in a histone deacetylase-dependent manner, and thus the regulation of E-cadherin levels. Contributes to transcriptional repression by BCL6. {ECO:0000269|PubMed:12705869, ECO:0000269|PubMed:15454082}.FUNCTION: Potassium channel activated by both membrane depolarization or increase in cytosolic Ca(2+) that mediates export of K(+) (PubMed:29330545, PubMed:31152168). It is also activated by the concentration of cytosolic Mg(2+). Its activation dampens the excitatory events that elevate the cytosolic Ca(2+) concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity. In smooth muscles, its activation by high level of Ca(2+), caused by ryanodine receptors in the sarcoplasmic reticulum, regulates the membrane potential. In cochlea cells, its number and kinetic properties partly determine the characteristic frequency of each hair cell and thereby helps to establish a tonotopic map. Kinetics of KCNMA1 channels are determined by alternative splicing, phosphorylation status and its combination with modulating beta subunits. Highly sensitive to both iberiotoxin (IbTx) and charybdotoxin (CTX). {ECO:0000269|PubMed:29330545, ECO:0000269|PubMed:31152168}.

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 MTA3-KCNMA1


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 MTA3-KCNMA1


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 MTA3-KCNMA1


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 MTA3-KCNMA1


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