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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:KCNIP3-KCNIP3 (FusionGDB2 ID:41415)

Fusion Gene Summary for KCNIP3-KCNIP3

check button Fusion gene summary
Fusion gene informationFusion gene name: KCNIP3-KCNIP3
Fusion gene ID: 41415
HgeneTgene
Gene symbol

KCNIP3

KCNIP3

Gene ID

30818

30818

Gene namepotassium voltage-gated channel interacting protein 3potassium voltage-gated channel interacting protein 3
SynonymsCSEN|DREAM|KCHIP3CSEN|DREAM|KCHIP3
Cytomap

2q11.1

2q11.1

Type of geneprotein-codingprotein-coding
DescriptioncalsenilinA-type potassium channel modulatory protein 3DRE-antagonist modulatorKv channel interacting protein 3, calsenilincalsenilin, presenilin-binding protein, EF hand transcription factorkv channel-interacting protein 3potassium channel interactcalsenilinA-type potassium channel modulatory protein 3DRE-antagonist modulatorKv channel interacting protein 3, calsenilincalsenilin, presenilin-binding protein, EF hand transcription factorkv channel-interacting protein 3potassium channel interact
Modification date2020032020200320
UniProtAcc

Q9Y2W7

Q9Y2W7

Ensembl transtripts involved in fusion geneENST00000295225, ENST00000360990, 
ENST00000377181, ENST00000468529, 
ENST00000295225, ENST00000360990, 
ENST00000377181, ENST00000468529, 
Fusion gene scores* DoF score2 X 3 X 1=64 X 5 X 3=60
# samples 36
** MAII scorelog2(3/6*10)=2.32192809488736log2(6/60*10)=0
Context

PubMed: KCNIP3 [Title/Abstract] AND KCNIP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKCNIP3(95996105)-KCNIP3(95995707), # samples:1
KCNIP3(95969228)-KCNIP3(95967435), # 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

check buttonFusion gene breakpoints across KCNIP3 (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 KCNIP3 (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/AAA666181KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
ChiTaRS5.0N/ABC019877KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+


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Fusion Gene ORF analysis for KCNIP3-KCNIP3

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-intronENST00000295225ENST00000295225KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000295225ENST00000295225KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000295225ENST00000360990KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000295225ENST00000360990KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000295225ENST00000377181KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000295225ENST00000377181KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000295225ENST00000468529KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000295225ENST00000468529KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000360990ENST00000295225KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000360990ENST00000295225KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000360990ENST00000360990KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000360990ENST00000360990KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000360990ENST00000377181KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000360990ENST00000377181KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000360990ENST00000468529KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000360990ENST00000468529KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000377181ENST00000295225KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000377181ENST00000295225KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000377181ENST00000360990KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000377181ENST00000360990KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000377181ENST00000377181KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000377181ENST00000377181KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000377181ENST00000468529KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000377181ENST00000468529KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000468529ENST00000295225KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000468529ENST00000295225KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000468529ENST00000360990KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000468529ENST00000360990KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000468529ENST00000377181KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000468529ENST00000377181KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+
intron-intronENST00000468529ENST00000468529KCNIP3chr2

95996105

+KCNIP3chr2

95995707

-
intron-intronENST00000468529ENST00000468529KCNIP3chr2

95969228

+KCNIP3chr2

95967435

+

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 KCNIP3-KCNIP3


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 KCNIP3-KCNIP3


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/:95996105/:95995707)
- 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
KCNIP3

Q9Y2W7

KCNIP3

Q9Y2W7

FUNCTION: Calcium-dependent transcriptional repressor that binds to the DRE element of genes including PDYN and FOS. Affinity for DNA is reduced upon binding to calcium and enhanced by binding to magnesium. Seems to be involved in nociception (By similarity). {ECO:0000250|UniProtKB:Q9QXT8}.; FUNCTION: Regulatory subunit of Kv4/D (Shal)-type voltage-gated rapidly inactivating A-type potassium channels, such as KCND2/Kv4.2 and KCND3/Kv4.3. Modulates channel expression at the cell membrane, gating characteristics, inactivation kinetics and rate of recovery from inactivation in a calcium-dependent and isoform-specific manner. {ECO:0000269|PubMed:10676964, ECO:0000269|PubMed:12829703, ECO:0000269|PubMed:15485870, ECO:0000269|PubMed:16123112, ECO:0000269|PubMed:18957440}.; FUNCTION: May play a role in the regulation of PSEN2 proteolytic processing and apoptosis. Together with PSEN2 involved in modulation of amyloid-beta formation. {ECO:0000269|PubMed:11259376, ECO:0000269|PubMed:11988022, ECO:0000269|PubMed:9771752}.FUNCTION: Calcium-dependent transcriptional repressor that binds to the DRE element of genes including PDYN and FOS. Affinity for DNA is reduced upon binding to calcium and enhanced by binding to magnesium. Seems to be involved in nociception (By similarity). {ECO:0000250|UniProtKB:Q9QXT8}.; FUNCTION: Regulatory subunit of Kv4/D (Shal)-type voltage-gated rapidly inactivating A-type potassium channels, such as KCND2/Kv4.2 and KCND3/Kv4.3. Modulates channel expression at the cell membrane, gating characteristics, inactivation kinetics and rate of recovery from inactivation in a calcium-dependent and isoform-specific manner. {ECO:0000269|PubMed:10676964, ECO:0000269|PubMed:12829703, ECO:0000269|PubMed:15485870, ECO:0000269|PubMed:16123112, ECO:0000269|PubMed:18957440}.; FUNCTION: May play a role in the regulation of PSEN2 proteolytic processing and apoptosis. Together with PSEN2 involved in modulation of amyloid-beta formation. {ECO:0000269|PubMed:11259376, ECO:0000269|PubMed:11988022, ECO:0000269|PubMed:9771752}.

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 KCNIP3-KCNIP3


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 KCNIP3-KCNIP3


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 KCNIP3-KCNIP3


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 KCNIP3-KCNIP3


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