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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:NEK7-ATP2B4 (FusionGDB2 ID:58534)

Fusion Gene Summary for NEK7-ATP2B4

check button Fusion gene summary
Fusion gene informationFusion gene name: NEK7-ATP2B4
Fusion gene ID: 58534
HgeneTgene
Gene symbol

NEK7

ATP2B4

Gene ID

140609

493

Gene nameNIMA related kinase 7ATPase plasma membrane Ca2+ transporting 4
Synonyms-ATP2B2|MXRA1|PMCA4|PMCA4b|PMCA4x
Cytomap

1q31.3

1q32.1

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase Nek7NIMA (never in mitosis gene a)-related kinase 7never in mitosis A-related kinase 7nimA-related protein kinase 7plasma membrane calcium-transporting ATPase 4ATPase, Ca++ transporting, plasma membrane 4matrix-remodeling-associated protein 1sarcolemmal calcium pump
Modification date2020031320200327
UniProtAcc.

P23634

Ensembl transtripts involved in fusion geneENST00000367383, ENST00000367385, 
ENST00000417895, ENST00000538004, 
ENST00000357681, ENST00000367218, 
ENST00000367219, ENST00000391954, 
ENST00000341360, ENST00000466407, 
Fusion gene scores* DoF score12 X 5 X 8=48013 X 15 X 8=1560
# samples 1216
** MAII scorelog2(12/480*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1560*10)=-3.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NEK7 [Title/Abstract] AND ATP2B4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNEK7(198126406)-ATP2B4(203651870), # samples:2
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
HgeneNEK7

GO:0006468

protein phosphorylation

12840024

TgeneATP2B4

GO:0006874

cellular calcium ion homeostasis

19278978|25798335

TgeneATP2B4

GO:0010629

negative regulation of gene expression

25147342

TgeneATP2B4

GO:0010751

negative regulation of nitric oxide mediated signal transduction

19278978

TgeneATP2B4

GO:0016525

negative regulation of angiogenesis

25147342

TgeneATP2B4

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19278978

TgeneATP2B4

GO:0043537

negative regulation of blood vessel endothelial cell migration

25147342

TgeneATP2B4

GO:0045019

negative regulation of nitric oxide biosynthetic process

11591728|19278978

TgeneATP2B4

GO:0051001

negative regulation of nitric-oxide synthase activity

11591728|17242280|19278978|19287093

TgeneATP2B4

GO:0070885

negative regulation of calcineurin-NFAT signaling cascade

19287093|25147342

TgeneATP2B4

GO:0071872

cellular response to epinephrine stimulus

19278978

TgeneATP2B4

GO:0098736

negative regulation of the force of heart contraction

17242280

TgeneATP2B4

GO:0140199

negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process

17242280

TgeneATP2B4

GO:1900082

negative regulation of arginine catabolic process

19278978

TgeneATP2B4

GO:1901660

calcium ion export

25798335

TgeneATP2B4

GO:1902548

negative regulation of cellular response to vascular endothelial growth factor stimulus

25147342

TgeneATP2B4

GO:1903078

positive regulation of protein localization to plasma membrane

15955804

TgeneATP2B4

GO:1903249

negative regulation of citrulline biosynthetic process

19278978

TgeneATP2B4

GO:2000481

positive regulation of cAMP-dependent protein kinase activity

19278978


check buttonFusion gene breakpoints across NEK7 (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 ATP2B4 (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
ChimerDB4LUSCTCGA-39-5034-01ANEK7chr1

198126406

-ATP2B4chr1

203651870

+
ChimerDB4LUSCTCGA-39-5034-01ANEK7chr1

198126406

+ATP2B4chr1

203651870

+


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Fusion Gene ORF analysis for NEK7-ATP2B4

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
5UTR-5UTRENST00000367383ENST00000357681NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367383ENST00000367218NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367383ENST00000367219NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367383ENST00000391954NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367385ENST00000357681NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367385ENST00000367218NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367385ENST00000367219NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-5UTRENST00000367385ENST00000391954NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-intronENST00000367383ENST00000341360NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-intronENST00000367383ENST00000466407NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-intronENST00000367385ENST00000341360NEK7chr1

198126406

+ATP2B4chr1

203651870

+
5UTR-intronENST00000367385ENST00000466407NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000417895ENST00000357681NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000417895ENST00000367218NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000417895ENST00000367219NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000417895ENST00000391954NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000538004ENST00000357681NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000538004ENST00000367218NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000538004ENST00000367219NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-5UTRENST00000538004ENST00000391954NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-intronENST00000417895ENST00000341360NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-intronENST00000417895ENST00000466407NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-intronENST00000538004ENST00000341360NEK7chr1

198126406

+ATP2B4chr1

203651870

+
intron-intronENST00000538004ENST00000466407NEK7chr1

198126406

+ATP2B4chr1

203651870

+

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 NEK7-ATP2B4


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)
NEK7chr1198126406+ATP2B4chr1203651869+0.0002223380.9997776
NEK7chr1198126406+ATP2B4chr1203651869+0.0002223380.9997776

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.
genomic feature of top 1%

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Fusion Protein Features for NEK7-ATP2B4


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/:198126406/:203651870)
- 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
.ATP2B4

P23634

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Calcium/calmodulin-regulated and magnesium-dependent enzyme that catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell (PubMed:8530416). By regulating sperm cell calcium homeostasis, may play a role in sperm motility (By similarity). {ECO:0000250|UniProtKB:Q6Q477, ECO:0000269|PubMed:8530416}.

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 NEK7-ATP2B4


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 NEK7-ATP2B4


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 NEK7-ATP2B4


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 NEK7-ATP2B4


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