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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:ATP2C1-CPNE4 (FusionGDB2 ID:7885)

Fusion Gene Summary for ATP2C1-CPNE4

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP2C1-CPNE4
Fusion gene ID: 7885
HgeneTgene
Gene symbol

ATP2C1

CPNE4

Gene ID

27032

131034

Gene nameATPase secretory pathway Ca2+ transporting 1copine 4
SynonymsATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1COPN4|CPN4
Cytomap

3q22.1

3q22.1

Type of geneprotein-codingprotein-coding
Descriptioncalcium-transporting ATPase type 2C member 1ATP-dependent Ca(2+) pump PMR1ATPase 2C1ATPase, Ca(2+)-sequesteringATPase, Ca++ transporting, type 2C, member 1HUSSY-28secretory pathway Ca2+/Mn2+ ATPase 1copine-4copine 8copine IV
Modification date2020031320200320
UniProtAcc

P98194

Q96A23

Ensembl transtripts involved in fusion geneENST00000328560, ENST00000359644, 
ENST00000393221, ENST00000422190, 
ENST00000428331, ENST00000504381, 
ENST00000504948, ENST00000505330, 
ENST00000507488, ENST00000508532, 
ENST00000510168, ENST00000513801, 
ENST00000533801, ENST00000509150, 
ENST00000512055, ENST00000429747, 
ENST00000502818, ENST00000503204, 
ENST00000511604, ENST00000512332, 
Fusion gene scores* DoF score16 X 17 X 10=272016 X 15 X 6=1440
# samples 1921
** MAII scorelog2(19/2720*10)=-3.83953532780675
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/1440*10)=-2.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATP2C1 [Title/Abstract] AND CPNE4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP2C1(130675023)-CPNE4(131759165), # samples:3
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
HgeneATP2C1

GO:0006816

calcium ion transport

12810057

HgeneATP2C1

GO:0006874

cellular calcium ion homeostasis

12810057


check buttonFusion gene breakpoints across ATP2C1 (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 CPNE4 (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
ChimerDB4PRADTCGA-V1-A9O9-01AATP2C1chr3

130675023

-CPNE4chr3

131759165

-
ChimerDB4PRADTCGA-V1-A9O9-01AATP2C1chr3

130675023

+CPNE4chr3

131759165

-
ChimerDB4PRADTCGA-V1-A9O9ATP2C1chr3

130675023

+CPNE4chr3

131759165

-


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Fusion Gene ORF analysis for ATP2C1-CPNE4

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-5UTRENST00000328560ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000359644ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000393221ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000422190ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000428331ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000504381ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000504948ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000505330ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000507488ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000508532ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000510168ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000513801ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-5UTRENST00000533801ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000328560ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000328560ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000328560ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000328560ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000328560ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000359644ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000359644ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000359644ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000359644ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000359644ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000393221ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000393221ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000393221ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000393221ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000393221ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000422190ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000422190ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000422190ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000422190ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000422190ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000428331ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000428331ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000428331ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000428331ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000428331ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504381ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504381ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504381ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504381ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504381ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504948ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504948ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504948ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504948ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000504948ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000505330ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000505330ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000505330ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000505330ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000505330ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000507488ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000507488ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000507488ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000507488ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000507488ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000508532ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000508532ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000508532ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000508532ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000508532ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000510168ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000510168ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000510168ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000510168ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000510168ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000513801ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000513801ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000513801ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000513801ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000513801ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000533801ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000533801ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000533801ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000533801ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
5CDS-intronENST00000533801ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
intron-5UTRENST00000509150ENST00000512055ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
intron-intronENST00000509150ENST00000429747ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
intron-intronENST00000509150ENST00000502818ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
intron-intronENST00000509150ENST00000503204ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
intron-intronENST00000509150ENST00000511604ATP2C1chr3

130675023

+CPNE4chr3

131759165

-
intron-intronENST00000509150ENST00000512332ATP2C1chr3

130675023

+CPNE4chr3

131759165

-

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 ATP2C1-CPNE4


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 ATP2C1-CPNE4


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/:130675023/:131759165)
- 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
ATP2C1

P98194

CPNE4

Q96A23

FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of the calcium.FUNCTION: Probable calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.

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 ATP2C1-CPNE4


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 ATP2C1-CPNE4


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 ATP2C1-CPNE4


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 ATP2C1-CPNE4


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