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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:BLCAP-CPNE1 (FusionGDB2 ID:9782)

Fusion Gene Summary for BLCAP-CPNE1

check button Fusion gene summary
Fusion gene informationFusion gene name: BLCAP-CPNE1
Fusion gene ID: 9782
HgeneTgene
Gene symbol

BLCAP

CPNE1

Gene ID

10904

8904

Gene nameBLCAP apoptosis inducing factorcopine 1
SynonymsBC10COPN1|CPN1
Cytomap

20q11.23

20q11.22

Type of geneprotein-codingprotein-coding
Descriptionbladder cancer-associated proteinbladder cancer associated proteinbladder cancer related protein (10kD)copine-1chromobindin 17copine I
Modification date2020031320200320
UniProtAcc

P62952

Q99829

Ensembl transtripts involved in fusion geneENST00000373537, ENST00000397131, 
ENST00000397134, ENST00000397135, 
ENST00000397137, ENST00000411780, 
ENST00000414542, 		ENST00000317619, 
ENST00000317677, ENST00000352393, 
ENST00000397442, ENST00000397443, 
ENST00000397445, ENST00000397446, 
ENST00000475146, 
Fusion gene scores* DoF score12 X 8 X 5=48017 X 7 X 8=952
# samples 1217
** MAII scorelog2(12/480*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/952*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BLCAP [Title/Abstract] AND CPNE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBLCAP(36147634)-CPNE1(34220845), # 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
HgeneBLCAP

GO:0030262

apoptotic nuclear changes

17031575

TgeneCPNE1

GO:0043392

negative regulation of DNA binding

18212740

TgeneCPNE1

GO:0045666

positive regulation of neuron differentiation

23263657

TgeneCPNE1

GO:0051897

positive regulation of protein kinase B signaling

23263657

TgeneCPNE1

GO:1990138

neuron projection extension

23263657


check buttonFusion gene breakpoints across BLCAP (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 CPNE1 (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
ChimerDB4STADTCGA-HU-A4GH-01ABLCAPchr20

36147634

-CPNE1chr20

34220845

-


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Fusion Gene ORF analysis for BLCAP-CPNE1

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-3CDSENST00000373537ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000373537ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000373537ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000373537ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000373537ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000373537ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000373537ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397131ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397134ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397135ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000397137ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000411780ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000317619BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000317677BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000352393BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000397442BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000397443BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000397445BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-3CDSENST00000414542ENST00000397446BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000373537ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000397131ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000397134ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000397135ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000397137ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000411780ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-
intron-intronENST00000414542ENST00000475146BLCAPchr20

36147634

-CPNE1chr20

34220845

-

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 BLCAP-CPNE1


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 BLCAP-CPNE1


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/:36147634/:34220845)
- 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
BLCAP

P62952

CPNE1

Q99829

FUNCTION: May regulate cell proliferation and coordinate apoptosis and cell cycle progression via a novel mechanism independent of both p53/TP53 and NF-kappa-B. {ECO:0000269|PubMed:17031575}.FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes (PubMed:14674885). Involved in the TNF-alpha receptor signaling pathway in a calcium-dependent manner (PubMed:14674885). Exhibits calcium-dependent phospholipid binding properties (PubMed:9430674, PubMed:19539605). Plays a role in neuronal progenitor cell differentiation; induces neurite outgrowth via a AKT-dependent signaling cascade and calcium-independent manner (PubMed:23263657, PubMed:25450385). May recruit target proteins to the cell membrane in a calcium-dependent manner (PubMed:12522145). May function in membrane trafficking (PubMed:9430674). Involved in TNF-alpha-induced NF-kappa-B transcriptional repression by inducing endoprotease processing of the transcription factor NF-kappa-B p65/RELA subunit (PubMed:18212740). Also induces endoprotease processing of NF-kappa-B p50/NFKB1, p52/NFKB2, RELB and REL (PubMed:18212740). {ECO:0000269|PubMed:12522145, ECO:0000269|PubMed:14674885, ECO:0000269|PubMed:18212740, ECO:0000269|PubMed:19539605, ECO:0000269|PubMed:23263657, ECO:0000269|PubMed:25450385, ECO:0000269|PubMed:9430674}.

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 BLCAP-CPNE1


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 BLCAP-CPNE1


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 BLCAP-CPNE1


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 BLCAP-CPNE1


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