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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:ZRANB3-CPNE1 (FusionGDB2 ID:102510)

Fusion Gene Summary for ZRANB3-CPNE1

check button Fusion gene summary
Fusion gene informationFusion gene name: ZRANB3-CPNE1
Fusion gene ID: 102510
HgeneTgene
Gene symbol

ZRANB3

CPNE1

Gene ID

84083

8904

Gene namezinc finger RANBP2-type containing 3copine 1
Synonyms4933425L19Rik|AH2COPN1|CPN1
Cytomap

2q21.3

20q11.22

Type of geneprotein-codingprotein-coding
DescriptionDNA annealing helicase and endonuclease ZRANB3annealing helicase 2zinc finger Ran-binding domain-containing protein 3zinc finger, RAN-binding domain containing 3copine-1chromobindin 17copine I
Modification date2020031320200320
UniProtAcc.

Q99829

Ensembl transtripts involved in fusion geneENST00000412849, ENST00000401392, 
ENST00000264159, ENST00000536680, 
ENST00000352393, ENST00000317677, 
ENST00000397445, ENST00000317619, 
ENST00000397443, ENST00000397446, 
ENST00000397442, ENST00000475146, 
Fusion gene scores* DoF score6 X 7 X 3=12617 X 7 X 8=952
# samples 817
** MAII scorelog2(8/126*10)=-0.655351828612554
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: ZRANB3 [Title/Abstract] AND CPNE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointZRANB3(135949432)-CPNE1(34223472), # 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
HgeneZRANB3

GO:0006281

DNA repair

22759634

HgeneZRANB3

GO:0006974

cellular response to DNA damage stimulus

22704558|22705370|22759634

HgeneZRANB3

GO:0009411

response to UV

22704558

HgeneZRANB3

GO:0031297

replication fork processing

22704558|22705370

HgeneZRANB3

GO:0036292

DNA rewinding

21078962|22705370

HgeneZRANB3

GO:0045910

negative regulation of DNA recombination

22704558

HgeneZRANB3

GO:0048478

replication fork protection

22704558|22705370

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 ZRANB3 (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
ChiTaRS5.0N/ACV344396ZRANB3chr2

135949432

-CPNE1chr20

34223472

+


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Fusion Gene ORF analysis for ZRANB3-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-intronENST00000412849ENST00000352393ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000317677ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000397445ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000317619ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000397443ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000397446ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000397442ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000412849ENST00000475146ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000352393ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000317677ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000397445ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000317619ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000397443ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000397446ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000397442ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000401392ENST00000475146ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000352393ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000317677ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000397445ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000317619ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000397443ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000397446ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000397442ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000264159ENST00000475146ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000352393ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000317677ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000397445ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000317619ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000397443ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000397446ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000397442ZRANB3chr2

135949432

-CPNE1chr20

34223472

+
intron-intronENST00000536680ENST00000475146ZRANB3chr2

135949432

-CPNE1chr20

34223472

+

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 ZRANB3-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 ZRANB3-CPNE1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CPNE1

Q99829

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.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 ZRANB3-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 ZRANB3-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 ZRANB3-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
TgeneCPNE1Q99829DB00277TheophyllineSmall moleculeApproved
TgeneCPNE1Q99829DB00277TheophyllineSmall moleculeApproved

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Related Diseases for ZRANB3-CPNE1


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