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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:CUX1-ZNF394 (FusionGDB2 ID:20747)

Fusion Gene Summary for CUX1-ZNF394

check button Fusion gene summary
Fusion gene informationFusion gene name: CUX1-ZNF394
Fusion gene ID: 20747
HgeneTgene
Gene symbol

CUX1

ZNF394

Gene ID

1523

84124

Gene namecut like homeobox 1zinc finger protein 394
SynonymsCASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75ZKSCAN14|ZSCAN46
Cytomap

7q22.1

7q22.1

Type of geneprotein-codingprotein-coding
Descriptionprotein CASPHomeobox protein cut-like 1CCAAT displacement proteinCUX1 gene Alternatively Spliced Productcut homologgolgi integral membrane protein 6homeobox protein cux-1putative protein product of Nbla10317zinc finger protein 394zinc finger protein 99zinc finger protein with KRAB and SCAN domains 14
Modification date2020032020200313
UniProtAcc

P39880

.
Ensembl transtripts involved in fusion geneENST00000560541, ENST00000292535, 
ENST00000292538, ENST00000360264, 
ENST00000393824, ENST00000425244, 
ENST00000437600, ENST00000546411, 
ENST00000547394, ENST00000549414, 
ENST00000550008, ENST00000556210, 
ENST00000337673, ENST00000426306, 
ENST00000394177, 
Fusion gene scores* DoF score32 X 26 X 13=108162 X 2 X 2=8
# samples 372
** MAII scorelog2(37/10816*10)=-4.86949797576587
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: CUX1 [Title/Abstract] AND ZNF394 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCUX1(101821937)-ZNF394(99092254), # samples:1
Anticipated loss of major functional domain due to fusion event.CUX1-ZNF394 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CUX1-ZNF394 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CUX1-ZNF394 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
CUX1-ZNF394 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CUX1-ZNF394 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
CUX1-ZNF394 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
* 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 CUX1 (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 ZNF394 (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-BR-8284-01ACUX1chr7

101821937

+ZNF394chr7

99092254

-


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Fusion Gene ORF analysis for CUX1-ZNF394

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
3UTR-3CDSENST00000560541ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
3UTR-3CDSENST00000560541ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
3UTR-5UTRENST00000560541ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000292535ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000292538ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000360264ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000393824ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000425244ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000437600ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000546411ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000547394ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000549414ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000550008ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
5CDS-5UTRENST00000556210ENST00000394177CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000292535ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000292535ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000292538ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000292538ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000360264ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000360264ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000393824ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000393824ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000425244ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000425244ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000437600ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000437600ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000546411ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000546411ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000547394ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000547394ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000549414ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000549414ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000550008ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000550008ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000556210ENST00000337673CUX1chr7

101821937

+ZNF394chr7

99092254

-
Frame-shiftENST00000556210ENST00000426306CUX1chr7

101821937

+ZNF394chr7

99092254

-

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 CUX1-ZNF394


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 CUX1-ZNF394


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/:101821937/:99092254)
- 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
CUX1

P39880

.
FUNCTION: Transcription factor involved in the control of neuronal differentiation in the brain. Regulates dendrite development and branching, and dendritic spine formation in cortical layers II-III. Also involved in the control of synaptogenesis. In addition, it has probably a broad role in mammalian development as a repressor of developmentally regulated gene expression. May act by preventing binding of positively-activing CCAAT factors to promoters. Component of nf-munr repressor; binds to the matrix attachment regions (MARs) (5' and 3') of the immunoglobulin heavy chain enhancer. Represses T-cell receptor (TCR) beta enhancer function by binding to MARbeta, an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Binds to the TH enhancer; may require the basic helix-loop-helix protein TCF4 as a coactivator. {ECO:0000250|UniProtKB:P53564}.; FUNCTION: [CDP/Cux p110]: Plays a role in cell cycle progression, in particular at the G1/S transition. As cells progress into S phase, a fraction of CUX1 molecules is proteolytically processed into N-terminally truncated proteins of 110 kDa. While CUX1 only transiently binds to DNA and carries the CCAAT-displacement activity, CDP/Cux p110 makes a stable interaction with DNA and stimulates expression of genes such as POLA1. {ECO:0000269|PubMed:15099520}.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}.

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 CUX1-ZNF394


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 CUX1-ZNF394


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 CUX1-ZNF394


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 CUX1-ZNF394


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