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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:CIZ1-SWI5 (FusionGDB2 ID:16881)

Fusion Gene Summary for CIZ1-SWI5

check button Fusion gene summary
Fusion gene informationFusion gene name: CIZ1-SWI5
Fusion gene ID: 16881
HgeneTgene
Gene symbol

CIZ1

SWI5

Gene ID

25792

375757

Gene nameCDKN1A interacting zinc finger protein 1SWI5 homologous recombination repair protein
SynonymsLSFR1|NP94|ZNF356C9orf119|SAE3
Cytomap

9q34.11

9q34.11

Type of geneprotein-codingprotein-coding
Descriptioncip1-interacting zinc finger proteinnuclear protein NP94zinc finger protein 356DNA repair protein SWI5 homologHBV DNAPTP1-transactivated protein ASWI5 recombination repair homologprotein SAE3 homolog
Modification date2020031320200329
UniProtAcc

Q9ULV3

SFR1

Ensembl transtripts involved in fusion geneENST00000476727, ENST00000325721, 
ENST00000357558, ENST00000372938, 
ENST00000372954, ENST00000538431, 
ENST00000541172, ENST00000277465, 
ENST00000372948, ENST00000393608, 
ENST00000320188, ENST00000418976, 
ENST00000419867, ENST00000495313, 
ENST00000608796, 
Fusion gene scores* DoF score8 X 7 X 2=1124 X 3 X 2=24
# samples 74
** MAII scorelog2(7/112*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CIZ1 [Title/Abstract] AND SWI5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCIZ1(130947826)-SWI5(131046789), # samples:2
Anticipated loss of major functional domain due to fusion event.CIZ1-SWI5 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CIZ1-SWI5 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CIZ1-SWI5 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneSWI5

GO:0071479

cellular response to ionizing radiation

23754376


check buttonFusion gene breakpoints across CIZ1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across SWI5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4SARCTCGA-DX-A23Z-01ACIZ1chr9

130947826

-SWI5chr9

131046789

+
ChimerDB4SARCTCGA-QQ-A8VD-01ACIZ1chr9

130947826

-SWI5chr9

131046789

+


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Fusion Gene ORF analysis for CIZ1-SWI5

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-3CDSENST00000476727ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
5UTR-3CDSENST00000476727ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
5UTR-3CDSENST00000476727ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
5UTR-3CDSENST00000476727ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
5UTR-3CDSENST00000476727ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000325721ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000325721ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000325721ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000325721ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000325721ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000357558ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000357558ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000357558ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000357558ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000357558ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372938ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372938ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372938ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372938ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372938ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372954ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372954ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372954ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372954ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000372954ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000538431ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000538431ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000538431ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000538431ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000538431ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000541172ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000541172ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000541172ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000541172ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
Frame-shiftENST00000541172ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000277465ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000277465ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000277465ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000277465ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000277465ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000372948ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000372948ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000372948ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000372948ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000372948ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000393608ENST00000320188CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000393608ENST00000418976CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000393608ENST00000419867CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000393608ENST00000495313CIZ1chr9

130947826

-SWI5chr9

131046789

+
In-frameENST00000393608ENST00000608796CIZ1chr9

130947826

-SWI5chr9

131046789

+

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 CIZ1-SWI5


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)
CIZ1chr9130947825-SWI5chr9131046788+1.03E-101
CIZ1chr9130947825-SWI5chr9131046788+1.03E-101
CIZ1chr9130947825-SWI5chr9131046788+1.03E-101
CIZ1chr9130947825-SWI5chr9131046788+1.03E-101

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.
genomic feature

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 CIZ1-SWI5


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/chr9:130947826/chr9:131046789)
- 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
CIZ1

Q9ULV3

SWI5

SFR1

FUNCTION: May regulate the subcellular localization of CIP/WAF1.245

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
HgeneCIZ1chr9:130947826chr9:131046789ENST00000325721-4164_44172870.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372938-5174_44196899.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372948-5184_44196843.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372954-4174_44172819.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000393608-5174_44196899.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000541172-4164_4495798.0Compositional biasNote=Gln-rich
TgeneSWI5chr9:130947826chr9:131046789ENST0000032018815156_183142236.0Coiled coilOntology_term=ECO:0000255

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCIZ1chr9:130947826chr9:131046789ENST00000325721-416276_470172870.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000325721-416741_761172870.0Compositional biasNote=Glu-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372938-517276_470196899.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372938-517741_761196899.0Compositional biasNote=Glu-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372948-518276_470196843.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372948-518741_761196843.0Compositional biasNote=Glu-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372954-417276_470172819.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372954-417741_761172819.0Compositional biasNote=Glu-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000393608-517276_470196899.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000393608-517741_761196899.0Compositional biasNote=Glu-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000541172-416276_47095798.0Compositional biasNote=Gln-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000541172-416741_76195798.0Compositional biasNote=Glu-rich
HgeneCIZ1chr9:130947826chr9:131046789ENST00000325721-416799_830172870.0Zinc fingerMatrin-type
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372938-517799_830196899.0Zinc fingerMatrin-type
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372948-518799_830196843.0Zinc fingerMatrin-type
HgeneCIZ1chr9:130947826chr9:131046789ENST00000372954-417799_830172819.0Zinc fingerMatrin-type
HgeneCIZ1chr9:130947826chr9:131046789ENST00000393608-517799_830196899.0Zinc fingerMatrin-type
HgeneCIZ1chr9:130947826chr9:131046789ENST00000541172-416799_83095798.0Zinc fingerMatrin-type


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Fusion Gene Sequence for CIZ1-SWI5


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 CIZ1-SWI5


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 CIZ1-SWI5


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 CIZ1-SWI5


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