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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:ATF7-CDC42SE2 (FusionGDB2 ID:7461)

Fusion Gene Summary for ATF7-CDC42SE2

check button Fusion gene summary
Fusion gene informationFusion gene name: ATF7-CDC42SE2
Fusion gene ID: 7461
HgeneTgene
Gene symbol

ATF7

CDC42SE2

Gene ID

11016

56990

Gene nameactivating transcription factor 7CDC42 small effector 2
SynonymsATFASPEC2
Cytomap

12q13.13

5q31.1

Type of geneprotein-codingprotein-coding
Descriptioncyclic AMP-dependent transcription factor ATF-7transcription factor ATF-ACDC42 small effector protein 2non-kinase Cdc42 effector protein SPEC2small effector of CDC42 protein 2
Modification date2020031320200313
UniProtAcc

P17544

Q9NRR3

Ensembl transtripts involved in fusion geneENST00000328463, ENST00000415113, 
ENST00000420353, ENST00000456903, 
ENST00000546661, ENST00000548118, 
ENST00000548446, ENST00000591397, 
ENST00000360515, ENST00000395246, 
ENST00000503291, ENST00000504701, 
ENST00000505065, 
Fusion gene scores* DoF score12 X 11 X 10=13208 X 9 X 3=216
# samples 1810
** MAII scorelog2(18/1320*10)=-2.87446911791614
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/216*10)=-1.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATF7 [Title/Abstract] AND CDC42SE2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATF7(53906606)-CDC42SE2(130608356), # 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
HgeneATF7

GO:0006355

regulation of transcription, DNA-templated

8288576

TgeneCDC42SE2

GO:0009966

regulation of signal transduction

10816584


check buttonFusion gene breakpoints across ATF7 (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 CDC42SE2 (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/AFN076796ATF7chr12

53906606

+CDC42SE2chr5

130608356

+


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Fusion Gene ORF analysis for ATF7-CDC42SE2

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-intronENST00000328463ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000328463ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000328463ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000328463ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000328463ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000415113ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000415113ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000415113ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000415113ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000415113ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000420353ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000420353ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000420353ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000420353ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000420353ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000456903ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000456903ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000456903ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000456903ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000456903ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000546661ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000546661ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000546661ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000546661ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000546661ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548118ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548118ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548118ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548118ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548118ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548446ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548446ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548446ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548446ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000548446ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000591397ENST00000360515ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000591397ENST00000395246ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000591397ENST00000503291ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000591397ENST00000504701ATF7chr12

53906606

+CDC42SE2chr5

130608356

+
intron-intronENST00000591397ENST00000505065ATF7chr12

53906606

+CDC42SE2chr5

130608356

+

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 ATF7-CDC42SE2


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 ATF7-CDC42SE2


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/:53906606/:130608356)
- 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
ATF7

P17544

CDC42SE2

Q9NRR3

FUNCTION: Stress-responsive chromatin regulator that plays a role in various biological processes including innate immunological memory, adipocyte differentiation or telomerase regulation (PubMed:29490055). In absence of stress, contributes to the formation of heterochromatin and heterochromatin-like structure by recruiting histone H3K9 tri- and di-methyltransferases thus silencing the transcription of target genes such as STAT1 in adipocytes, or genes involved in innate immunity in macrophages and adipocytes (By similarity). Stress induces ATF7 phosphorylation that disrupts interactions with histone methyltransferase and enhances the association with coactivators containing histone acetyltransferase and/or histone demethylase, leading to disruption of the heterochromatin-like structure and subsequently transcriptional activation (By similarity). In response to TNF-alpha, which is induced by various stresses, phosphorylated ATF7 and telomerase are released from telomeres leading to telomere shortening (PubMed:29490055). Plays also a role in maintaining epithelial regenerative capacity and protecting against cell death during intestinal epithelial damage and repair (By similarity). {ECO:0000250|UniProtKB:Q8R0S1, ECO:0000269|PubMed:29490055}.; FUNCTION: [Isoform 4]: Acts as a dominant repressor of the E-selectin/NF-ELAM1/delta-A promoter.; FUNCTION: [Isoform 5]: Acts as a negative regulator, inhibiting both ATF2 and ATF7 transcriptional activities. It may exert these effects by sequestrating in the cytoplasm the Thr-53 phosphorylating kinase, preventing activation. {ECO:0000269|PubMed:21858082}.FUNCTION: Probably involved in the organization of the actin cytoskeleton by acting downstream of CDC42, inducing actin filament assembly. Alters CDC42-induced cell shape changes. In activated T-cells, may play a role in CDC42-mediated F-actin accumulation at the immunological synapse. May play a role in early contractile events in phagocytosis in macrophages. {ECO:0000269|PubMed:10816584, ECO:0000269|PubMed:15840583}.

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 ATF7-CDC42SE2


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 ATF7-CDC42SE2


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 ATF7-CDC42SE2


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 ATF7-CDC42SE2


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