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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:EWSR1-CHN1 (FusionGDB2 ID:27819)

Fusion Gene Summary for EWSR1-CHN1

check button Fusion gene summary
Fusion gene informationFusion gene name: EWSR1-CHN1
Fusion gene ID: 27819
HgeneTgene
Gene symbol

EWSR1

CHN1

Gene ID

2130

1959

Gene nameEWS RNA binding protein 1early growth response 2
SynonymsEWS|EWS-FLI1|bK984G1.4AT591|CHN1|CMT1D|CMT4E|KROX20
Cytomap

22q12.2

10q21.3

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein EWSEWS RNA-binding protein variant 6Ewing sarcoma breakpoint region 1Ewings sarcoma EWS-Fli1 (type 1) oncogeneE3 SUMO-protein ligase EGR2E3 SUMO-protein transferase ERG2KROX-20, Drosophila, homolog (early growth response-2)early growth response protein 2zinc finger protein Krox-20
Modification date2020032920200328
UniProtAcc

Q01844

P15882

Ensembl transtripts involved in fusion geneENST00000331029, ENST00000332035, 
ENST00000332050, ENST00000333395, 
ENST00000397938, ENST00000406548, 
ENST00000414183, 		ENST00000295497, 
ENST00000409156, ENST00000409597, 
ENST00000409900, ENST00000488080, 
Fusion gene scores* DoF score44 X 91 X 16=640649 X 8 X 6=432
# samples 988
** MAII scorelog2(98/64064*10)=-6.03058831983342
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/432*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EWSR1 [Title/Abstract] AND CHN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint
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
TgeneCHN1

GO:0045944

positive regulation of transcription by RNA polymerase II

12687019


check buttonFusion gene breakpoints across EWSR1 (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 CHN1 (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
ChimerKB4..EWSR1chr22

29678378

+CHN1chr2

29678378

-


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Fusion Gene ORF analysis for EWSR1-CHN1

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-intronENST00000331029ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000331029ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000331029ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000331029ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000331029ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332035ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332035ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332035ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332035ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332035ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332050ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332050ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332050ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332050ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000332050ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000333395ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000333395ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000333395ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000333395ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000333395ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000397938ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000397938ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000397938ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000397938ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000397938ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000406548ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000406548ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000406548ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000406548ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000406548ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000414183ENST00000295497EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000414183ENST00000409156EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000414183ENST00000409597EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000414183ENST00000409900EWSR1chr22

29678378

+CHN1chr2

29678378

-
intron-intronENST00000414183ENST00000488080EWSR1chr22

29678378

+CHN1chr2

29678378

-

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 EWSR1-CHN1


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 EWSR1-CHN1


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/:/:)
- 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
EWSR1

Q01844

CHN1

P15882

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: GTPase-activating protein for p21-rac and a phorbol ester receptor. Involved in the assembly of neuronal locomotor circuits as a direct effector of EPHA4 in axon guidance.

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 EWSR1-CHN1


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 EWSR1-CHN1


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 EWSR1-CHN1


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 EWSR1-CHN1


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