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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:MSRA-ESCO2 (FusionGDB2 ID:55081)

Fusion Gene Summary for MSRA-ESCO2

check button Fusion gene summary
Fusion gene informationFusion gene name: MSRA-ESCO2
Fusion gene ID: 55081
HgeneTgene
Gene symbol

MSRA

ESCO2

Gene ID

4482

157570

Gene namemethionine sulfoxide reductase Aestablishment of sister chromatid cohesion N-acetyltransferase 2
SynonymsPMSR2410004I17Rik|EFO2|EFO2p|RBS|hEFO2
Cytomap

8p23.1

8p21.1

Type of geneprotein-codingprotein-coding
Descriptionmitochondrial peptide methionine sulfoxide reductasecytosolic methionine-S-sulfoxide reductasepeptide Met(O) reductasepeptide met (O) reductasepeptide-methionine (S)-S-oxide reductaseN-acetyltransferase ESCO2ECO1 homolog 2establishment factor-like protein 2
Modification date2020031320200328
UniProtAcc.

Q56NI9

Ensembl transtripts involved in fusion geneENST00000317173, ENST00000441698, 
ENST00000518255, ENST00000521209, 
ENST00000528246, ENST00000382490, 
ENST00000517594, 		ENST00000305188, 
ENST00000397418, ENST00000523910, 
Fusion gene scores* DoF score12 X 9 X 6=6483 X 3 X 2=18
# samples 133
** MAII scorelog2(13/648*10)=-2.31748218985617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: MSRA [Title/Abstract] AND ESCO2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMSRA(9912168)-ESCO2(27657058), # samples:1
Anticipated loss of major functional domain due to fusion event.MSRA-ESCO2 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

check buttonFusion gene breakpoints across MSRA (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 ESCO2 (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
ChimerDB4PRADTCGA-CH-5741-01AMSRAchr8

9912168

-ESCO2chr8

27657058

+


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Fusion Gene ORF analysis for MSRA-ESCO2

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
Frame-shiftENST00000317173ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
Frame-shiftENST00000317173ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
5CDS-intronENST00000317173ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+
Frame-shiftENST00000441698ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
Frame-shiftENST00000441698ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
5CDS-intronENST00000441698ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+
Frame-shiftENST00000518255ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
Frame-shiftENST00000518255ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
5CDS-intronENST00000518255ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000521209ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000521209ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-intronENST00000521209ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000528246ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000528246ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-intronENST00000528246ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000382490ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000382490ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-intronENST00000382490ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000517594ENST00000305188MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-3CDSENST00000517594ENST00000397418MSRAchr8

9912168

-ESCO2chr8

27657058

+
intron-intronENST00000517594ENST00000523910MSRAchr8

9912168

-ESCO2chr8

27657058

+

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 MSRA-ESCO2


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 MSRA-ESCO2


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
.ESCO2

Q56NI9

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: Acetyltransferase required for the establishment of sister chromatid cohesion (PubMed:15821733, PubMed:15958495). Couples the processes of cohesion and DNA replication to ensure that only sister chromatids become paired together. In contrast to the structural cohesins, the deposition and establishment factors are required only during the S phase. Acetylates the cohesin component SMC3 (PubMed:21111234). {ECO:0000269|PubMed:15821733, ECO:0000269|PubMed:15958495, ECO:0000269|PubMed:19907496, ECO:0000269|PubMed:21111234}.

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 MSRA-ESCO2


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 MSRA-ESCO2


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 MSRA-ESCO2


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 MSRA-ESCO2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMSRAC0036341Schizophrenia2PSYGENET
HgeneMSRAC0013146Drug abuse1CTD_human
HgeneMSRAC0013170Drug habituation1CTD_human
HgeneMSRAC0013222Drug Use Disorders1CTD_human
HgeneMSRAC0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneMSRAC0038580Substance Dependence1CTD_human
HgeneMSRAC0038586Substance Use Disorders1CTD_human
HgeneMSRAC0236969Substance-Related Disorders1CTD_human
HgeneMSRAC0740858Substance abuse problem1CTD_human
HgeneMSRAC1510472Drug Dependence1CTD_human
HgeneMSRAC4316881Prescription Drug Abuse1CTD_human
TgeneESCO2C0392475Roberts-SC phocomelia syndrome7CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneESCO2C0022665Kidney Neoplasm1CTD_human
TgeneESCO2C0740457Malignant neoplasm of kidney1CTD_human