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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:GMEB2-RALY (FusionGDB2 ID:33487)

Fusion Gene Summary for GMEB2-RALY

check button Fusion gene summary
Fusion gene informationFusion gene name: GMEB2-RALY
Fusion gene ID: 33487
HgeneTgene
Gene symbol

GMEB2

RALY

Gene ID

26205

22913

Gene nameglucocorticoid modulatory element binding protein 2RALY heterogeneous nuclear ribonucleoprotein
SynonymsGMEB-2|P79PIF|PIF79HNRPCL2|P542
Cytomap

20q13.33

20q11.22

Type of geneprotein-codingprotein-coding
Descriptionglucocorticoid modulatory element-binding protein 2DNA-binding protein p79PIFPIF p79parvovirus initiation factor, p79RNA-binding protein RalyRNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog)RNA-binding protein (autoantigenic)RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)autoantigen p542heterogeneous nuclear r
Modification date2020031320200327
UniProtAcc

Q9UKD1

.
Ensembl transtripts involved in fusion geneENST00000266068, ENST00000370069, 
ENST00000370077, 		ENST00000246194, 
ENST00000375114, ENST00000493399, 
Fusion gene scores* DoF score7 X 7 X 5=24524 X 15 X 13=4680
# samples 837
** MAII scorelog2(8/245*10)=-1.61470984411521
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(37/4680*10)=-3.66091135395445
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GMEB2 [Title/Abstract] AND RALY [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGMEB2(62234318)-RALY(32659872), # samples:3
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

check buttonFusion gene breakpoints across GMEB2 (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 RALY (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
ChimerDB4READTCGA-DY-A1DD-01AGMEB2chr20

62234318

-RALYchr20

32659872

+
ChimerDB4READTCGA-DY-A1DDGMEB2chr20

62234318

-RALYchr20

32652850

+
ChimerDB4READTCGA-DY-A1DDGMEB2chr20

62234318

-RALYchr20

32659872

+


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Fusion Gene ORF analysis for GMEB2-RALY

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
5CDS-5UTRENST00000266068ENST00000246194GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000266068ENST00000375114GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000266068ENST00000493399GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000370069ENST00000246194GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000370069ENST00000375114GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000370069ENST00000493399GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000370077ENST00000246194GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000370077ENST00000375114GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-5UTRENST00000370077ENST00000493399GMEB2chr20

62234318

-RALYchr20

32659872

+
5CDS-intronENST00000266068ENST00000246194GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000266068ENST00000375114GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000266068ENST00000493399GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000370069ENST00000246194GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000370069ENST00000375114GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000370069ENST00000493399GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000370077ENST00000246194GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000370077ENST00000375114GMEB2chr20

62234318

-RALYchr20

32652850

+
5CDS-intronENST00000370077ENST00000493399GMEB2chr20

62234318

-RALYchr20

32652850

+

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 GMEB2-RALY


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)
GMEB2chr2062234317-RALYchr2032659871+2.62E-060.9999974
GMEB2chr2062234317-RALYchr2032659871+2.62E-060.9999974
GMEB2chr2062234317-RALYchr2032659871+2.62E-060.9999974
GMEB2chr2062234317-RALYchr2032659871+2.62E-060.9999974

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.
genomic feature of top 1%

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Fusion Protein Features for GMEB2-RALY


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/:62234318/:32659872)
- 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
GMEB2

Q9UKD1

.
FUNCTION: Trans-acting factor that binds to glucocorticoid modulatory elements (GME) present in the TAT (tyrosine aminotransferase) promoter and increases sensitivity to low concentrations of glucocorticoids. Binds also to the transferrin receptor promoter. Essential auxiliary factor for the replication of parvoviruses.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 GMEB2-RALY


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 GMEB2-RALY


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 GMEB2-RALY


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 GMEB2-RALY


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