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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:BRF1-GYS1 (FusionGDB2 ID:10249)

Fusion Gene Summary for BRF1-GYS1

check button Fusion gene summary
Fusion gene informationFusion gene name: BRF1-GYS1
Fusion gene ID: 10249
HgeneTgene
Gene symbol

BRF1

GYS1

Gene ID

2972

2997

Gene nameBRF1 RNA polymerase III transcription initiation factor subunitglycogen synthase 1
SynonymsBRF|BRF-1|CFDS|GTF3B|HEL-S-76p|TAF3B2|TAF3C|TAFIII90|TF3B90|TFIIIB90|hBRFGSY|GYS
Cytomap

14q32.33

19q13.33

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor IIIB 90 kDa subunitB - related factor 1BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIBBRF1, RNA polymerase III transcription initiation factor 90 kDa subunitTATA box binding protein (TBP)-associateglycogen [starch] synthase, muscleglycogen synthase 1 (muscle)
Modification date2020031320200313
UniProtAcc

Q92994

P13807

Ensembl transtripts involved in fusion geneENST00000327359, ENST00000379932, 
ENST00000379937, ENST00000392557, 
ENST00000440513, ENST00000446501, 
ENST00000546474, ENST00000547530, 
ENST00000548421, ENST00000549044, 
ENST00000551787, 		ENST00000263276, 
ENST00000323798, ENST00000457974, 
ENST00000540532, ENST00000541188, 
ENST00000544287, 
Fusion gene scores* DoF score7 X 8 X 3=16811 X 11 X 4=484
# samples 811
** MAII scorelog2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/484*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BRF1 [Title/Abstract] AND GYS1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBRF1(105716895)-GYS1(49471453), # 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
TgeneGYS1

GO:0005978

glycogen biosynthetic process

16275910


check buttonFusion gene breakpoints across BRF1 (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 GYS1 (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/ABU601594BRF1chr14

105716895

+GYS1chr19

49471453

-


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Fusion Gene ORF analysis for BRF1-GYS1

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-3UTRENST00000327359ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000327359ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000379932ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000379932ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000379937ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000379937ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000392557ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000392557ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000440513ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000440513ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000446501ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000446501ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000546474ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000546474ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000547530ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000547530ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000548421ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000548421ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000549044ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000549044ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000551787ENST00000263276BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-3UTRENST00000551787ENST00000323798BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000327359ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000327359ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000327359ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000327359ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379932ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379932ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379932ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379932ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379937ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379937ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379937ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000379937ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000392557ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000392557ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000392557ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000392557ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000440513ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000440513ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000440513ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000440513ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000446501ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000446501ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000446501ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000446501ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000546474ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000546474ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000546474ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000546474ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000547530ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000547530ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000547530ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000547530ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000548421ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000548421ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000548421ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000548421ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000549044ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000549044ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000549044ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000549044ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000551787ENST00000457974BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000551787ENST00000540532BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000551787ENST00000541188BRF1chr14

105716895

+GYS1chr19

49471453

-
intron-intronENST00000551787ENST00000544287BRF1chr14

105716895

+GYS1chr19

49471453

-

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 BRF1-GYS1


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 BRF1-GYS1


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/:105716895/:49471453)
- 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
BRF1

Q92994

GYS1

P13807

FUNCTION: General activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. The isoform 1 is involved in the transcription of tRNA, adenovirus VA1, 7SL and 5S RNA. Isoform 2 is required for transcription of the U6 promoter.FUNCTION: Transfers the glycosyl residue from UDP-Glc to the non-reducing end of alpha-1,4-glucan.

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 BRF1-GYS1


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 BRF1-GYS1


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 BRF1-GYS1


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 BRF1-GYS1


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