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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:BRF1-GRAP2 (FusionGDB2 ID:10248)

Fusion Gene Summary for BRF1-GRAP2

Fusion gene summary

Fusion gene information	Fusion gene name: BRF1-GRAP2
	Fusion gene ID: 10248
		Hgene	Tgene
	Gene symbol	BRF1	GRAP2
	Gene ID	2972	9402
	Gene name	BRF1 RNA polymerase III transcription initiation factor subunit	GRB2 related adaptor protein 2
	Synonyms	BRF\|BRF-1\|CFDS\|GTF3B\|HEL-S-76p\|TAF3B2\|TAF3C\|TAFIII90\|TF3B90\|TFIIIB90\|hBRF	GADS\|GRAP-2\|GRB2L\|GRBLG\|GRID\|GRPL\|GrbX\|Grf40\|Mona\|P38
	Cytomap	14q32.33	22q13.1
	Type of gene	protein-coding	protein-coding
	Description	transcription 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)-associate	GRB2-related adapter protein 2GRB-2-like proteinGRB2-related protein with insert domainSH3-SH2-SH3 adapter MonaSH3-SH2-SH3 adaptor moleculeadapter protein GRIDgrf-40grf40 adapter proteingrowth factor receptor-binding proteingrowth factor receptor
	Modification date	20200313	20200327
	UniProtAcc	Q92994	O75791
	Ensembl transtripts involved in fusion gene	ENST00000327359, ENST00000379932, ENST00000379937, ENST00000392557, ENST00000440513, ENST00000446501, ENST00000546474, ENST00000547530, ENST00000548421, ENST00000549044, ENST00000551787,	ENST00000344138, ENST00000399090, ENST00000407075, ENST00000478445, ENST00000540310, ENST00000543252, ENST00000544756,
Fusion gene scores	* DoF score	7 X 8 X 3=168	12 X 12 X 7=1008
	# samples	8	14
	** MAII score	log2(8/168*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1008*10)=-2.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: BRF1 [Title/Abstract] AND GRAP2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	BRF1(105711627)-GRAP2(40328604), # 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Fusion 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.

Fusion gene breakpoints across GRAP2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS5.0	N/A	EC575591	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+

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Fusion Gene ORF analysis for BRF1-GRAP2

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.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-intron	ENST00000327359	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000327359	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000327359	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000327359	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000327359	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000327359	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000327359	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379932	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000379937	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000392557	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000440513	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000446501	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000546474	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000547530	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000548421	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000549044	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000344138	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000399090	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000407075	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000478445	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000540310	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000543252	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+
intron-intron	ENST00000551787	ENST00000544756	BRF1	chr14	105711627	+	GRAP2	chr22	40328604	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

DeepORF 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.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for BRF1-GRAP2

FusionAI 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.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution 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.

Distribution 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-GRAP2

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:105711627/:40328604)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
BRF1 Q92994	GRAP2 O75791
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: Interacts with SLP-76 to regulate NF-AT activation. Binds to tyrosine-phosphorylated shc.

Retention 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.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for BRF1-GRAP2

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-GRAP2

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for BRF1-GRAP2

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for BRF1-GRAP2

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source