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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:TCF3-TCF3 (FusionGDB2 ID:89780)

Fusion Gene Summary for TCF3-TCF3

Fusion gene summary

Fusion gene information	Fusion gene name: TCF3-TCF3
	Fusion gene ID: 89780
		Hgene	Tgene
	Gene symbol	TCF3	TCF3
	Gene ID	83439	83439
	Gene name	transcription factor 7 like 1	transcription factor 7 like 1
	Synonyms	TCF-3\|TCF3	TCF-3\|TCF3
	Cytomap	2p11.2	2p11.2
	Type of gene	protein-coding	protein-coding
	Description	transcription factor 7-like 1HMG box transcription factor 3transcription factor 7-like 1 (T-cell specific, HMG-box)	transcription factor 7-like 1HMG box transcription factor 3transcription factor 7-like 1 (T-cell specific, HMG-box)
	Modification date	20200313	20200313
	UniProtAcc	TFPT	TFPT
	Ensembl transtripts involved in fusion gene	ENST00000262965, ENST00000344749, ENST00000395423, ENST00000453954, ENST00000588136,	ENST00000262965, ENST00000344749, ENST00000395423, ENST00000453954, ENST00000588136,
Fusion gene scores	* DoF score	21 X 26 X 9=4914	12 X 15 X 8=1440
	# samples	27	17
	** MAII score	log2(27/4914*10)=-4.18586654531133 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(17/1440*10)=-3.08246216019197 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: TCF3 [Title/Abstract] AND TCF3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	TCF3(1627299)-TCF3(1622708), # samples:2
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 TCF3 (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 TCF3 (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	AA773093	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
ChiTaRS5.0	N/A	AL079531	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
ChiTaRS5.0	N/A	CN419071	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
ChiTaRS5.0	N/A	DL056923	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-

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Fusion Gene ORF analysis for TCF3-TCF3

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-3UTR	ENST00000262965	ENST00000262965	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000262965	ENST00000262965	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000262965	ENST00000344749	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000262965	ENST00000344749	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000262965	ENST00000395423	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000344749	ENST00000262965	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000344749	ENST00000262965	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000344749	ENST00000344749	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000344749	ENST00000344749	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000344749	ENST00000395423	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000395423	ENST00000262965	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000395423	ENST00000262965	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000395423	ENST00000344749	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000395423	ENST00000344749	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000395423	ENST00000395423	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000453954	ENST00000262965	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000453954	ENST00000262965	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000453954	ENST00000344749	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000453954	ENST00000344749	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000453954	ENST00000395423	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000588136	ENST00000262965	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000588136	ENST00000262965	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000588136	ENST00000344749	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-3UTR	ENST00000588136	ENST00000344749	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-3UTR	ENST00000588136	ENST00000395423	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000262965	ENST00000262965	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000262965	ENST00000344749	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000262965	ENST00000395423	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000262965	ENST00000395423	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000262965	ENST00000453954	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000262965	ENST00000453954	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000262965	ENST00000453954	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000262965	ENST00000588136	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000262965	ENST00000588136	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000262965	ENST00000588136	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000344749	ENST00000262965	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000344749	ENST00000344749	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000344749	ENST00000395423	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000344749	ENST00000395423	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000344749	ENST00000453954	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000344749	ENST00000453954	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000344749	ENST00000453954	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000344749	ENST00000588136	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000344749	ENST00000588136	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000344749	ENST00000588136	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000395423	ENST00000262965	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000395423	ENST00000344749	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000395423	ENST00000395423	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000395423	ENST00000395423	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000395423	ENST00000453954	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000395423	ENST00000453954	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000395423	ENST00000453954	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000395423	ENST00000588136	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000395423	ENST00000588136	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000395423	ENST00000588136	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000453954	ENST00000262965	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000453954	ENST00000344749	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000453954	ENST00000395423	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000453954	ENST00000395423	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000453954	ENST00000453954	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000453954	ENST00000453954	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000453954	ENST00000453954	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000453954	ENST00000588136	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000453954	ENST00000588136	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000453954	ENST00000588136	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000588136	ENST00000262965	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000588136	ENST00000344749	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000588136	ENST00000395423	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000588136	ENST00000395423	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000588136	ENST00000453954	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000588136	ENST00000453954	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000588136	ENST00000453954	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-
intron-intron	ENST00000588136	ENST00000588136	TCF3	chr19	1627299	+	TCF3	chr19	1622708	-
intron-intron	ENST00000588136	ENST00000588136	TCF3	chr19	1611629	+	TCF3	chr19	1611585	-
intron-intron	ENST00000588136	ENST00000588136	TCF3	chr19	1610080	-	TCF3	chr19	1610764	-

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 TCF3-TCF3

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 TCF3-TCF3

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:1627299/:1622708)
- 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
TCF3 TFPT	TCF3 TFPT
253	253

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 TCF3-TCF3

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 TCF3-TCF3

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 TCF3-TCF3

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 TCF3-TCF3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source