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Fusion Protein:ST3GAL3-TGFBR3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ST3GAL3-TGFBR3
	FusionPDB ID: 86945
	FusionGDB2.0 ID: 86945
		Hgene	Tgene
	Gene symbol	ST3GAL3	TGFBR3
	Gene ID	6487	7049
	Gene name	ST3 beta-galactoside alpha-2,3-sialyltransferase 3	transforming growth factor beta receptor 3
	Synonyms	EIEE15\|MRT12\|SIAT6\|ST3GALII\|ST3Gal III\|ST3GalIII\|ST3N	BGCAN\|betaglycan
	Cytomap	1p34.1	1p22.1
	Type of gene	protein-coding	protein-coding
	Description	CMP-N-acetylneuraminate-beta-1,4-galactoside alpha-2,3-sialyltransferaseGal beta-1,3(4)GlcNAc alpha-2,3 sialyltransferasealpha 2,3-ST 3alpha 2,3-sialyltransferase IIIalpha-2,3-sialyltransferase IIsialyltransferase 6 (N-acetyllacosaminide alpha 2,3-si	transforming growth factor beta receptor type 3TGF-beta receptor type 3TGF-beta receptor type IIITGFR-3betaglycan proteoglycantransforming growth factor beta receptor III
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000461375, ENST00000262915, ENST00000330208, ENST00000332628, ENST00000347631, ENST00000353126, ENST00000361392, ENST00000361746, ENST00000361812, ENST00000372362, ENST00000372365, ENST00000372368, ENST00000372369, ENST00000372374, ENST00000372375, ENST00000372377, ENST00000533933, ENST00000545417, ENST00000335430, ENST00000351035, ENST00000361400, ENST00000372366, ENST00000372367, ENST00000372372, ENST00000528371, ENST00000531451, ENST00000531816, ENST00000531993,	ENST00000212355, ENST00000370399, ENST00000525962, ENST00000468996,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	11 X 9 X 8=792	10 X 9 X 9=810
	# samples	12	10
	** MAII score	log2(12/792*10)=-2.72246602447109 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/810*10)=-3.01792190799726 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ST3GAL3 [Title/Abstract] AND TGFBR3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ST3GAL3 [Title/Abstract] AND TGFBR3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ST3GAL3(44257820)-TGFBR3(92195530), # samples:1
Anticipated loss of major functional domain due to fusion event.	ST3GAL3-TGFBR3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. ST3GAL3-TGFBR3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* 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
Tgene	TGFBR3	GO:0001837	epithelial to mesenchymal transition	18184661
Tgene	TGFBR3	GO:0007179	transforming growth factor beta receptor signaling pathway	12958365
Tgene	TGFBR3	GO:0030509	BMP signaling pathway	18184661
Tgene	TGFBR3	GO:0032354	response to follicle-stimulating hormone	14557487
Tgene	TGFBR3	GO:0034695	response to prostaglandin E	14557487
Tgene	TGFBR3	GO:0034699	response to luteinizing hormone	14557487
Tgene	TGFBR3	GO:0051271	negative regulation of cellular component movement	17999987
Tgene	TGFBR3	GO:0060317	cardiac epithelial to mesenchymal transition	18184661

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:44257820/chr1:92195530)
- 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.

Retention analysis results 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, are available here.

Fusion gene breakpoints across ST3GAL3 (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 TGFBR3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

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)
ENST00000262915	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5770	388	177	2375	732
ENST00000262915	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3686	388	177	2372	731
ENST00000262915	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3685	388	177	2375	732
ENST00000372375	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5725	343	177	2330	717
ENST00000372375	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3641	343	177	2327	716
ENST00000372375	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3640	343	177	2330	717
ENST00000372374	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5725	343	177	2330	717
ENST00000372374	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3641	343	177	2327	716
ENST00000372374	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3640	343	177	2330	717
ENST00000353126	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5725	343	177	2330	717
ENST00000353126	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3641	343	177	2327	716
ENST00000353126	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3640	343	177	2330	717
ENST00000545417	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5770	388	177	2375	732
ENST00000545417	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3686	388	177	2372	731
ENST00000545417	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3685	388	177	2375	732
ENST00000330208	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5725	343	177	2330	717
ENST00000330208	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3641	343	177	2327	716
ENST00000330208	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3640	343	177	2330	717
ENST00000372377	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5725	343	177	2330	717
ENST00000372377	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3641	343	177	2327	716
ENST00000372377	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3640	343	177	2330	717
ENST00000361392	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5725	343	177	2330	717
ENST00000361392	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3641	343	177	2327	716
ENST00000361392	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3640	343	177	2330	717
ENST00000347631	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5744	362	151	2349	732
ENST00000347631	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3660	362	151	2346	731
ENST00000347631	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3659	362	151	2349	732
ENST00000361812	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5593	211	0	2198	732
ENST00000361812	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3509	211	0	2195	731
ENST00000361812	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3508	211	0	2198	732
ENST00000372362	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5548	166	0	2153	717
ENST00000372362	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3464	166	0	2150	716
ENST00000372362	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3463	166	0	2153	717
ENST00000372365	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5548	166	0	2153	717
ENST00000372365	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3464	166	0	2150	716
ENST00000372365	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3463	166	0	2153	717
ENST00000372368	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5548	166	0	2153	717
ENST00000372368	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3464	166	0	2150	716
ENST00000372368	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3463	166	0	2153	717
ENST00000332628	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5548	166	0	2153	717
ENST00000332628	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3464	166	0	2150	716
ENST00000332628	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3463	166	0	2153	717
ENST00000372369	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5548	166	0	2153	717
ENST00000372369	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3464	166	0	2150	716
ENST00000372369	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3463	166	0	2153	717
ENST00000361746	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5593	211	0	2198	732
ENST00000361746	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3509	211	0	2195	731
ENST00000361746	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3508	211	0	2198	732
ENST00000533933	ST3GAL3	chr1	44257820	-	ENST00000212355	TGFBR3	chr1	92195530	-	5548	166	0	2153	717
ENST00000533933	ST3GAL3	chr1	44257820	-	ENST00000370399	TGFBR3	chr1	92195530	-	3464	166	0	2150	716
ENST00000533933	ST3GAL3	chr1	44257820	-	ENST00000525962	TGFBR3	chr1	92195530	-	3463	166	0	2153	717

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
ENST00000262915	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00013701	0.999863
ENST00000262915	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000423113	0.99957687
ENST00000262915	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000509491	0.9994905
ENST00000372375	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	8.46E-05	0.99991536
ENST00000372375	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000358937	0.99964106
ENST00000372375	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000357522	0.9996425
ENST00000372374	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	8.46E-05	0.99991536
ENST00000372374	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000358937	0.99964106
ENST00000372374	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000357522	0.9996425
ENST00000353126	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	8.46E-05	0.99991536
ENST00000353126	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000358937	0.99964106
ENST00000353126	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000357522	0.9996425
ENST00000545417	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00013701	0.999863
ENST00000545417	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000423113	0.99957687
ENST00000545417	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000509491	0.9994905
ENST00000330208	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	8.46E-05	0.99991536
ENST00000330208	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000358937	0.99964106
ENST00000330208	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000357522	0.9996425
ENST00000372377	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	8.46E-05	0.99991536
ENST00000372377	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000358937	0.99964106
ENST00000372377	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000357522	0.9996425
ENST00000361392	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	8.46E-05	0.99991536
ENST00000361392	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000358937	0.99964106
ENST00000361392	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000357522	0.9996425
ENST00000347631	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000134467	0.99986553
ENST00000347631	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000402004	0.99959797
ENST00000347631	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000485244	0.9995148
ENST00000361812	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000130302	0.9998697
ENST00000361812	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000420653	0.99957937
ENST00000361812	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000506023	0.99949396
ENST00000372362	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	7.99E-05	0.99992
ENST00000372362	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000350673	0.9996493
ENST00000372362	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00034807	0.9996519
ENST00000372365	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	7.99E-05	0.99992
ENST00000372365	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000350673	0.9996493
ENST00000372365	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00034807	0.9996519
ENST00000372368	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	7.99E-05	0.99992
ENST00000372368	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000350673	0.9996493
ENST00000372368	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00034807	0.9996519
ENST00000332628	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	7.99E-05	0.99992
ENST00000332628	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000350673	0.9996493
ENST00000332628	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00034807	0.9996519
ENST00000372369	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	7.99E-05	0.99992
ENST00000372369	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000350673	0.9996493
ENST00000372369	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00034807	0.9996519
ENST00000361746	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000130302	0.9998697
ENST00000361746	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000420653	0.99957937
ENST00000361746	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000506023	0.99949396
ENST00000533933	ENST00000212355	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	7.99E-05	0.99992
ENST00000533933	ENST00000370399	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.000350673	0.9996493
ENST00000533933	ENST00000525962	ST3GAL3	chr1	44257820	-	TGFBR3	chr1	92195530	-	0.00034807	0.9996519

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for ST3GAL3-TGFBR3

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
ST3GAL3	chr1	44257820	TGFBR3	chr1	92195530	166	54	VVLSFDSAGQTLGSDQVFPPKCNIGK
ST3GAL3	chr1	44257820	TGFBR3	chr1	92195530	211	69	VVLSFDSAGQTLGSDQVFPPKCNIGK
ST3GAL3	chr1	44257820	TGFBR3	chr1	92195530	343	54	VVLSFDSAGQTLGSDQVFPPKCNIGK
ST3GAL3	chr1	44257820	TGFBR3	chr1	92195530	362	69	VVLSFDSAGQTLGSDQVFPPKCNIGK
ST3GAL3	chr1	44257820	TGFBR3	chr1	92195530	388	69	VVLSFDSAGQTLGSDQVFPPKCNIGK

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Potential FusionNeoAntigen Information of ST3GAL3-TGFBR3 in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

ST3GAL3-TGFBR3_44257820_92195530.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:17	QTLGSDQVF	0.9634	0.8228	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:16	QTLGSDQVF	0.9554	0.8265	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B58:01	QTLGSDQVF	0.918	0.8863	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B58:02	QTLGSDQVF	0.8461	0.8822	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B57:03	QTLGSDQVF	0.7991	0.955	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B13:02	GQTLGSDQV	0.6613	0.9194	8	17
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-A32:13	QTLGSDQVF	0.3922	0.8184	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:01	GQTLGSDQVF	0.9987	0.729	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B13:01	GQTLGSDQVF	0.9156	0.9251	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:03	GQTLGSDQVF	0.9119	0.6463	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:05	QTLGSDQVF	0.8132	0.7235	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:05	GQTLGSDQVF	0.7302	0.6328	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B57:04	QTLGSDQVF	0.9424	0.6325	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B58:06	QTLGSDQVF	0.9222	0.8734	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B57:02	QTLGSDQVF	0.9142	0.8928	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:20	QTLGSDQVF	0.8149	0.7952	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B35:28	QTLGSDQVF	0.7633	0.8107	9	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:135	GQTLGSDQVF	0.9988	0.7783	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:27	GQTLGSDQVF	0.9988	0.7796	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:125	GQTLGSDQVF	0.9987	0.729	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:34	GQTLGSDQVF	0.9987	0.729	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:33	GQTLGSDQVF	0.9987	0.729	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:24	GQTLGSDQVF	0.9986	0.8584	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:53	GQTLGSDQVF	0.9943	0.7352	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:50	GQTLGSDQVF	0.9917	0.6797	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:54	GQTLGSDQVF	0.9882	0.6675	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:12	GQTLGSDQVF	0.983	0.6364	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B48:02	GQTLGSDQVF	0.847	0.7018	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B15:20	GQTLGSDQVF	0.7208	0.7233	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B35:28	GQTLGSDQVF	0.7182	0.748	8	18
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	388	HLA-B57:02	AGQTLGSDQVF	0.9971	0.8802	7	18

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Potential FusionNeoAntigen Information of ST3GAL3-TGFBR3 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of ST3GAL3-TGFBR3

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8390	SAGQTLGSDQVFPP	ST3GAL3	TGFBR3	chr1	44257820	chr1	92195530	388

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ST3GAL3-TGFBR3

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	8390	SAGQTLGSDQVFPP	-6.89175	-7.02525
HLA-B14:02	3BVN	8390	SAGQTLGSDQVFPP	-3.76353	-4.82823
HLA-B14:02	3BVN	8390	SAGQTLGSDQVFPP	-3.54463	-5.51563
HLA-B52:01	3W39	8390	SAGQTLGSDQVFPP	-6.8236	-6.9571
HLA-B52:01	3W39	8390	SAGQTLGSDQVFPP	-6.55289	-7.61759
HLA-B52:01	3W39	8390	SAGQTLGSDQVFPP	-6.49618	-7.56088
HLA-B52:01	3W39	8390	SAGQTLGSDQVFPP	-5.06042	-7.03142
HLA-B52:01	3W39	8390	SAGQTLGSDQVFPP	-4.70921	-4.84271
HLA-B52:01	3W39	8390	SAGQTLGSDQVFPP	-4.01048	-5.98148
HLA-A11:01	4UQ2	8390	SAGQTLGSDQVFPP	-5.86092	-6.92562
HLA-A11:01	4UQ2	8390	SAGQTLGSDQVFPP	-3.84862	-5.81962
HLA-A24:02	5HGA	8390	SAGQTLGSDQVFPP	-8.52398	-8.65748
HLA-A24:02	5HGA	8390	SAGQTLGSDQVFPP	-6.68848	-8.65948
HLA-A24:02	5HGA	8390	SAGQTLGSDQVFPP	-5.15302	-6.21772
HLA-B27:05	6PYJ	8390	SAGQTLGSDQVFPP	-6.45407	-6.58757
HLA-B27:05	6PYJ	8390	SAGQTLGSDQVFPP	-5.58769	-7.55869
HLA-B44:05	3DX8	8390	SAGQTLGSDQVFPP	-7.7023	-7.8358
HLA-B44:05	3DX8	8390	SAGQTLGSDQVFPP	-7.44739	-7.58089
HLA-B44:05	3DX8	8390	SAGQTLGSDQVFPP	-5.65528	-7.62628
HLA-B44:05	3DX8	8390	SAGQTLGSDQVFPP	-3.72784	-4.79254
HLA-B44:05	3DX8	8390	SAGQTLGSDQVFPP	-2.8034	-3.8681
HLA-B44:05	3DX8	8390	SAGQTLGSDQVFPP	-1.97925	-3.95025
HLA-A02:01	6TDR	8390	SAGQTLGSDQVFPP	-6.15445	-7.21915
HLA-A02:01	6TDR	8390	SAGQTLGSDQVFPP	-4.70104	-5.76574

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Vaccine Design for the FusionNeoAntigens of ST3GAL3-TGFBR3

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	7	18	AGQTLGSDQVF	GACAAACACTAGGCTCAGATCAAGTGTTCCCTC
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	8	17	GQTLGSDQV	AAACACTAGGCTCAGATCAAGTGTTCC
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	8	18	GQTLGSDQVF	AAACACTAGGCTCAGATCAAGTGTTCCCTC
ST3GAL3-TGFBR3	chr1	44257820	chr1	92195530	9	18	QTLGSDQVF	CACTAGGCTCAGATCAAGTGTTCCCTC

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of ST3GAL3-TGFBR3

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
LIHC	ST3GAL3-TGFBR3	chr1	44257820	ENST00000262915	chr1	92195530	ENST00000212355	TCGA-LG-A6GG-01A

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Potential target of CAR-T therapy development for ST3GAL3-TGFBR3

Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000262915

9_28

445.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000330208

9_28

156.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000332628

9_28

345.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000347631

9_28

391.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000353126

9_28

278.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000361392

9_28

376.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000361746

9_28

445.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000361812

9_28

171.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372362

9_28

156.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372365

9_28

177.66666666666666

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372368

9_28

430.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372369

9_28

346.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372374

9_28

345.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372375

9_28

430.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000372377

9_28

445.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000533933

9_28

278.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Hgene

ST3GAL3

chr1:44257820

chr1:92195530

ENST00000545417

9_28

171.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

TGFBR3

chr1:44257820

chr1:92195530

ENST00000212355

788_809

852.0

Transmembrane

Helical

Tgene

TGFBR3

chr1:44257820

chr1:92195530

ENST00000370399

788_809

851.0

Transmembrane

Helical

Tgene

TGFBR3

chr1:44257820

chr1:92195530

ENST00000525962

788_809

852.0

Transmembrane

Helical

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to ST3GAL3-TGFBR3

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to ST3GAL3-TGFBR3

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)