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Fusion Protein:TGFBR3-LRTM1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TGFBR3-LRTM1
	FusionPDB ID: 90477
	FusionGDB2.0 ID: 90477
		Hgene	Tgene
	Gene symbol	TGFBR3	LRTM1
	Gene ID	7049	57408
	Gene name	transforming growth factor beta receptor 3	leucine rich repeats and transmembrane domains 1
	Synonyms	BGCAN\|betaglycan	HT017
	Cytomap	1p22.1	3p14.3
	Type of gene	protein-coding	protein-coding
	Description	transforming growth factor beta receptor type 3TGF-beta receptor type 3TGF-beta receptor type IIITGFR-3betaglycan proteoglycantransforming growth factor beta receptor III	leucine-rich repeat and transmembrane domain-containing protein 1
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000212355, ENST00000370399, ENST00000525962, ENST00000468996,	ENST00000493075, ENST00000273286,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 13 X 6=1092	3 X 2 X 3=18
	# samples	15	4
	** MAII score	log2(15/1092*10)=-2.86393845042397 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/18*10)=1.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: TGFBR3 [Title/Abstract] AND LRTM1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TGFBR3 [Title/Abstract] AND LRTM1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TGFBR3(92174220)-LRTM1(54959242), # samples:2
Anticipated loss of major functional domain due to fusion event.	TGFBR3-LRTM1 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. TGFBR3-LRTM1 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. TGFBR3-LRTM1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. TGFBR3-LRTM1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted 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
Hgene	TGFBR3	GO:0001837	epithelial to mesenchymal transition	18184661
Hgene	TGFBR3	GO:0007179	transforming growth factor beta receptor signaling pathway	12958365
Hgene	TGFBR3	GO:0030509	BMP signaling pathway	18184661
Hgene	TGFBR3	GO:0032354	response to follicle-stimulating hormone	14557487
Hgene	TGFBR3	GO:0034695	response to prostaglandin E	14557487
Hgene	TGFBR3	GO:0034699	response to luteinizing hormone	14557487
Hgene	TGFBR3	GO:0051271	negative regulation of cellular component movement	17999987
Hgene	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/chr1:92174220/chr3:54959242)
- 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 TGFBR3 (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 LRTM1 (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)
ENST00000525962	TGFBR3	chr1	92174220	-	ENST00000273286	LRTM1	chr3	54959242	-	3602	2349	62	3379	1105
ENST00000525962	TGFBR3	chr1	92174219	-	ENST00000273286	LRTM1	chr3	54959242	-	3602	2349	62	3379	1105

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
ENST00000525962	ENST00000273286	TGFBR3	chr1	92174220	-	LRTM1	chr3	54959242	-	0.000231926	0.9997681
ENST00000525962	ENST00000273286	TGFBR3	chr1	92174219	-	LRTM1	chr3	54959242	-	0.000231926	0.9997681

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 TGFBR3-LRTM1

+/-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
TGFBR3	chr1	92174219	LRTM1	chr3	54959242	2349	762	KPLAVIHHEAESKGELLLFSSVIVLL
TGFBR3	chr1	92174220	LRTM1	chr3	54959242	2349	762	KPLAVIHHEAESKGELLLFSSVIVLL

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Potential FusionNeoAntigen Information of TGFBR3-LRTM1 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.

TGFBR3-LRTM1_92174219_54959242.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)
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:13	AESKGELL	0.9278	0.9655	9	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:02	AESKGELLL	0.9849	0.696	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:03	AESKGELLL	0.978	0.9862	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:02	HEAESKGEL	0.9772	0.642	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B13:01	AESKGELLL	0.9706	0.9145	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:03	HEAESKGEL	0.9214	0.9757	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B47:01	AESKGELLL	0.9151	0.7548	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B18:01	HEAESKGEL	0.9039	0.927	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B45:01	AESKGELLL	0.8808	0.9284	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:16	ESKGELLLF	0.8701	0.6088	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B47:01	HEAESKGEL	0.8004	0.595	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B45:01	HEAESKGEL	0.7386	0.8099	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:13	HEAESKGEL	0.7367	0.9443	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B58:02	ESKGELLLF	0.6437	0.8601	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:01	HEAESKGEL	0.5643	0.5926	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:03	ESKGELLLF	0.5627	0.8895	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:01	HEAESKGEL	0.5279	0.9234	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:10	HEAESKGEL	0.3898	0.6475	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:37	HEAESKGEL	0.3293	0.6551	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:01	AESKGELLL	0.3176	0.9117	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:13	AESKGELLL	0.2224	0.9745	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:01	AESKGELLL	0.1571	0.7739	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:03	AESKGELLLF	0.9993	0.9805	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B47:01	AESKGELLLF	0.9989	0.6948	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:01	HHEAESKGEL	0.9966	0.9645	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:01	HHEAESKGEL	0.9932	0.9761	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:02	HHEAESKGEL	0.993	0.9797	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:01	AESKGELLLF	0.9824	0.9508	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:10	HHEAESKGEL	0.9668	0.5863	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:03	AESKGELLLF	0.922	0.943	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:13	HEAESKGELL	0.8652	0.9558	7	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:37	HHEAESKGEL	0.8174	0.5884	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:01	HHEAESKGELL	0.9997	0.9737	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:01	IHHEAESKGEL	0.9996	0.8563	5	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:02	HHEAESKGELL	0.9996	0.9841	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:01	HHEAESKGELL	0.9995	0.9818	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:01	IHHEAESKGEL	0.9991	0.8985	5	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:02	IHHEAESKGEL	0.9991	0.91	5	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B47:01	HEAESKGELLL	0.9974	0.6168	7	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:13	HEAESKGELLL	0.9873	0.9632	7	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:08	AESKGELL	0.9572	0.7631	9	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:06	HEAESKGEL	0.9992	0.5422	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:06	AESKGELLL	0.9968	0.6944	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:10	AESKGELLL	0.9939	0.514	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:08	HEAESKGEL	0.8093	0.8001	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:05	HEAESKGEL	0.6423	0.923	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:08	AESKGELLL	0.363	0.7936	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:09	HHEAESKGEL	0.996	0.676	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:05	HHEAESKGEL	0.9931	0.9599	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:10	AESKGELLLF	0.9855	0.5338	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:08	HEAESKGELL	0.9682	0.8487	7	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:08	HHEAESKGEL	0.9604	0.8954	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:10	HEAESKGELL	0.9398	0.5012	7	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:10	EAESKGELLL	0.3902	0.5271	8	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:09	HHEAESKGELL	0.9995	0.761	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:05	HHEAESKGELL	0.9995	0.9699	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:05	IHHEAESKGEL	0.9991	0.8396	5	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:08	HEAESKGELLL	0.9983	0.8741	7	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:10	HEAESKGELLL	0.9965	0.5386	7	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:04	AESKGELL	0.9996	0.7002	9	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:04	HEAESKGEL	0.999	0.6254	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:04	AESKGELLL	0.9973	0.73	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-A25:01	ESKGELLLF	0.9824	0.8255	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:26	AESKGELLL	0.978	0.9862	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:13	AESKGELLL	0.978	0.9862	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:07	AESKGELLL	0.978	0.9862	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B18:11	HEAESKGEL	0.9338	0.9442	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:13	HEAESKGEL	0.9214	0.9757	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:07	HEAESKGEL	0.9214	0.9757	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:26	HEAESKGEL	0.9214	0.9757	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B18:05	HEAESKGEL	0.9039	0.927	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:02	ESKGELLLF	0.901	0.9259	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B18:06	HEAESKGEL	0.8966	0.9325	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B18:03	HEAESKGEL	0.8692	0.9205	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:13	ESKGELLLF	0.8461	0.6823	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:03	HEAESKGEL	0.8261	0.5406	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:11	HEAESKGEL	0.82	0.7777	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:31	HEAESKGEL	0.7389	0.9368	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:02	HEAESKGEL	0.7239	0.9468	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B58:06	ESKGELLLF	0.7144	0.7258	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:04	HEAESKGEL	0.5643	0.5926	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:05	HEAESKGEL	0.5643	0.5926	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:03	AESKGELLL	0.4673	0.5264	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:11	AESKGELLL	0.4087	0.7688	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:02	AESKGELLL	0.2339	0.9764	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:09	HEAESKGEL	0.2018	0.5276	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:04	AESKGELLL	0.1571	0.7739	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B50:05	AESKGELLL	0.1571	0.7739	9	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-C02:02	ESKGELLLF	0.0373	0.9604	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-C02:10	ESKGELLLF	0.0373	0.9604	10	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:53	HEAESKGEL	0.0151	0.8376	7	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:07	AESKGELLLF	0.9993	0.9805	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:13	AESKGELLLF	0.9993	0.9805	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B44:26	AESKGELLLF	0.9993	0.9805	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:31	HHEAESKGEL	0.9957	0.9643	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:04	HEAESKGELL	0.9953	0.6422	7	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:05	HHEAESKGEL	0.9932	0.9761	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:10	AESKGELLLF	0.9824	0.9508	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:53	AESKGELLLF	0.9811	0.7725	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:11	HHEAESKGEL	0.9698	0.8666	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:04	AESKGELLLF	0.9664	0.8339	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B58:06	AESKGELLLF	0.9456	0.8284	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B48:02	AESKGELLLF	0.9447	0.8467	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:09	HHEAESKGEL	0.9431	0.5931	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B57:02	AESKGELLLF	0.9364	0.9402	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:02	HEAESKGELL	0.8819	0.9577	7	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:03	AESKGELLLF	0.8758	0.5081	9	19
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:03	HEAESKGELL	0.8586	0.5888	7	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:03	HHEAESKGEL	0.4157	0.6281	6	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B40:04	HEAESKGELLL	0.9996	0.6653	7	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:05	HHEAESKGELL	0.9995	0.9818	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B38:05	IHHEAESKGEL	0.9991	0.8985	5	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:11	HHEAESKGELL	0.997	0.9114	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B15:09	HHEAESKGELL	0.9947	0.6064	6	17
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:11	IHHEAESKGEL	0.9929	0.6949	5	16
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B41:03	HEAESKGELLL	0.9912	0.62	7	18
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	HLA-B39:02	HEAESKGELLL	0.9901	0.9647	7	18

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Potential FusionNeoAntigen Information of TGFBR3-LRTM1 in HLA II

TGFBR3-LRTM1_92174219_54959242.msa

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)
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	DRB1-0806	KPLAVIHHEAESKGE	0	15
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	DRB1-0822	KPLAVIHHEAESKGE	0	15
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	DRB1-1358	KPLAVIHHEAESKGE	0	15
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	2349	DRB5-0106	KPLAVIHHEAESKGE	0	15

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Fusion breakpoint peptide structures of TGFBR3-LRTM1

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
3345	HHEAESKGELLLFS	TGFBR3	LRTM1	chr1	92174219	chr3	54959242	2349

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TGFBR3-LRTM1

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	3345	HHEAESKGELLLFS	-7.9962	-8.1096
HLA-B14:02	3BVN	3345	HHEAESKGELLLFS	-5.70842	-6.74372
HLA-B52:01	3W39	3345	HHEAESKGELLLFS	-6.83737	-6.95077
HLA-B52:01	3W39	3345	HHEAESKGELLLFS	-4.4836	-5.5189
HLA-A11:01	4UQ2	3345	HHEAESKGELLLFS	-10.0067	-10.1201
HLA-A11:01	4UQ2	3345	HHEAESKGELLLFS	-9.03915	-10.0745
HLA-A24:02	5HGA	3345	HHEAESKGELLLFS	-6.56204	-6.67544
HLA-A24:02	5HGA	3345	HHEAESKGELLLFS	-5.42271	-6.45801
HLA-B44:05	3DX8	3345	HHEAESKGELLLFS	-7.85648	-8.89178
HLA-B44:05	3DX8	3345	HHEAESKGELLLFS	-5.3978	-5.5112
HLA-A02:01	6TDR	3345	HHEAESKGELLLFS	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of TGFBR3-LRTM1

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
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	10	19	ESKGELLLF	AATCTAAAGGTGAACTGCTCCTGTTTT
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	5	16	IHHEAESKGEL	TCCACCATGAAGCAGAATCTAAAGGTGAACTGC
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	6	16	HHEAESKGEL	ACCATGAAGCAGAATCTAAAGGTGAACTGC
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	6	17	HHEAESKGELL	ACCATGAAGCAGAATCTAAAGGTGAACTGCTCC
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	7	16	HEAESKGEL	ATGAAGCAGAATCTAAAGGTGAACTGC
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	7	17	HEAESKGELL	ATGAAGCAGAATCTAAAGGTGAACTGCTCC
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	7	18	HEAESKGELLL	ATGAAGCAGAATCTAAAGGTGAACTGCTCCTGT
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	8	18	EAESKGELLL	AAGCAGAATCTAAAGGTGAACTGCTCCTGT
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	9	17	AESKGELL	CAGAATCTAAAGGTGAACTGCTCC
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	9	18	AESKGELLL	CAGAATCTAAAGGTGAACTGCTCCTGT
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	9	19	AESKGELLLF	CAGAATCTAAAGGTGAACTGCTCCTGTTTT

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
TGFBR3-LRTM1	chr1	92174219	chr3	54959242	0	15	KPLAVIHHEAESKGE	AGCCCCTTGCTGTGATCCACCATGAAGCAGAATCTAAAGGTGAAC

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Information of the samples that have these potential fusion neoantigens of TGFBR3-LRTM1

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
OV	TGFBR3-LRTM1	chr1	92174219	ENST00000525962	chr3	54959242	ENST00000273286	TCGA-30-1861

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Potential target of CAR-T therapy development for TGFBR3-LRTM1

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

Tgene

LRTM1

chr1:92174219

chr3:54959242

ENST00000273286

289_309

346.0

Transmembrane

Helical

Tgene

LRTM1

chr1:92174219

chr3:54959242

ENST00000493075

289_309

270.0

Transmembrane

Helical

Tgene

LRTM1

chr1:92174220

chr3:54959242

ENST00000273286

289_309

346.0

Transmembrane

Helical

Tgene

LRTM1

chr1:92174220

chr3:54959242

ENST00000493075

289_309

270.0

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 TGFBR3-LRTM1

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 TGFBR3-LRTM1

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)