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Fusion Protein:LIFR-C9

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LIFR-C9
	FusionPDB ID: 44655
	FusionGDB2.0 ID: 44655
		Hgene	Tgene
	Gene symbol	LIFR	C9
	Gene ID	3977	1645
	Gene name	LIF receptor subunit alpha	aldo-keto reductase family 1 member C1
	Synonyms	CD118\|LIF-R\|SJS2\|STWS\|SWS	2-ALPHA-HSD\|20-ALPHA-HSD\|C9\|DD1\|DD1/DD2\|DDH\|DDH1\|H-37\|HAKRC\|HBAB\|MBAB
	Cytomap	5p13.1	10p15.1
	Type of gene	protein-coding	protein-coding
	Description	leukemia inhibitory factor receptorCD118 antigenLIF receptorLIF receptor alphaleukemia inhibitory factor receptor alpha	aldo-keto reductase family 1 member C120 alpha-hydroxysteroid dehydrogenasealdo-keto reductase Cchlordecone reductase homolog HAKRCdihydrodiol dehydrogenase 1dihydrodiol dehydrogenase 1/2dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid
	Modification date	20200313	20200313
	UniProtAcc	P42702 Main function of 5'-partner protein: FUNCTION: Signal-transducing molecule. May have a common pathway with IL6ST. The soluble form inhibits the biological activity of LIF by blocking its binding to receptors on target cells.	A6NGG3 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000263409, ENST00000453190, ENST00000503088,	ENST00000509186, ENST00000263408,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 7 X 7=392	7 X 6 X 4=168
	# samples	8	8
	** MAII score	log2(8/392*10)=-2.29278174922785 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(8/168*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: LIFR [Title/Abstract] AND C9 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: LIFR [Title/Abstract] AND C9 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LIFR(38493708)-C9(39316131), # samples:3
Anticipated loss of major functional domain due to fusion event.	LIFR-C9 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. LIFR-C9 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. LIFR-C9 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. LIFR-C9 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. LIFR-C9 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. LIFR-C9 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. LIFR-C9 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	LIFR	GO:0008284	positive regulation of cell proliferation	7957045\|8999038
Hgene	LIFR	GO:0019221	cytokine-mediated signaling pathway	7957045
Hgene	LIFR	GO:0034097	response to cytokine	8999038
Hgene	LIFR	GO:0048861	leukemia inhibitory factor signaling pathway	8999038\|12643274
Hgene	LIFR	GO:0070120	ciliary neurotrophic factor-mediated signaling pathway	12643274
Tgene	C9	GO:0007586	digestion	8486699
Tgene	C9	GO:0008206	bile acid metabolic process	8486699
Tgene	C9	GO:0030855	epithelial cell differentiation	21492153
Tgene	C9	GO:0042448	progesterone metabolic process	21232532
Tgene	C9	GO:0042574	retinal metabolic process	21851338
Tgene	C9	GO:0055114	oxidation-reduction process	8486699\|19442656\|21232532
Tgene	C9	GO:0071395	cellular response to jasmonic acid stimulus	19487289

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:38493708/chr5:39316131)
- 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 LIFR (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 C9 (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)

ENST00000263409

LIFR

chr5

38493708

ENST00000263408

chr5

39316131

4230

2228

163

2277

704

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
ENST00000263409	ENST00000263408	LIFR	chr5	38493708	-	C9	chr5	39316131	-	0.000172859	0.9998272

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 LIFR-C9

+/-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
LIFR	chr5	38493708	C9	chr5	39316131	2228	688	KVPSNSTETVIESDQRREKFQNRTLR

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Potential FusionNeoAntigen Information of LIFR-C9 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.

LIFR-C9_38493708_39316131.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)
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A66:01	ETVIESDQR	0.9964	0.5739	7	16
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A26:03	ETVIESDQR	0.9921	0.6011	7	16
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-B44:03	IESDQRREKF	0.9986	0.7726	10	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A66:01	ETVIESDQRR	0.9938	0.6852	7	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:24	ETVIESDQRR	0.9931	0.5566	7	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:03	ETVIESDQRR	0.991	0.5357	7	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A26:03	ETVIESDQRR	0.9868	0.7229	7	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:05	ETVIESDQRR	0.9386	0.5326	7	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:08	TETVIESDQRR	0.9967	0.5364	6	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:24	TETVIESDQRR	0.9957	0.5476	6	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:03	TETVIESDQRR	0.9955	0.5364	6	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:05	TETVIESDQRR	0.9954	0.5446	6	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:01	ETVIESDQRR	0.9931	0.5566	7	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-A68:01	TETVIESDQRR	0.9957	0.5476	6	17
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-B44:07	IESDQRREKF	0.9986	0.7726	10	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-B44:13	IESDQRREKF	0.9986	0.7726	10	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	HLA-B44:26	IESDQRREKF	0.9986	0.7726	10	20

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Potential FusionNeoAntigen Information of LIFR-C9 in HLA II

LIFR-C9_38493708_39316131.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)
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0301	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0301	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0301	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0301	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0303	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0303	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0305	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0305	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0307	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0307	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0307	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0307	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0310	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0313	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0313	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0313	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0313	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0315	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0315	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0315	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0318	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0318	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0318	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0318	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0320	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0320	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0320	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0320	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0322	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0322	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0322	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0322	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0324	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0324	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0326	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0326	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0328	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0328	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0328	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0328	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0330	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0330	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0330	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0330	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0332	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0332	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0332	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0332	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0334	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0334	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0334	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0334	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0336	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0336	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0336	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0336	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0340	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0340	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0344	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0344	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0344	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0344	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0346	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0346	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0346	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0346	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0348	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0348	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0348	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0348	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0350	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0350	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0350	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0350	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0352	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0352	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0352	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0352	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0354	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0354	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0354	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-0354	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-1107	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-1107	TETVIESDQRREKFQ	6	21
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-1107	STETVIESDQRREKF	5	20
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-1107	TVIESDQRREKFQNR	8	23
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-1371	ETVIESDQRREKFQN	7	22
LIFR-C9	chr5	38493708	chr5	39316131	2228	DRB1-1421	ETVIESDQRREKFQN	7	22

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Fusion breakpoint peptide structures of LIFR-C9

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
9322	TETVIESDQRREKF	LIFR	C9	chr5	38493708	chr5	39316131	2228

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LIFR-C9

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	9322	TETVIESDQRREKF	-7.9962	-8.1096
HLA-B14:02	3BVN	9322	TETVIESDQRREKF	-5.70842	-6.74372
HLA-B52:01	3W39	9322	TETVIESDQRREKF	-6.83737	-6.95077
HLA-B52:01	3W39	9322	TETVIESDQRREKF	-4.4836	-5.5189
HLA-A11:01	4UQ2	9322	TETVIESDQRREKF	-10.0067	-10.1201
HLA-A11:01	4UQ2	9322	TETVIESDQRREKF	-9.03915	-10.0745
HLA-A24:02	5HGA	9322	TETVIESDQRREKF	-6.56204	-6.67544
HLA-A24:02	5HGA	9322	TETVIESDQRREKF	-5.42271	-6.45801
HLA-B44:05	3DX8	9322	TETVIESDQRREKF	-7.85648	-8.89178
HLA-B44:05	3DX8	9322	TETVIESDQRREKF	-5.3978	-5.5112
HLA-A02:01	6TDR	9322	TETVIESDQRREKF	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of LIFR-C9

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
LIFR-C9	chr5	38493708	chr5	39316131	10	20	IESDQRREKF	TAGAATCTGACCAAAGGCGAGAAAAATTTC
LIFR-C9	chr5	38493708	chr5	39316131	6	17	TETVIESDQRR	CTGAAACTGTAATAGAATCTGACCAAAGGCGAG
LIFR-C9	chr5	38493708	chr5	39316131	7	16	ETVIESDQR	AAACTGTAATAGAATCTGACCAAAGGC
LIFR-C9	chr5	38493708	chr5	39316131	7	17	ETVIESDQRR	AAACTGTAATAGAATCTGACCAAAGGCGAG

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
LIFR-C9	chr5	38493708	chr5	39316131	5	20	STETVIESDQRREKF	GCACTGAAACTGTAATAGAATCTGACCAAAGGCGAGAAAAATTTC
LIFR-C9	chr5	38493708	chr5	39316131	6	21	TETVIESDQRREKFQ	CTGAAACTGTAATAGAATCTGACCAAAGGCGAGAAAAATTTCAGA
LIFR-C9	chr5	38493708	chr5	39316131	7	22	ETVIESDQRREKFQN	AAACTGTAATAGAATCTGACCAAAGGCGAGAAAAATTTCAGAACC
LIFR-C9	chr5	38493708	chr5	39316131	8	23	TVIESDQRREKFQNR	CTGTAATAGAATCTGACCAAAGGCGAGAAAAATTTCAGAACCGAA

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Information of the samples that have these potential fusion neoantigens of LIFR-C9

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
BRCA	LIFR-C9	chr5	38493708	ENST00000263409	chr5	39316131	ENST00000263408	TCGA-A7-A26G-01A

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Potential target of CAR-T therapy development for LIFR-C9

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

chr5:38493708

chr5:39316131

ENST00000263408

314_330

560.0

Transmembrane

Beta stranded

Tgene

chr5:38493708

chr5:39316131

ENST00000263408

335_354

560.0

Transmembrane

Beta stranded

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 LIFR-C9

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 LIFR-C9

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)