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Fusion Protein:LRTOMT-NFIC

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: LRTOMT-NFIC
	FusionPDB ID: 50147
	FusionGDB2.0 ID: 50147
		Hgene	Tgene
	Gene symbol	LRTOMT	NFIC
	Gene ID	220074	4782
	Gene name	leucine rich transmembrane and O-methyltransferase domain containing	nuclear factor I C
	Synonyms	CFAP111\|DFNB63\|LRRC51	CTF\|CTF5\|NF-I\|NFI
	Cytomap	11q13.4	19p13.3
	Type of gene	protein-coding	protein-coding
	Description	transmembrane O-methyltransferaseleucine-rich repeat-containing protein 51leucine rich transmembrane and 0-methyltransferase domain containing	nuclear factor 1 C-typeCCAAT-box-binding transcription factorNF-I/CNF1-CTGGCA-binding proteinnuclear factor I/C (CCAAT-binding transcription factor)
	Modification date	20200313	20200313
	UniProtAcc	Q96E66 Main function of 5'-partner protein:	P08651 Main function of 5'-partner protein: FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000289488, ENST00000324866, ENST00000439209, ENST00000447974, ENST00000536917, ENST00000538478, ENST00000541614, ENST00000419228, ENST00000435085, ENST00000307198, ENST00000423494, ENST00000440313, ENST00000539271, ENST00000539587,	ENST00000588839, ENST00000341919, ENST00000346156, ENST00000395111, ENST00000443272, ENST00000586919, ENST00000589123, ENST00000590282,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 9 X 3=216	24 X 21 X 9=4536
	# samples	11	27
	** MAII score	log2(11/216*10)=-0.973527788638809 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(27/4536*10)=-4.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: LRTOMT [Title/Abstract] AND NFIC [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: LRTOMT [Title/Abstract] AND NFIC [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	LRTOMT(71800211)-NFIC(3449012), # samples:3
Anticipated loss of major functional domain due to fusion event.	LRTOMT-NFIC 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. LRTOMT-NFIC 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. LRTOMT-NFIC 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. LRTOMT-NFIC 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	NFIC	GO:0000122	negative regulation of transcription by RNA polymerase II	19706729
Tgene	NFIC	GO:0045944	positive regulation of transcription by RNA polymerase II	1524678\|19706729

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:71800211/chr19:3449012)
- 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 LRTOMT (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 NFIC (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)
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7477	460	2198	1371	275
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1711	460	1344	847	165
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	1248	460	378	821	147
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	822	460	378	821	147
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	987	460	378	788	136
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	1006	460	378	821	147
ENST00000447974	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	1167	460	378	1028	216
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7477	460	2198	1371	275
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1711	460	1344	847	165
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	1248	460	378	821	147
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	822	460	378	821	147
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	987	460	378	788	136
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	1006	460	378	821	147
ENST00000289488	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	1167	460	378	1028	216
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7236	219	1957	1130	275
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1470	219	1103	606	165
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	1007	219	137	580	147
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	581	219	137	580	148
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	746	219	137	547	136
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	765	219	137	580	147
ENST00000538478	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	926	219	137	787	216
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7265	248	1986	1159	275
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1499	248	1132	635	165
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	1036	248	166	609	147
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	610	248	166	609	148
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	775	248	166	576	136
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	794	248	166	609	147
ENST00000324866	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	955	248	166	816	216
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7265	248	1986	1159	275
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1499	248	1132	635	165
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	1036	248	166	609	147
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	610	248	166	609	148
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	775	248	166	576	136
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	794	248	166	609	147
ENST00000439209	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	955	248	166	816	216
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7215	198	1936	1109	275
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1449	198	1082	585	165
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	986	198	116	559	147
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	560	198	116	559	148
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	725	198	116	526	136
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	744	198	116	559	147
ENST00000541614	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	905	198	116	766	216
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000589123	NFIC	chr19	3449012	+	7116	99	1837	1010	275
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000346156	NFIC	chr19	3449012	+	1350	99	983	486	165
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000395111	NFIC	chr19	3449012	+	887	99	17	460	147
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000586919	NFIC	chr19	3449012	+	461	99	17	460	148
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000341919	NFIC	chr19	3449012	+	626	99	17	427	136
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000590282	NFIC	chr19	3449012	+	645	99	17	460	147
ENST00000536917	LRTOMT	chr11	71800211	+	ENST00000443272	NFIC	chr19	3449012	+	806	99	17	667	216

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
ENST00000447974	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.2522071	0.74779284
ENST00000447974	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.26784945	0.7321506
ENST00000447974	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.0922913	0.9077087
ENST00000447974	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.044536583	0.95546347
ENST00000447974	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.047592457	0.9524076
ENST00000447974	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.048845064	0.9511549
ENST00000447974	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.048112866	0.95188713
ENST00000289488	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.2522071	0.74779284
ENST00000289488	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.26784945	0.7321506
ENST00000289488	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.0922913	0.9077087
ENST00000289488	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.044536583	0.95546347
ENST00000289488	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.047592457	0.9524076
ENST00000289488	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.048845064	0.9511549
ENST00000289488	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.048112866	0.95188713
ENST00000538478	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.2630797	0.73692024
ENST00000538478	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.30404183	0.6959582
ENST00000538478	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.11590851	0.88409144
ENST00000538478	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.034431856	0.9655682
ENST00000538478	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.041349623	0.9586504
ENST00000538478	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.0448453	0.9551547
ENST00000538478	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.04738001	0.95262
ENST00000324866	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.2636922	0.7363078
ENST00000324866	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.30246946	0.6975305
ENST00000324866	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.14371084	0.8562892
ENST00000324866	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.043091152	0.9569088
ENST00000324866	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.045663927	0.95433605
ENST00000324866	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.052244004	0.947756
ENST00000324866	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.05812959	0.94187045
ENST00000439209	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.2636922	0.7363078
ENST00000439209	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.30246946	0.6975305
ENST00000439209	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.14371084	0.8562892
ENST00000439209	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.043091152	0.9569088
ENST00000439209	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.045663927	0.95433605
ENST00000439209	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.052244004	0.947756
ENST00000439209	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.05812959	0.94187045
ENST00000541614	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.26444975	0.7355503
ENST00000541614	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.38468784	0.61531216
ENST00000541614	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.112246804	0.8877532
ENST00000541614	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.037344076	0.96265596
ENST00000541614	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.04031248	0.9596875
ENST00000541614	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.039173815	0.96082616
ENST00000541614	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.047165196	0.9528348
ENST00000536917	ENST00000589123	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.2650684	0.7349315
ENST00000536917	ENST00000346156	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.26607996	0.73392
ENST00000536917	ENST00000395111	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.100793086	0.89920694
ENST00000536917	ENST00000586919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.06831824	0.93168175
ENST00000536917	ENST00000341919	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.036096767	0.96390325
ENST00000536917	ENST00000590282	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.04500419	0.9549958
ENST00000536917	ENST00000443272	LRTOMT	chr11	71800211	+	NFIC	chr19	3449012	+	0.046224307	0.9537757

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 LRTOMT-NFIC

+/-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
LRTOMT	chr11	71800211	NFIC	chr19	3449012	198	27	PLDYSFRSIHVIQGISSPVKKTEMDK
LRTOMT	chr11	71800211	NFIC	chr19	3449012	219	27	PLDYSFRSIHVIQGISSPVKKTEMDK
LRTOMT	chr11	71800211	NFIC	chr19	3449012	248	27	PLDYSFRSIHVIQGISSPVKKTEMDK
LRTOMT	chr11	71800211	NFIC	chr19	3449012	460	27	PLDYSFRSIHVIQGISSPVKKTEMDK
LRTOMT	chr11	71800211	NFIC	chr19	3449012	99	27	PLDYSFRSIHVIQGISSPVKKTEMDK

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Potential FusionNeoAntigen Information of LRTOMT-NFIC 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.

LRTOMT-NFIC_71800211_3449012.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)
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B57:01	RSIHVIQGI	0.9977	0.9626	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B57:03	RSIHVIQGI	0.9972	0.9763	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B58:02	RSIHVIQGI	0.9971	0.8395	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B58:01	RSIHVIQGI	0.9967	0.8827	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B15:16	RSIHVIQGI	0.9961	0.724	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B15:17	RSIHVIQGI	0.9958	0.876	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A30:08	RSIHVIQGI	0.992	0.7692	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A32:13	RSIHVIQGI	0.9848	0.9001	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B13:02	RSIHVIQGI	0.8619	0.6824	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B52:01	RSIHVIQGI	0.4543	0.8951	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:03	VIQGISSPVK	0.9941	0.5163	10	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:03	HVIQGISSPVK	0.9995	0.5719	9	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:03	VIQGISSPVKK	0.9988	0.5849	10	21
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A03:25	HVIQGISSPVK	0.9979	0.5363	9	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A03:12	HVIQGISSPVK	0.9979	0.5773	9	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C15:04	RSIHVIQGI	0.9997	0.831	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C15:06	RSIHVIQGI	0.9996	0.8399	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C06:03	RSIHVIQGI	0.9753	0.9791	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C12:04	RSIHVIQGI	0.9745	0.9754	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C02:06	RSIHVIQGI	0.8968	0.9163	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:01	HVIQGISSPVK	0.9995	0.5151	9	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:01	VIQGISSPVKK	0.9981	0.5471	10	21
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A03:01	HVIQGISSPVK	0.9979	0.5363	9	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C15:02	RSIHVIQGI	0.9997	0.8201	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C15:09	RSIHVIQGI	0.9997	0.831	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-C15:05	RSIHVIQGI	0.9996	0.894	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B57:10	RSIHVIQGI	0.9977	0.9626	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-B58:06	RSIHVIQGI	0.9974	0.7611	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A32:01	RSIHVIQGI	0.9954	0.9232	6	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A68:02	HVIQGISSPV	0.9976	0.5698	9	19
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A69:01	HVIQGISSPV	0.9953	0.6494	9	19
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:02	HVIQGISSPVK	0.9995	0.5151	9	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	HLA-A11:02	VIQGISSPVKK	0.9981	0.5471	10	21

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Potential FusionNeoAntigen Information of LRTOMT-NFIC in HLA II

LRTOMT-NFIC_71800211_3449012.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)
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0102	FRSIHVIQGISSPVK	5	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0123	FRSIHVIQGISSPVK	5	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0401	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0407	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0407	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0419	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0419	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0431	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0431	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0433	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0434	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0435	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0435	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0438	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0438	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0443	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0443	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0447	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0447	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0447	PLDYSFRSIHVIQGI	0	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0454	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0454	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0454	PLDYSFRSIHVIQGI	0	15
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0461	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0461	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0463	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0474	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0475	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0476	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0482	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-0486	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1001	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1001	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1003	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1003	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1130	DYSFRSIHVIQGISS	2	17
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1130	LDYSFRSIHVIQGIS	1	16
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB1-1615	FRSIHVIQGISSPVK	5	20
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB5-0106	IHVIQGISSPVKKTE	8	23
LRTOMT-NFIC	chr11	71800211	chr19	3449012	460	DRB5-0205	IHVIQGISSPVKKTE	8	23

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Fusion breakpoint peptide structures of LRTOMT-NFIC

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
8223	RSIHVIQGISSPVK	LRTOMT	NFIC	chr11	71800211	chr19	3449012	460

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LRTOMT-NFIC

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	8223	RSIHVIQGISSPVK	-6.07233	-6.07953
HLA-B52:01	3W39	8223	RSIHVIQGISSPVK	-5.45645	-5.46365
HLA-A24:02	5HGA	8223	RSIHVIQGISSPVK	-3.85827	-3.86547
HLA-B44:05	3DX8	8223	RSIHVIQGISSPVK	-4.76301	-4.77021

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Vaccine Design for the FusionNeoAntigens of LRTOMT-NFIC

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
LRTOMT-NFIC	chr11	71800211	chr19	3449012	10	20	VIQGISSPVK	TCATTCAAGGCATCTCGTCCCCGGTGAAGA
LRTOMT-NFIC	chr11	71800211	chr19	3449012	10	21	VIQGISSPVKK	TCATTCAAGGCATCTCGTCCCCGGTGAAGAAGA
LRTOMT-NFIC	chr11	71800211	chr19	3449012	6	15	RSIHVIQGI	GAAGCATCCACGTCATTCAAGGCATCT
LRTOMT-NFIC	chr11	71800211	chr19	3449012	9	19	HVIQGISSPV	ACGTCATTCAAGGCATCTCGTCCCCGGTGA
LRTOMT-NFIC	chr11	71800211	chr19	3449012	9	20	HVIQGISSPVK	ACGTCATTCAAGGCATCTCGTCCCCGGTGAAGA

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
LRTOMT-NFIC	chr11	71800211	chr19	3449012	0	15	PLDYSFRSIHVIQGI	CTCTTGACTACTCCTTCAGAAGCATCCACGTCATTCAAGGCATCT
LRTOMT-NFIC	chr11	71800211	chr19	3449012	1	16	LDYSFRSIHVIQGIS	TTGACTACTCCTTCAGAAGCATCCACGTCATTCAAGGCATCTCGT
LRTOMT-NFIC	chr11	71800211	chr19	3449012	2	17	DYSFRSIHVIQGISS	ACTACTCCTTCAGAAGCATCCACGTCATTCAAGGCATCTCGTCCC
LRTOMT-NFIC	chr11	71800211	chr19	3449012	5	20	FRSIHVIQGISSPVK	TCAGAAGCATCCACGTCATTCAAGGCATCTCGTCCCCGGTGAAGA
LRTOMT-NFIC	chr11	71800211	chr19	3449012	8	23	IHVIQGISSPVKKTE	TCCACGTCATTCAAGGCATCTCGTCCCCGGTGAAGAAGACAGAGA

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Information of the samples that have these potential fusion neoantigens of LRTOMT-NFIC

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	LRTOMT-NFIC	chr11	71800211	ENST00000289488	chr19	3449012	ENST00000341919	TCGA-A8-A097-01A

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Potential target of CAR-T therapy development for LRTOMT-NFIC

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

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 LRTOMT-NFIC

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 LRTOMT-NFIC

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)