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Fusion Protein:KMT2E-SRSF7

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KMT2E-SRSF7
	FusionPDB ID: 43293
	FusionGDB2.0 ID: 43293
		Hgene	Tgene
	Gene symbol	KMT2E	SRSF7
	Gene ID	55904	6432
	Gene name	lysine methyltransferase 2E (inactive)	serine and arginine rich splicing factor 7
	Synonyms	HDCMC04P\|MLL5\|NKp44L\|ODLURO	9G8\|AAG3\|SFRS7
	Cytomap	7q22.3	2p22.1
	Type of gene	protein-coding	protein-coding
	Description	inactive histone-lysine N-methyltransferase 2Ehistone-lysine N-methyltransferase 2Ehistone-lysine N-methyltransferase MLL5inactive lysine N-methyltransferase 2Elysine (K)-specific methyltransferase 2Emyeloid/lymphoid or mixed-lineage leukemia 5 (trit	serine/arginine-rich splicing factor 7SR splicing factor 7aging-associated protein 3splicing factor 9G8splicing factor, arginine/serine-rich 7, 35kDa
	Modification date	20200314	20200313
	UniProtAcc	Q8IZD2 Main function of 5'-partner protein: FUNCTION: Associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription (PubMed:23629655, PubMed:24130829, PubMed:23798402). Chromatin interaction is mediated via the binding to tri-methylated histone H3 at 'Lys-4' (H3K4me3) (PubMed:24130829, PubMed:23798402). Key regulator of hematopoiesis involved in terminal myeloid differentiation and in the regulation of hematopoietic stem cell (HSCs) self-renewal by a mechanism that involves DNA methylation (By similarity). Also acts as an important cell cycle regulator, participating in cell cycle regulatory network machinery at multiple cell cycle stages including G1/S transition, S phase progression and mitotic entry (PubMed:14718661, PubMed:18573682, PubMed:19264965, PubMed:23629655). Recruited to E2F1 responsive promoters by HCFC1 where it stimulates tri-methylation of histone H3 at 'Lys-4' and transcriptional activation and thereby facilitates G1 to S phase transition (PubMed:23629655). During myoblast differentiation, required to suppress inappropriate expression of S-phase-promoting genes and maintain expression of determination genes in quiescent cells (By similarity). {ECO:0000250\|UniProtKB:Q3UG20, ECO:0000269\|PubMed:14718661, ECO:0000269\|PubMed:18573682, ECO:0000269\|PubMed:23629655, ECO:0000269\|PubMed:23798402, ECO:0000269\|PubMed:24130829}.; FUNCTION: [Isoform NKp44L]: Cellular ligand for NCR2/NKp44, may play a role as a danger signal in cytotoxicity and NK-cell-mediated innate immunity. {ECO:0000269\|PubMed:23958951}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000334914, ENST00000257745, ENST00000311117, ENST00000334877, ENST00000476671, ENST00000480368,	ENST00000313117, ENST00000409276, ENST00000446327,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	18 X 21 X 9=3402	10 X 5 X 7=350
	# samples	28	10
	** MAII score	log2(28/3402*10)=-3.60288440871842 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/350*10)=-1.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: KMT2E [Title/Abstract] AND SRSF7 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: KMT2E [Title/Abstract] AND SRSF7 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KMT2E(104704027)-SRSF7(38975795), # samples:1
Anticipated loss of major functional domain due to fusion event.	KMT2E-SRSF7 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. KMT2E-SRSF7 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. KMT2E-SRSF7 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. KMT2E-SRSF7 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	SRSF7	GO:0008380	RNA splicing	8013463
Tgene	SRSF7	GO:0048025	negative regulation of mRNA splicing, via spliceosome	15009664

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr7:104704027/chr2:38975795)
- 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 KMT2E (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 SRSF7 (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)
ENST00000311117	KMT2E	chr7	104704027	+	ENST00000313117	SRSF7	chr2	38975795	-	2826	961	545	1291	248
ENST00000311117	KMT2E	chr7	104704027	+	ENST00000446327	SRSF7	chr2	38975795	-	1639	961	545	1255	236
ENST00000311117	KMT2E	chr7	104704027	+	ENST00000409276	SRSF7	chr2	38975795	-	1523	961	545	1282	245
ENST00000257745	KMT2E	chr7	104704027	+	ENST00000313117	SRSF7	chr2	38975795	-	2667	802	386	1132	248
ENST00000257745	KMT2E	chr7	104704027	+	ENST00000446327	SRSF7	chr2	38975795	-	1480	802	386	1096	236
ENST00000257745	KMT2E	chr7	104704027	+	ENST00000409276	SRSF7	chr2	38975795	-	1364	802	386	1123	245
ENST00000334877	KMT2E	chr7	104704027	+	ENST00000313117	SRSF7	chr2	38975795	-	2815	950	534	1280	248
ENST00000334877	KMT2E	chr7	104704027	+	ENST00000446327	SRSF7	chr2	38975795	-	1628	950	534	1244	236
ENST00000334877	KMT2E	chr7	104704027	+	ENST00000409276	SRSF7	chr2	38975795	-	1512	950	534	1271	245
ENST00000476671	KMT2E	chr7	104704027	+	ENST00000313117	SRSF7	chr2	38975795	-	2787	922	506	1252	248
ENST00000476671	KMT2E	chr7	104704027	+	ENST00000446327	SRSF7	chr2	38975795	-	1600	922	506	1216	236
ENST00000476671	KMT2E	chr7	104704027	+	ENST00000409276	SRSF7	chr2	38975795	-	1484	922	506	1243	245

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
ENST00000311117	ENST00000313117	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.11410933	0.8858907
ENST00000311117	ENST00000446327	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.032826778	0.9671733
ENST00000311117	ENST00000409276	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.038281344	0.9617186
ENST00000257745	ENST00000313117	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.13378324	0.8662168
ENST00000257745	ENST00000446327	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.039619952	0.9603801
ENST00000257745	ENST00000409276	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.045264397	0.95473564
ENST00000334877	ENST00000313117	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.13309975	0.86690027
ENST00000334877	ENST00000446327	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.044693533	0.9553065
ENST00000334877	ENST00000409276	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.052476894	0.9475231
ENST00000476671	ENST00000313117	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.10974206	0.89025795
ENST00000476671	ENST00000446327	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.038377155	0.96162283
ENST00000476671	ENST00000409276	KMT2E	chr7	104704027	+	SRSF7	chr2	38975795	-	0.04690493	0.9530951

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 KMT2E-SRSF7

+/-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
KMT2E	chr7	104704027	SRSF7	chr2	38975795	802	136	GFTHDDGYMICCDKCRSRSRSHSRSR
KMT2E	chr7	104704027	SRSF7	chr2	38975795	802	170	SRSRGRRSRSASPRRSRSISLRRSRS
KMT2E	chr7	104704027	SRSF7	chr2	38975795	922	136	GFTHDDGYMICCDKCRSRSRSHSRSR
KMT2E	chr7	104704027	SRSF7	chr2	38975795	922	170	SRSRGRRSRSASPRRSRSISLRRSRS
KMT2E	chr7	104704027	SRSF7	chr2	38975795	950	136	GFTHDDGYMICCDKCRSRSRSHSRSR
KMT2E	chr7	104704027	SRSF7	chr2	38975795	950	170	SRSRGRRSRSASPRRSRSISLRRSRS
KMT2E	chr7	104704027	SRSF7	chr2	38975795	961	136	GFTHDDGYMICCDKCRSRSRSHSRSR
KMT2E	chr7	104704027	SRSF7	chr2	38975795	961	170	SRSRGRRSRSASPRRSRSISLRRSRS

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Potential FusionNeoAntigen Information of KMT2E-SRSF7 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.

KMT2E-SRSF7_104704027_38975795.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)
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A30:08	RSRSASPRR	0.9961	0.8224	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:09	RSRSASPRR	0.992	0.7225	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:11	RSRSASPRR	0.992	0.7225	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:03	RSRSASPRR	0.992	0.7225	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A30:08	RSASPRRSR	0.9878	0.768	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:09	RSASPRRSR	0.9836	0.6114	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:11	RSASPRRSR	0.9836	0.6114	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:03	RSASPRRSR	0.9836	0.6114	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:02	RSRSASPRR	0.9186	0.6803	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:06	RSASPRRSR	0.8559	0.5053	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:02	RSASPRRSR	0.8518	0.577	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:06	RSRSASPRR	0.8411	0.6224	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A03:12	RSRSASPRR	0.7746	0.559	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B07:10	SPRRSRSISL	0.9996	0.5072	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B14:01	SPRRSRSISL	0.9183	0.6177	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B14:02	SPRRSRSISL	0.9183	0.6177	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A30:08	RSRSASPRRSR	0.9937	0.797	6	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B07:02	ASPRRSRSISL	0.9923	0.5744	10	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:06	RSRSASPRRSR	0.849	0.5507	6	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:01	RSRSASPRR	0.9927	0.6358	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:01	RSASPRRSR	0.9844	0.5282	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B14:03	PRRSRSISL	0.7826	0.5783	12	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:30	ASPRRSRSI	0.2879	0.9565	10	19
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:17	ASPRRSRSI	0.2828	0.962	10	19
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B07:12	SPRRSRSISL	0.9989	0.6194	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B14:03	SPRRSRSISL	0.9662	0.8158	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:01	SRSASPRRSR	0.622	0.537	7	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B39:10	SPRRSRSISL	0.5819	0.8338	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B07:04	ASPRRSRSISL	0.9945	0.5172	10	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:30	ASPRRSRSISL	0.9921	0.9613	10	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:17	ASPRRSRSISL	0.9917	0.9665	10	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A31:01	RSRSASPRRSR	0.9898	0.6138	6	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A30:01	RSRSASPRR	0.9968	0.9087	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B27:10	RRSRSASPR	0.9949	0.7991	5	14
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:01	RSRSASPRR	0.992	0.7225	6	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A30:01	RSASPRRSR	0.9907	0.876	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A74:01	RSASPRRSR	0.9836	0.6114	8	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:02	ASPRRSRSI	0.3192	0.962	10	19
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:03	ASPRRSRSI	0.0517	0.9618	10	19
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B27:10	RRSRSASPRR	0.9985	0.7785	5	15
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B67:01	SPRRSRSISL	0.529	0.6847	11	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-A30:01	RSRSASPRRSR	0.9951	0.8838	6	17
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-B07:22	ASPRRSRSISL	0.9923	0.5744	10	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:02	ASPRRSRSISL	0.9894	0.9662	10	21
KMT2E-SRSF7	chr7	104704027	chr2	38975795	802	HLA-C01:03	ASPRRSRSISL	0.9876	0.962	10	21

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Potential FusionNeoAntigen Information of KMT2E-SRSF7 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 KMT2E-SRSF7

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
8248	RSRSASPRRSRSIS	KMT2E	SRSF7	chr7	104704027	chr2	38975795	802

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KMT2E-SRSF7

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	8248	RSRSASPRRSRSIS	-7.9962	-8.1096
HLA-B14:02	3BVN	8248	RSRSASPRRSRSIS	-5.70842	-6.74372
HLA-B52:01	3W39	8248	RSRSASPRRSRSIS	-6.83737	-6.95077
HLA-B52:01	3W39	8248	RSRSASPRRSRSIS	-4.4836	-5.5189
HLA-A11:01	4UQ2	8248	RSRSASPRRSRSIS	-10.0067	-10.1201
HLA-A11:01	4UQ2	8248	RSRSASPRRSRSIS	-9.03915	-10.0745
HLA-A24:02	5HGA	8248	RSRSASPRRSRSIS	-6.56204	-6.67544
HLA-A24:02	5HGA	8248	RSRSASPRRSRSIS	-5.42271	-6.45801
HLA-B44:05	3DX8	8248	RSRSASPRRSRSIS	-7.85648	-8.89178
HLA-B44:05	3DX8	8248	RSRSASPRRSRSIS	-5.3978	-5.5112
HLA-A02:01	6TDR	8248	RSRSASPRRSRSIS	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of KMT2E-SRSF7

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
KMT2E-SRSF7	chr7	104704027	chr2	38975795	10	19	ASPRRSRSI	CAAATGCAGGTCACGGTCTAGATCACA
KMT2E-SRSF7	chr7	104704027	chr2	38975795	10	21	ASPRRSRSISL	CAAATGCAGGTCACGGTCTAGATCACATTCTCG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	11	21	SPRRSRSISL	ATGCAGGTCACGGTCTAGATCACATTCTCG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	12	21	PRRSRSISL	CAGGTCACGGTCTAGATCACATTCTCG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	5	14	RRSRSASPR	CATGATCTGTTGTGACAAATGCAGGTC
KMT2E-SRSF7	chr7	104704027	chr2	38975795	5	15	RRSRSASPRR	CATGATCTGTTGTGACAAATGCAGGTCACG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	6	15	RSRSASPRR	GATCTGTTGTGACAAATGCAGGTCACG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	6	17	RSRSASPRRSR	GATCTGTTGTGACAAATGCAGGTCACGGTCTAG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	7	17	SRSASPRRSR	CTGTTGTGACAAATGCAGGTCACGGTCTAG
KMT2E-SRSF7	chr7	104704027	chr2	38975795	8	17	RSASPRRSR	TTGTGACAAATGCAGGTCACGGTCTAG

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 KMT2E-SRSF7

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
Non-Cancer	KMT2E-SRSF7	chr7	104704027	ENST00000257745	chr2	38975795	ENST00000409276	ERR315487

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Potential target of CAR-T therapy development for KMT2E-SRSF7

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 KMT2E-SRSF7

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 KMT2E-SRSF7

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)