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Fusion Protein:CBFB-NUTF2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CBFB-NUTF2
	FusionPDB ID: 13375
	FusionGDB2.0 ID: 13375
		Hgene	Tgene
	Gene symbol	CBFB	NUTF2
	Gene ID	865	10204
	Gene name	core-binding factor subunit beta	nuclear transport factor 2
	Synonyms	PEBP2B	NTF-2\|NTF2\|PP15
	Cytomap	16q22.1	16q22.1
	Type of gene	protein-coding	protein-coding
	Description	core-binding factor subunit betaCBF-betaPEA2-betaPEBP2-betaSL3-3 enhancer factor 1 beta subunitSL3-3 enhancer factor 1 subunit betaSL3/AKV core-binding factor beta subunitcore-binding factor beta subunitpolyomavirus enhancer binding protein 2, bet	nuclear transport factor 2placental protein 15
	Modification date	20200320	20200313
	UniProtAcc	Q13951 Main function of 5'-partner protein: FUNCTION: Forms the heterodimeric complex core-binding factor (CBF) with RUNX family proteins (RUNX1, RUNX2, and RUNX3). RUNX members modulate the transcription of their target genes through recognizing the core consensus binding sequence 5'-TGTGGT-3', or very rarely, 5'-TGCGGT-3', within their regulatory regions via their runt domain, while CBFB is a non-DNA-binding regulatory subunit that allosterically enhances the sequence-specific DNA-binding capacity of RUNX. The heterodimers bind to the core site of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL3 and GM-CSF promoters. CBF complexes repress ZBTB7B transcription factor during cytotoxic (CD8+) T cell development. They bind to RUNX-binding sequence within the ZBTB7B locus acting as transcriptional silencer and allowing for cytotoxic T cell differentiation. {ECO:0000250\|UniProtKB:Q08024}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000561924, ENST00000290858, ENST00000412916, ENST00000568858,	ENST00000219169, ENST00000568396, ENST00000569436,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	17 X 18 X 12=3672	12 X 9 X 6=648
	# samples	33	15
	** MAII score	log2(33/3672*10)=-3.47602812916799 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/648*10)=-2.11103131238874 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CBFB [Title/Abstract] AND NUTF2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CBFB [Title/Abstract] AND NUTF2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CBFB(67070658)-NUTF2(67902243), # samples:2
Anticipated loss of major functional domain due to fusion event.	CBFB-NUTF2 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. CBFB-NUTF2 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	NUTF2	GO:0006606	protein import into nucleus	7744965\|10679025
Tgene	NUTF2	GO:0006611	protein export from nucleus	16449645

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:67070658/chr16:67902243)
- 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 CBFB (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 NUTF2 (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)
ENST00000290858	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902243	+	2482	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902243	+	1238	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902243	+	1238	543	261	827	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902243	+	2384	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902243	+	1140	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902243	+	1140	445	163	729	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902242	+	2482	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902242	+	1238	543	261	827	188
ENST00000290858	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902242	+	1238	543	261	827	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000219169	NUTF2	chr16	67902242	+	2384	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000569436	NUTF2	chr16	67902242	+	1140	445	163	729	188
ENST00000412916	CBFB	chr16	67070658	+	ENST00000568396	NUTF2	chr16	67902242	+	1140	445	163	729	188

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
ENST00000290858	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.004257829	0.99574214
ENST00000290858	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.005475971	0.994524
ENST00000290858	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.005475971	0.994524
ENST00000412916	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.005038908	0.99496114
ENST00000412916	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.004547407	0.9954526
ENST00000412916	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902243	+	0.004547407	0.9954526
ENST00000290858	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.004257829	0.99574214
ENST00000290858	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.005475971	0.994524
ENST00000290858	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.005475971	0.994524
ENST00000412916	ENST00000219169	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.005038908	0.99496114
ENST00000412916	ENST00000569436	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.004547407	0.9954526
ENST00000412916	ENST00000568396	CBFB	chr16	67070658	+	NUTF2	chr16	67902242	+	0.004547407	0.9954526

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 CBFB-NUTF2

+/-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
CBFB	chr16	67070658	NUTF2	chr16	67902242	445	94	SREYVDLEREAGKIDASCLTWEGQQF
CBFB	chr16	67070658	NUTF2	chr16	67902242	543	94	SREYVDLEREAGKIDASCLTWEGQQF
CBFB	chr16	67070658	NUTF2	chr16	67902243	445	94	SREYVDLEREAGKIDASCLTWEGQQF
CBFB	chr16	67070658	NUTF2	chr16	67902243	543	94	SREYVDLEREAGKIDASCLTWEGQQF

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Potential FusionNeoAntigen Information of CBFB-NUTF2 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.

CBFB-NUTF2_67070658_67902242.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)
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B58:01	KIDASCLTW	0.9965	0.9835	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B57:01	KIDASCLTW	0.9932	0.9912	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B58:02	KIDASCLTW	0.9831	0.975	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-A32:13	KIDASCLTW	0.9561	0.9822	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B57:03	KIDASCLTW	0.9526	0.9951	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B41:01	REAGKIDAS	0.2063	0.6154	8	17
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B50:01	REAGKIDAS	0.0185	0.5988	8	17
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B50:01	LEREAGKIDA	0.7729	0.6505	6	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B57:04	KIDASCLTW	0.9944	0.8012	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B57:10	KIDASCLTW	0.9932	0.9912	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-A32:01	KIDASCLTW	0.9824	0.9934	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B57:02	KIDASCLTW	0.9543	0.8963	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B58:06	KIDASCLTW	0.9467	0.979	12	21
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B50:05	REAGKIDAS	0.0185	0.5988	8	17
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B50:04	REAGKIDAS	0.0185	0.5988	8	17
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B50:05	LEREAGKIDA	0.7729	0.6505	6	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B50:04	LEREAGKIDA	0.7729	0.6505	6	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	HLA-B41:03	REAGKIDASCL	0.9922	0.6305	8	19

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Potential FusionNeoAntigen Information of CBFB-NUTF2 in HLA II

CBFB-NUTF2_67070658_67902242.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)
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0466	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0801	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0802	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0802	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0803	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0805	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0805	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0807	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0808	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0809	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0809	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0811	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0813	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0813	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0814	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0815	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0815	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0816	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0818	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0821	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0821	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0823	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0824	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0824	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0826	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0827	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0829	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0830	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0830	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0831	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0832	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0833	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0835	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0836	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0837	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0838	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0839	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-0840	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1101	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1101	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1105	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1105	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1108	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1108	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1109	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1109	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1110	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1110	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1111	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1112	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1112	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1115	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1115	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1119	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1119	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1124	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1124	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1127	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1127	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1128	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1128	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1129	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1129	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1130	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1131	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1131	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1132	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1132	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1133	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1133	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1137	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1137	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1139	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1139	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1145	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1149	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1149	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1151	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1151	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1153	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1161	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1161	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1162	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1162	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1164	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1164	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1166	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1166	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1169	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1169	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1172	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1172	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1173	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1173	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1174	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1174	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1175	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1175	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1179	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1180	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1180	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1181	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1181	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1182	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1183	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1187	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1187	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1190	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1190	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1191	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1191	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1193	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1193	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1194	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1194	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1195	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1195	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1196	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1196	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1303	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1305	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1305	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1307	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1307	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-13100	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-13100	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-13101	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1310	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1312	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1313	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1314	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1314	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1321	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1321	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1326	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1326	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1330	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1337	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1337	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1346	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1346	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1347	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1347	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1349	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1349	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1350	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1350	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1355	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1356	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1356	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1360	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1360	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1362	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1362	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1363	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1366	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1382	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1382	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1385	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1385	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1386	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1386	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1388	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1390	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1395	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1402	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1402	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1403	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1409	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1409	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1413	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1419	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1422	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1422	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1425	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1425	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1427	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1427	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1430	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1430	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1440	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1441	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1441	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1446	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1449	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1451	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1453	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1453	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1463	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1467	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1469	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1469	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1477	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1485	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1489	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1494	SREYVDLEREAGKID	0	15
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1494	REYVDLEREAGKIDA	1	16
CBFB-NUTF2	chr16	67070658	chr16	67902242	543	DRB1-1498	SREYVDLEREAGKID	0	15

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Fusion breakpoint peptide structures of CBFB-NUTF2

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
4928	LEREAGKIDASCLT	CBFB	NUTF2	chr16	67070658	chr16	67902242	543

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CBFB-NUTF2

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	4928	LEREAGKIDASCLT	-6.01316	-6.12656
HLA-B14:02	3BVN	4928	LEREAGKIDASCLT	-3.92858	-4.96388
HLA-B52:01	3W39	4928	LEREAGKIDASCLT	-5.92102	-6.95632
HLA-B52:01	3W39	4928	LEREAGKIDASCLT	-4.84472	-4.95812
HLA-A24:02	5HGA	4928	LEREAGKIDASCLT	-8.26357	-9.29887
HLA-A24:02	5HGA	4928	LEREAGKIDASCLT	-7.03366	-7.14706
HLA-B44:05	3DX8	4928	LEREAGKIDASCLT	-6.13971	-6.25311
HLA-B44:05	3DX8	4928	LEREAGKIDASCLT	-5.20728	-6.24258
HLA-A02:01	6TDR	4928	LEREAGKIDASCLT	-5.28864	-5.40204

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Vaccine Design for the FusionNeoAntigens of CBFB-NUTF2

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
CBFB-NUTF2	chr16	67070658	chr16	67902242	12	21	KIDASCLTW	AAGATTGACGCGTCATGCCTTACGTGG
CBFB-NUTF2	chr16	67070658	chr16	67902242	6	16	LEREAGKIDA	TTAGAAAGAGAAGCAGGCAAGATTGACGCG
CBFB-NUTF2	chr16	67070658	chr16	67902242	8	17	REAGKIDAS	AGAGAAGCAGGCAAGATTGACGCGTCA
CBFB-NUTF2	chr16	67070658	chr16	67902242	8	19	REAGKIDASCL	AGAGAAGCAGGCAAGATTGACGCGTCATGCCTT

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
CBFB-NUTF2	chr16	67070658	chr16	67902242	0	15	SREYVDLEREAGKID	AGCCGAGAGTATGTCGACTTAGAAAGAGAAGCAGGCAAGATTGAC
CBFB-NUTF2	chr16	67070658	chr16	67902242	1	16	REYVDLEREAGKIDA	CGAGAGTATGTCGACTTAGAAAGAGAAGCAGGCAAGATTGACGCG

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Information of the samples that have these potential fusion neoantigens of CBFB-NUTF2

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
LUAD	CBFB-NUTF2	chr16	67070658	ENST00000290858	chr16	67902242	ENST00000219169	TCGA-78-8660

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Potential target of CAR-T therapy development for CBFB-NUTF2

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 CBFB-NUTF2

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 CBFB-NUTF2

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
Hgene	CBFB	C0023467	Leukemia, Myelocytic, Acute	2	CTD_human
Hgene	CBFB	C0023479	Acute myelomonocytic leukemia	2	CTD_human;ORPHANET
Hgene	CBFB	C0026998	Acute Myeloid Leukemia, M1	2	CTD_human
Hgene	CBFB	C1879321	Acute Myeloid Leukemia (AML-M2)	2	CTD_human
Hgene	CBFB	C0005941	Bone Diseases, Developmental	1	CTD_human
Hgene	CBFB	C0008925	Cleft Palate	1	CTD_human
Hgene	CBFB	C0018798	Congenital Heart Defects	1	CTD_human
Hgene	CBFB	C0029396	Heterotopic Ossification	1	CTD_human
Hgene	CBFB	C1837218	Cleft palate, isolated	1	CTD_human

	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)