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Fusion Protein:TRAF3IP2-FYN

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TRAF3IP2-FYN
	FusionPDB ID: 93663
	FusionGDB2.0 ID: 93663
		Hgene	Tgene
	Gene symbol	TRAF3IP2	FYN
	Gene ID	10758	2534
	Gene name	TRAF3 interacting protein 2	FYN proto-oncogene, Src family tyrosine kinase
	Synonyms	ACT1\|C6orf2\|C6orf4\|C6orf5\|C6orf6\|CANDF8\|CIKS\|PSORS13	SLK\|SYN\|p59-FYN
	Cytomap	6q21	6q21
	Type of gene	protein-coding	protein-coding
	Description	adapter protein CIKSNFkB-activating protein ACT1connection to IKK and SAPK/JNKnuclear factor NF-kappa-B activator 1symbol withdrawn, see C6orf4	tyrosine-protein kinase FynFYN oncogene related to SRC, FGR, YESOKT3-induced calcium influx regulatorc-syn protooncogeneproto-oncogene Synproto-oncogene c-Fynsrc-like kinasesrc/yes-related noveltyrosine kinase p59fyn(T)
	Modification date	20200313	20200327
	UniProtAcc	.	C1orf168 Main function of 5'-partner protein: 728
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000340026, ENST00000359831, ENST00000368735, ENST00000368761, ENST00000392556, ENST00000368731,	ENST00000476769, ENST00000229470, ENST00000229471, ENST00000354650, ENST00000356013, ENST00000368667, ENST00000368678, ENST00000368682, ENST00000538466,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 4 X 4=48	19 X 14 X 12=3192
	# samples	4	27
	** MAII score	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(27/3192*10)=-3.56342933917152 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: TRAF3IP2 [Title/Abstract] AND FYN [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TRAF3IP2 [Title/Abstract] AND FYN [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TRAF3IP2(111887647)-FYN(111995833), # samples:2
Anticipated loss of major functional domain due to fusion event.	TRAF3IP2-FYN 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. TRAF3IP2-FYN 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. TRAF3IP2-FYN 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. TRAF3IP2-FYN 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. TRAF3IP2-FYN seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. TRAF3IP2-FYN seems lost the major protein functional domain in Tgene partner, which is a kinase 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	TRAF3IP2	GO:0002230	positive regulation of defense response to virus by host	23066157
Tgene	FYN	GO:0050852	T cell receptor signaling pathway	7722293

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:111887647/chr6:111995833)
- 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 TRAF3IP2 (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 FYN (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)
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000368682	FYN	chr6	111995833	-	3839	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000354650	FYN	chr6	111995833	-	3839	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000229471	FYN	chr6	111995833	-	2889	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000368667	FYN	chr6	111995833	-	2889	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000368678	FYN	chr6	111995833	-	2885	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000229470	FYN	chr6	111995833	-	2877	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000356013	FYN	chr6	111995833	-	2877	2091	588	2228	546
ENST00000392556	TRAF3IP2	chr6	111887647	-	ENST00000538466	FYN	chr6	111995833	-	2877	2091	588	2228	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000368682	FYN	chr6	111995833	-	3846	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000354650	FYN	chr6	111995833	-	3846	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000229471	FYN	chr6	111995833	-	2896	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000368667	FYN	chr6	111995833	-	2896	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000368678	FYN	chr6	111995833	-	2892	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000229470	FYN	chr6	111995833	-	2884	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000356013	FYN	chr6	111995833	-	2884	2098	595	2235	546
ENST00000340026	TRAF3IP2	chr6	111887647	-	ENST00000538466	FYN	chr6	111995833	-	2884	2098	595	2235	546

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
ENST00000392556	ENST00000368682	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.00258892	0.9974111
ENST00000392556	ENST00000354650	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.00258892	0.9974111
ENST00000392556	ENST00000229471	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.01238893	0.987611
ENST00000392556	ENST00000368667	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.01238893	0.987611
ENST00000392556	ENST00000368678	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.012327708	0.98767227
ENST00000392556	ENST00000229470	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.012919379	0.98708063
ENST00000392556	ENST00000356013	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.012919379	0.98708063
ENST00000392556	ENST00000538466	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.012919379	0.98708063
ENST00000340026	ENST00000368682	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.002675285	0.9973247
ENST00000340026	ENST00000354650	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.002675285	0.9973247
ENST00000340026	ENST00000229471	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.012683788	0.98731625
ENST00000340026	ENST00000368667	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.012683788	0.98731625
ENST00000340026	ENST00000368678	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.01262177	0.9873782
ENST00000340026	ENST00000229470	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.013256474	0.98674357
ENST00000340026	ENST00000356013	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.013256474	0.98674357
ENST00000340026	ENST00000538466	TRAF3IP2	chr6	111887647	-	FYN	chr6	111995833	-	0.013256474	0.98674357

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 TRAF3IP2-FYN

+/-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
TRAF3IP2	chr6	111887647	FYN	chr6	111995833	2091	380	LECPAELRPQVPQPPSPAAVPRPPSN
TRAF3IP2	chr6	111887647	FYN	chr6	111995833	2098	380	LECPAELRPQVPQPPSPAAVPRPPSN

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Potential FusionNeoAntigen Information of TRAF3IP2-FYN 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.

TRAF3IP2-FYN_111887647_111995833.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)
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:01	QPPSPAAV	0.9954	0.9722	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:02	QPPSPAAV	0.9897	0.9738	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:01	VPQPPSPA	0.985	0.5325	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:01	VPQPPSPA	0.9842	0.5587	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:05	VPQPPSPAA	0.997	0.7431	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:02	VPQPPSPAA	0.9964	0.7639	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:01	VPQPPSPAA	0.993	0.7974	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:01	VPQPPSPAA	0.9859	0.6992	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B39:06	VPQPPSPAA	0.9636	0.9503	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:03	VPQPPSPAA	0.9308	0.7996	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:08	VPQPPSPAA	0.8747	0.8503	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:02	VPQPPSPAA	0.8348	0.9746	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:04	VPQPPSPAA	0.8348	0.9746	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:02	VPQPPSPAA	0.8251	0.9073	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:01	VPQPPSPAA	0.8129	0.9278	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:01	VPQPPSPAA	0.8044	0.8188	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:05	VPQPPSPAA	0.802	0.7846	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B81:01	VPQPPSPAA	0.6774	0.8037	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B08:09	VPQPPSPAA	0.6745	0.8809	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B82:01	VPQPPSPAA	0.6386	0.754	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:05	VPQPPSPAAV	0.9962	0.7891	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:02	VPQPPSPAAV	0.996	0.8029	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:01	VPQPPSPAAV	0.9897	0.9366	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:02	VPQPPSPAAV	0.9831	0.9537	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B45:01	AELRPQVPQP	0.9806	0.9889	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:01	VPQPPSPAAV	0.9788	0.8727	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:01	VPQPPSPAAV	0.9762	0.9663	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B50:02	AELRPQVPQP	0.9561	0.8113	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:02	VPQPPSPAAV	0.9475	0.9753	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:04	VPQPPSPAAV	0.9475	0.9753	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:03	VPQPPSPAAV	0.9379	0.7691	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:01	QVPQPPSPAA	0.8909	0.8324	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:01	QVPQPPSPAA	0.8687	0.8935	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B82:01	QVPQPPSPAA	0.8532	0.8196	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:05	QVPQPPSPAA	0.8486	0.7971	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B41:01	AELRPQVPQP	0.8357	0.9814	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B81:01	VPQPPSPAAV	0.8083	0.8694	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B50:01	AELRPQVPQP	0.7706	0.8986	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B82:01	VPQPPSPAAV	0.6554	0.782	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:05	RPQVPQPPSPA	0.9964	0.7827	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:02	RPQVPQPPSPA	0.9961	0.7855	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:01	RPQVPQPPSPA	0.9726	0.5933	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:01	RPQVPQPPSPA	0.8937	0.6169	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:01	VPQPPSPA	0.9951	0.8763	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B54:01	VPQPPSPA	0.9916	0.7712	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:01	QPPSPAAV	0.9894	0.9795	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B39:10	QPPSPAAV	0.5568	0.991	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B54:01	VPQPPSPAA	0.997	0.9107	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:12	VPQPPSPAA	0.9959	0.7972	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:04	VPQPPSPAA	0.9641	0.8932	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:04	VPQPPSPAA	0.9637	0.7661	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B73:01	LRPQVPQPP	0.9402	0.9216	6	15
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:01	VPQPPSPAA	0.9096	0.9514	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:08	VPQPPSPAA	0.8497	0.7683	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:12	VPQPPSPAA	0.8348	0.9746	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B42:02	VPQPPSPAA	0.8139	0.7642	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B42:01	VPQPPSPAA	0.7245	0.7557	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B39:10	VPQPPSPAA	0.6489	0.974	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:12	VPQPPSPAAV	0.9949	0.8098	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B54:01	VPQPPSPAAV	0.9916	0.9642	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:01	VPQPPSPAAV	0.9885	0.9763	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:04	VPQPPSPAAV	0.976	0.7945	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B40:06	AELRPQVPQP	0.967	0.9221	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:04	VPQPPSPAAV	0.9594	0.963	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:08	VPQPPSPAAV	0.9502	0.8762	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:12	VPQPPSPAAV	0.9475	0.9753	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B42:02	VPQPPSPAAV	0.94	0.8308	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B42:01	VPQPPSPAAV	0.9248	0.8231	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B54:01	QVPQPPSPAA	0.9102	0.9418	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:12	QVPQPPSPAA	0.8035	0.7892	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B39:10	VPQPPSPAAV	0.7214	0.9847	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:04	QVPQPPSPAA	0.6139	0.9519	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:01	QVPQPPSPAA	0.557	0.98	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:12	RPQVPQPPSPA	0.9867	0.8391	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:04	RPQVPQPPSPA	0.9838	0.7941	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:02	VPQPPSPA	0.9959	0.9009	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:13	QPPSPAAV	0.9953	0.9473	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:14	QPPSPAAV	0.9938	0.9584	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:05	VPQPPSPA	0.9928	0.7771	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:21	QPPSPAAV	0.9849	0.9652	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:29	QPPSPAAV	0.982	0.8918	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	VPQPPSPA	0.9709	0.5928	10	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	PQPPSPAA	0.8832	0.8643	11	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B59:01	QPPSPAAV	0.8206	0.9683	12	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:22	VPQPPSPAA	0.9964	0.7639	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:09	VPQPPSPAA	0.9962	0.7974	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	VPQPPSPAA	0.9909	0.7783	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:05	VPQPPSPAA	0.9843	0.875	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B59:01	VPQPPSPAA	0.9776	0.7767	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:04	VPQPPSPAA	0.9744	0.7485	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:02	VPQPPSPAA	0.9641	0.8932	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:26	VPQPPSPAA	0.9355	0.6905	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:13	VPQPPSPAA	0.9189	0.8054	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:22	VPQPPSPAA	0.9095	0.8207	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:02	VPQPPSPAA	0.8831	0.945	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B67:01	VPQPPSPAA	0.8818	0.9734	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:29	VPQPPSPAA	0.8655	0.8445	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:09	VPQPPSPAA	0.8348	0.9746	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:14	VPQPPSPAA	0.8266	0.9054	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:30	VPQPPSPAA	0.8121	0.7869	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:17	VPQPPSPAA	0.8121	0.7869	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:11	VPQPPSPAA	0.809	0.8468	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:09	VPQPPSPAA	0.8087	0.9163	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:13	VPQPPSPAA	0.8073	0.9185	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:77	VPQPPSPAA	0.8044	0.8188	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:23	VPQPPSPAA	0.7968	0.8283	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:21	VPQPPSPAA	0.7128	0.9219	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:05	VPQPPSPAA	0.6718	0.629	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B82:02	VPQPPSPAA	0.6386	0.754	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:24	VPQPPSPAA	0.604	0.8443	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B18:07	VPQPPSPAA	0.1074	0.8547	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:43	VPQPPSPAA	0.0345	0.8901	10	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:22	VPQPPSPAAV	0.996	0.8029	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:09	VPQPPSPAAV	0.9957	0.8268	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:22	VPQPPSPAAV	0.9902	0.8803	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:05	VPQPPSPAAV	0.9863	0.9324	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:02	VPQPPSPAAV	0.9822	0.973	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:13	VPQPPSPAAV	0.9755	0.9473	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	VPQPPSPAAV	0.9716	0.9229	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:04	VPQPPSPAAV	0.9707	0.8203	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:14	VPQPPSPAAV	0.9703	0.9347	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:29	VPQPPSPAAV	0.9701	0.8826	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:09	VPQPPSPAAV	0.9674	0.9525	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B59:01	VPQPPSPAAV	0.9602	0.9217	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:02	VPQPPSPAAV	0.9594	0.963	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:06	VPQPPSPAAV	0.9532	0.9464	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B35:09	VPQPPSPAAV	0.9475	0.9753	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:26	VPQPPSPAAV	0.9352	0.727	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:05	VPQPPSPAAV	0.9294	0.7042	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B51:21	VPQPPSPAAV	0.9173	0.9632	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B82:02	QVPQPPSPAA	0.8532	0.8196	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	QVPQPPSPAA	0.8411	0.8549	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B67:01	VPQPPSPAAV	0.7981	0.9877	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:04	QVPQPPSPAA	0.7816	0.8641	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B50:04	AELRPQVPQP	0.7706	0.8986	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B50:05	AELRPQVPQP	0.7706	0.8986	4	14
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:05	QVPQPPSPAA	0.7057	0.9188	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B82:02	VPQPPSPAAV	0.6554	0.782	10	20
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	RPQVPQPPSP	0.6239	0.5202	7	17
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B56:02	QVPQPPSPAA	0.6139	0.9519	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B78:02	QVPQPPSPAA	0.4624	0.978	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B67:01	QVPQPPSPAA	0.3306	0.988	9	19
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B07:22	RPQVPQPPSPA	0.9961	0.7855	7	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	HLA-B55:02	RPQVPQPPSPA	0.9338	0.6733	7	18

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Potential FusionNeoAntigen Information of TRAF3IP2-FYN in HLA II

TRAF3IP2-FYN_111887647_111995833.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)
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	DRB4-0101	PAELRPQVPQPPSPA	3	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	DRB4-0103	PAELRPQVPQPPSPA	3	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	DRB4-0104	PAELRPQVPQPPSPA	3	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	DRB4-0106	PAELRPQVPQPPSPA	3	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	DRB4-0107	PAELRPQVPQPPSPA	3	18
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	2098	DRB4-0108	PAELRPQVPQPPSPA	3	18

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Fusion breakpoint peptide structures of TRAF3IP2-FYN

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
5548	LRPQVPQPPSPAAV	TRAF3IP2	FYN	chr6	111887647	chr6	111995833	2098

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TRAF3IP2-FYN

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	5548	LRPQVPQPPSPAAV	-7.15543	-7.26883
HLA-B14:02	3BVN	5548	LRPQVPQPPSPAAV	-4.77435	-5.80965
HLA-B52:01	3W39	5548	LRPQVPQPPSPAAV	-6.80875	-6.92215
HLA-B52:01	3W39	5548	LRPQVPQPPSPAAV	-4.20386	-5.23916
HLA-A11:01	4UQ2	5548	LRPQVPQPPSPAAV	-7.5194	-8.5547
HLA-A11:01	4UQ2	5548	LRPQVPQPPSPAAV	-6.9601	-7.0735
HLA-A24:02	5HGA	5548	LRPQVPQPPSPAAV	-7.52403	-7.63743
HLA-A24:02	5HGA	5548	LRPQVPQPPSPAAV	-5.82433	-6.85963
HLA-B27:05	6PYJ	5548	LRPQVPQPPSPAAV	-3.28285	-4.31815
HLA-B44:05	3DX8	5548	LRPQVPQPPSPAAV	-5.91172	-6.94702
HLA-B44:05	3DX8	5548	LRPQVPQPPSPAAV	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of TRAF3IP2-FYN

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
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	10	18	VPQPPSPA	CATCGAATGGTGCAAAGTTCCCCA
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	10	19	VPQPPSPAA	CATCGAATGGTGCAAAGTTCCCCATCA
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	10	20	VPQPPSPAAV	CATCGAATGGTGCAAAGTTCCCCATCAAGT
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	11	19	PQPPSPAA	CGAATGGTGCAAAGTTCCCCATCA
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	12	20	QPPSPAAV	ATGGTGCAAAGTTCCCCATCAAGT
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	4	14	AELRPQVPQP	TTACATACTAAGTACATTCATCGAATGGTG
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	6	15	LRPQVPQPP	ACTAAGTACATTCATCGAATGGTGCAA
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	7	17	RPQVPQPPSP	AAGTACATTCATCGAATGGTGCAAAGTTCC
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	7	18	RPQVPQPPSPA	AAGTACATTCATCGAATGGTGCAAAGTTCCCCA
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	9	19	QVPQPPSPAA	ATTCATCGAATGGTGCAAAGTTCCCCATCA

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
TRAF3IP2-FYN	chr6	111887647	chr6	111995833	3	18	PAELRPQVPQPPSPA	GGCTTACATACTAAGTACATTCATCGAATGGTGCAAAGTTCCCCA

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Information of the samples that have these potential fusion neoantigens of TRAF3IP2-FYN

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
UCEC	TRAF3IP2-FYN	chr6	111887647	ENST00000340026	chr6	111995833	ENST00000229470	TCGA-D1-A3DG-01A

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Potential target of CAR-T therapy development for TRAF3IP2-FYN

Predicted 3D structure. We used RoseTTAFold.

505_TRAF3IP2-FYN_4dd40_pred.pdb

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
TRAF3IP2	chr6	111887647	ENST00000340026	FYN	chr6	111995833	ENST00000229470

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Related Drugs to TRAF3IP2-FYN

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 TRAF3IP2-FYN

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)