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Fusion Protein:PAX3-MAML3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PAX3-MAML3
	FusionPDB ID: 62941
	FusionGDB2.0 ID: 62941
		Hgene	Tgene
	Gene symbol	PAX3	MAML3
	Gene ID	5077	55534
	Gene name	paired box 3	mastermind like transcriptional coactivator 3
	Synonyms	CDHS\|HUP2\|WS1\|WS3	CAGH3\|ERDA3\|GDN\|MAM-2\|MAM2\|TNRC3\|mam-3
	Cytomap	2q36.1	4q31.1
	Type of gene	protein-coding	protein-coding
	Description	paired box protein Pax-3paired box homeotic gene 3paired domain gene 3paired domain gene HuP2transcriptional factor PAX3	mastermind-like protein 3CAG repeat containing (glia-derived nexin I alpha)expanded repeat domain, CAG/CTG 3polyglutamine richtrinucleotide repeat containing 3
	Modification date	20200313	20200313
	UniProtAcc	PAXBP1 Main function of 5'-partner protein: 917	Q96JK9 Main function of 5'-partner protein: FUNCTION: Acts as a transcriptional coactivator for NOTCH proteins. Has been shown to amplify NOTCH-induced transcription of HES1. {ECO:0000269\|PubMed:12370315, ECO:0000269\|PubMed:12386158}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000336840, ENST00000344493, ENST00000350526, ENST00000392069, ENST00000392070, ENST00000409551, ENST00000464706, ENST00000258387, ENST00000409828,	ENST00000398940, ENST00000327122, ENST00000509479,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 10 X 5=350	13 X 13 X 8=1352
	# samples	8	16
	** MAII score	log2(8/350*10)=-2.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/1352*10)=-3.07895134139482 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PAX3 [Title/Abstract] AND MAML3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PAX3 [Title/Abstract] AND MAML3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PAX3(223096876)-MAML3(140812024), # samples:1 PAX3(223084859)-MAML3(140812124), # samples:1 PAX3(223096797)-MAML3(140812124), # samples:1
Anticipated loss of major functional domain due to fusion event.	PAX3-MAML3 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. PAX3-MAML3 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. PAX3-MAML3 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. PAX3-MAML3 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
Hgene	PAX3	GO:0045893	positive regulation of transcription, DNA-templated	11863357
Hgene	PAX3	GO:0045944	positive regulation of transcription by RNA polymerase II	11863357
Tgene	MAML3	GO:0007219	Notch signaling pathway	12370315
Tgene	MAML3	GO:0045944	positive regulation of transcription by RNA polymerase II	12370315

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:223096876/chr4:140812024)
- 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 PAX3 (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 MAML3 (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)
ENST00000392069	PAX3	chr2	223084859	-	ENST00000509479	MAML3	chr4	140812124	-	7058	1539	366	4487	1373
ENST00000392069	PAX3	chr2	223084859	-	ENST00000327122	MAML3	chr4	140812124	-	3168	1539	366	3167	934
ENST00000344493	PAX3	chr2	223084859	-	ENST00000509479	MAML3	chr4	140812124	-	7073	1554	381	4502	1373
ENST00000344493	PAX3	chr2	223084859	-	ENST00000327122	MAML3	chr4	140812124	-	3183	1554	381	3182	934
ENST00000350526	PAX3	chr2	223084859	-	ENST00000509479	MAML3	chr4	140812124	-	6829	1310	137	4258	1373
ENST00000350526	PAX3	chr2	223084859	-	ENST00000327122	MAML3	chr4	140812124	-	2939	1310	137	2938	934
ENST00000336840	PAX3	chr2	223084859	-	ENST00000509479	MAML3	chr4	140812124	-	7073	1554	381	4502	1373
ENST00000336840	PAX3	chr2	223084859	-	ENST00000327122	MAML3	chr4	140812124	-	3183	1554	381	3182	934
ENST00000392070	PAX3	chr2	223084859	-	ENST00000509479	MAML3	chr4	140812124	-	7073	1554	381	4502	1373
ENST00000392070	PAX3	chr2	223084859	-	ENST00000327122	MAML3	chr4	140812124	-	3183	1554	381	3182	934
ENST00000409551	PAX3	chr2	223084859	-	ENST00000509479	MAML3	chr4	140812124	-	6969	1450	280	4398	1372
ENST00000409551	PAX3	chr2	223084859	-	ENST00000327122	MAML3	chr4	140812124	-	3079	1450	280	3078	933
ENST00000392069	PAX3	chr2	223096797	-	ENST00000509479	MAML3	chr4	140812124	-	6677	1158	366	4106	1246
ENST00000392069	PAX3	chr2	223096797	-	ENST00000327122	MAML3	chr4	140812124	-	2787	1158	366	2786	807
ENST00000344493	PAX3	chr2	223096797	-	ENST00000509479	MAML3	chr4	140812124	-	6692	1173	381	4121	1246
ENST00000344493	PAX3	chr2	223096797	-	ENST00000327122	MAML3	chr4	140812124	-	2802	1173	381	2801	807
ENST00000350526	PAX3	chr2	223096797	-	ENST00000509479	MAML3	chr4	140812124	-	6448	929	137	3877	1246
ENST00000350526	PAX3	chr2	223096797	-	ENST00000327122	MAML3	chr4	140812124	-	2558	929	137	2557	807
ENST00000336840	PAX3	chr2	223096797	-	ENST00000509479	MAML3	chr4	140812124	-	6692	1173	381	4121	1246
ENST00000336840	PAX3	chr2	223096797	-	ENST00000327122	MAML3	chr4	140812124	-	2802	1173	381	2801	807
ENST00000392070	PAX3	chr2	223096797	-	ENST00000509479	MAML3	chr4	140812124	-	6692	1173	381	4121	1246
ENST00000392070	PAX3	chr2	223096797	-	ENST00000327122	MAML3	chr4	140812124	-	2802	1173	381	2801	807
ENST00000409551	PAX3	chr2	223096797	-	ENST00000509479	MAML3	chr4	140812124	-	6588	1069	280	4017	1245
ENST00000409551	PAX3	chr2	223096797	-	ENST00000327122	MAML3	chr4	140812124	-	2698	1069	280	2697	806

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
ENST00000392069	ENST00000509479	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.007691321	0.9923086
ENST00000392069	ENST00000327122	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.061968062	0.938032
ENST00000344493	ENST00000509479	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.007641885	0.99235815
ENST00000344493	ENST00000327122	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.063811004	0.936189
ENST00000350526	ENST00000509479	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.006162272	0.9938378
ENST00000350526	ENST00000327122	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.04372464	0.95627534
ENST00000336840	ENST00000509479	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.007641885	0.99235815
ENST00000336840	ENST00000327122	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.063811004	0.936189
ENST00000392070	ENST00000509479	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.007641885	0.99235815
ENST00000392070	ENST00000327122	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.063811004	0.936189
ENST00000409551	ENST00000509479	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.006683484	0.99331653
ENST00000409551	ENST00000327122	PAX3	chr2	223084859	-	MAML3	chr4	140812124	-	0.04928075	0.9507193
ENST00000392069	ENST00000509479	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.007079103	0.99292094
ENST00000392069	ENST00000327122	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.09174849	0.90825146
ENST00000344493	ENST00000509479	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.007020851	0.9929791
ENST00000344493	ENST00000327122	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.14151075	0.8584892
ENST00000350526	ENST00000509479	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.005645957	0.994354
ENST00000350526	ENST00000327122	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.1784306	0.8215694
ENST00000336840	ENST00000509479	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.007020851	0.9929791
ENST00000336840	ENST00000327122	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.14151075	0.8584892
ENST00000392070	ENST00000509479	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.007020851	0.9929791
ENST00000392070	ENST00000327122	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.14151075	0.8584892
ENST00000409551	ENST00000509479	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.006117674	0.9938823
ENST00000409551	ENST00000327122	PAX3	chr2	223096797	-	MAML3	chr4	140812124	-	0.4242044	0.5757956

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 PAX3-MAML3

+/-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
PAX3	chr2	223084859	MAML3	chr4	140812124	1310	390	NPMNPTIGNGLSPQLQETVKRKLEGA
PAX3	chr2	223084859	MAML3	chr4	140812124	1450	389	NPMNPTIGNGLSPQLQETVKRKLEGA
PAX3	chr2	223084859	MAML3	chr4	140812124	1539	390	NPMNPTIGNGLSPQLQETVKRKLEGA
PAX3	chr2	223084859	MAML3	chr4	140812124	1554	390	NPMNPTIGNGLSPQLQETVKRKLEGA
PAX3	chr2	223096797	MAML3	chr4	140812124	1069	262	ELAQRAKLTEARVQLQETVKRKLEGA
PAX3	chr2	223096797	MAML3	chr4	140812124	1158	263	ELAQRAKLTEARVQLQETVKRKLEGA
PAX3	chr2	223096797	MAML3	chr4	140812124	1173	263	ELAQRAKLTEARVQLQETVKRKLEGA
PAX3	chr2	223096797	MAML3	chr4	140812124	929	263	ELAQRAKLTEARVQLQETVKRKLEGA

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Potential FusionNeoAntigen Information of PAX3-MAML3 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.

PAX3-MAML3_223084859_140812124.msa
PAX3-MAML3_223096797_140812124.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)
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:22	GLSPQLQET	0.9778	0.5004	9	18
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:27	GLSPQLQET	0.9683	0.5766	9	18
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:13	GLSPQLQET	0.9672	0.6782	9	18
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:38	GLSPQLQET	0.9275	0.6548	9	18
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:22	GLSPQLQETV	0.9987	0.5236	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:13	GLSPQLQETV	0.9986	0.6937	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:27	GLSPQLQETV	0.9985	0.5728	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:60	GLSPQLQETV	0.9962	0.5163	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:30	GLSPQLQETV	0.9961	0.5236	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:67	GLSPQLQETV	0.9961	0.5236	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:24	GLSPQLQETV	0.9961	0.5236	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:11	GLSPQLQETV	0.9961	0.5457	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:21	GLSPQLQETV	0.9955	0.6289	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:38	GLSPQLQETV	0.9922	0.6497	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:04	GLSPQLQETV	0.9857	0.7158	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:19	GLSPQLQETV	0.9814	0.5313	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:35	GLSPQLQETV	0.912	0.5354	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:29	GLSPQLQETV	0.8255	0.5253	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:20	GLSPQLQETV	0.8184	0.531	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-B39:10	SPQLQETV	0.204	0.8755	11	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C03:19	IGNGLSPQL	0.9984	0.9732	6	15
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C08:13	IGNGLSPQL	0.938	0.9767	6	15
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C08:04	IGNGLSPQL	0.938	0.9767	6	15
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C01:17	LSPQLQETV	0.8957	0.9762	10	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C01:30	LSPQLQETV	0.7435	0.978	10	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:05	GLSPQLQETV	0.9983	0.5613	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:01	GLSPQLQETV	0.9961	0.5236	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-B51:21	SPQLQETV	0.8022	0.5308	11	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-B51:09	SPQLQETV	0.7937	0.543	11	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-B59:01	SPQLQETV	0.4218	0.6265	11	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C03:05	IGNGLSPQL	0.9974	0.8823	6	15
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:03	GLSPQLQET	0.973	0.6344	9	18
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C01:03	LSPQLQETV	0.97	0.9747	10	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-C01:02	LSPQLQETV	0.9212	0.9741	10	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-B35:13	IGNGLSPQL	0.8657	0.8676	6	15
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-B07:13	IGNGLSPQL	0.2257	0.7747	6	15
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:03	GLSPQLQETV	0.999	0.6532	9	19
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	HLA-A02:06	GLSPQLQETV	0.9955	0.6289	9	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:04	ARVQLQETV	0.9997	0.6505	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:07	ARVQLQETV	0.9996	0.5559	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:06	ARVQLQETV	0.9987	0.9562	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:24	ARVQLQETV	0.9983	0.8821	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:22	KLTEARVQL	0.9954	0.5249	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:01	ARVQLQETV	0.9949	0.9715	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:24	KLTEARVQL	0.9923	0.5715	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:60	KLTEARVQL	0.9923	0.565	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:67	KLTEARVQL	0.9923	0.5715	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:30	KLTEARVQL	0.9923	0.5715	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:11	KLTEARVQL	0.9918	0.585	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:13	KLTEARVQL	0.9898	0.6719	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:16	KLTEARVQL	0.989	0.5158	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B38:02	ARVQLQETV	0.9889	0.9922	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:27	KLTEARVQL	0.9876	0.5484	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:04	KLTEARVQL	0.9863	0.5421	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:21	KLTEARVQL	0.9839	0.6757	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:38	KLTEARVQL	0.9807	0.6834	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A32:13	KLTEARVQL	0.9404	0.9493	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:35	KLTEARVQL	0.9205	0.5777	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:29	KLTEARVQL	0.9197	0.5725	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:20	KLTEARVQL	0.8771	0.5776	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A31:02	VQLQETVKR	0.8339	0.6072	12	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B48:01	KLTEARVQL	0.5848	0.6438	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B13:02	KLTEARVQL	0.137	0.6912	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B13:01	KLTEARVQL	0.1064	0.96	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A74:11	RVQLQETVKR	0.96	0.5699	11	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A74:03	RVQLQETVKR	0.96	0.5699	11	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A74:09	RVQLQETVKR	0.96	0.5699	11	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A31:02	RVQLQETVKR	0.9124	0.5908	11	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B48:01	AKLTEARVQL	0.9022	0.6258	5	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:14	ARVQLQETV	0.9997	0.5325	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:09	ARVQLQETV	0.9961	0.9603	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B73:01	ARVQLQETV	0.9948	0.9356	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:12	ARVQLQETV	0.9938	0.9732	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:05	KLTEARVQL	0.9928	0.528	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:07	KLTEARVQL	0.9928	0.6262	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:01	KLTEARVQL	0.9923	0.5715	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C07:95	ARVQLQETV	0.9848	0.8464	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C01:17	KLTEARVQL	0.9833	0.976	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:05	ARVQLQETV	0.9798	0.9696	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C07:13	KLTEARVQL	0.9011	0.954	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C07:13	ARVQLQETV	0.8689	0.9555	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C01:30	KLTEARVQL	0.7807	0.9668	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C12:16	ARVQLQETV	0.0207	0.9759	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A31:01	RVQLQETVKR	0.9605	0.5463	11	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:06	ARVQLQETV	0.9997	0.7083	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:10	ARVQLQETV	0.9997	0.7096	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B39:31	ARVQLQETV	0.9954	0.9715	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:03	KLTEARVQL	0.9936	0.6112	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A30:01	RVQLQETVK	0.993	0.8672	11	20
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C01:03	KLTEARVQL	0.9911	0.9781	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C07:01	ARVQLQETV	0.989	0.78	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C06:08	ARVQLQETV	0.9847	0.9933	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C01:02	KLTEARVQL	0.9846	0.9742	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:14	KLTEARVQL	0.9841	0.6323	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A02:06	KLTEARVQL	0.9839	0.6757	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A32:01	KLTEARVQL	0.9818	0.9449	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B15:73	KLTEARVQL	0.888	0.8246	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C07:04	KLTEARVQL	0.8799	0.9631	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C17:01	KLTEARVQL	0.7633	0.9347	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B15:30	KLTEARVQL	0.7366	0.77	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C07:22	ARVQLQETV	0.7156	0.7872	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B07:13	KLTEARVQL	0.5044	0.8032	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C06:02	ARVQLQETV	0.1493	0.9956	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-C06:17	ARVQLQETV	0.1493	0.9956	10	19
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B40:21	KLTEARVQL	0.088	0.5167	6	15
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:10	ARVQLQETVK	0.9997	0.7813	10	20
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-A74:01	RVQLQETVKR	0.96	0.5699	11	21
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	HLA-B27:10	ARVQLQETVKR	0.9998	0.6198	10	21

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Potential FusionNeoAntigen Information of PAX3-MAML3 in HLA II

PAX3-MAML3_223084859_140812124.msa
PAX3-MAML3_223096797_140812124.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)
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1189	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1343	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1354	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1354	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1401	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1401	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1416	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1418	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1426	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1426	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1435	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1435	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1438	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1454	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1454	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1458	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1458	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1460	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1460	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1462	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1464	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1470	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1472	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1475	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1486	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1486	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1487	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1487	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1488	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1488	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1490	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1490	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1497	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1497	LSPQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223084859	chr4	140812124	1554	DRB1-1499	SPQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-0303	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1354	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1354	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1401	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1401	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1418	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1426	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1426	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1435	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1435	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1438	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1452	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1454	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1454	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1458	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1458	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1460	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1460	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1464	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1472	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1486	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1486	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1487	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1487	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1488	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1488	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1490	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1490	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1497	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1497	ARVQLQETVKRKLEG	10	25
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB1-1499	RVQLQETVKRKLEGA	11	26
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0106	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0106	TEARVQLQETVKRKL	8	23
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0106	LTEARVQLQETVKRK	7	22
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0111	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0202	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0204	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0205	EARVQLQETVKRKLE	9	24
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0205	TEARVQLQETVKRKL	8	23
PAX3-MAML3	chr2	223096797	chr4	140812124	1173	DRB5-0205	LTEARVQLQETVKRK	7	22

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Fusion breakpoint peptide structures of PAX3-MAML3

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
3696	IGNGLSPQLQETVK	PAX3	MAML3	chr2	223084859	chr4	140812124	1554

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
4409	KLTEARVQLQETVK	PAX3	MAML3	chr2	223096797	chr4	140812124	1173

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PAX3-MAML3

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	3696	IGNGLSPQLQETVK	-7.15543	-7.26883
HLA-B14:02	3BVN	3696	IGNGLSPQLQETVK	-4.77435	-5.80965
HLA-B52:01	3W39	3696	IGNGLSPQLQETVK	-6.80875	-6.92215
HLA-B52:01	3W39	3696	IGNGLSPQLQETVK	-4.20386	-5.23916
HLA-A11:01	4UQ2	3696	IGNGLSPQLQETVK	-7.5194	-8.5547
HLA-A11:01	4UQ2	3696	IGNGLSPQLQETVK	-6.9601	-7.0735
HLA-A24:02	5HGA	3696	IGNGLSPQLQETVK	-7.52403	-7.63743
HLA-A24:02	5HGA	3696	IGNGLSPQLQETVK	-5.82433	-6.85963
HLA-B27:05	6PYJ	3696	IGNGLSPQLQETVK	-3.28285	-4.31815
HLA-B44:05	3DX8	3696	IGNGLSPQLQETVK	-5.91172	-6.94702
HLA-B44:05	3DX8	3696	IGNGLSPQLQETVK	-4.24346	-4.35686
HLA-B14:02	3BVN	4409	KLTEARVQLQETVK	-7.9962	-8.1096
HLA-B14:02	3BVN	4409	KLTEARVQLQETVK	-5.70842	-6.74372
HLA-B52:01	3W39	4409	KLTEARVQLQETVK	-6.83737	-6.95077
HLA-B52:01	3W39	4409	KLTEARVQLQETVK	-4.4836	-5.5189
HLA-A11:01	4UQ2	4409	KLTEARVQLQETVK	-10.0067	-10.1201
HLA-A11:01	4UQ2	4409	KLTEARVQLQETVK	-9.03915	-10.0745
HLA-A24:02	5HGA	4409	KLTEARVQLQETVK	-6.56204	-6.67544
HLA-A24:02	5HGA	4409	KLTEARVQLQETVK	-5.42271	-6.45801
HLA-B44:05	3DX8	4409	KLTEARVQLQETVK	-7.85648	-8.89178
HLA-B44:05	3DX8	4409	KLTEARVQLQETVK	-5.3978	-5.5112
HLA-A02:01	6TDR	4409	KLTEARVQLQETVK	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of PAX3-MAML3

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
PAX3-MAML3	chr2	223084859	chr4	140812124	10	19	LSPQLQETV	TCACCTCAGCTACAAGAGACTGTGAAA
PAX3-MAML3	chr2	223084859	chr4	140812124	11	19	SPQLQETV	CCTCAGCTACAAGAGACTGTGAAA
PAX3-MAML3	chr2	223084859	chr4	140812124	6	15	IGNGLSPQL	GGCAATGGCCTCTCACCTCAGCTACAA
PAX3-MAML3	chr2	223084859	chr4	140812124	9	18	GLSPQLQET	CTCTCACCTCAGCTACAAGAGACTGTG
PAX3-MAML3	chr2	223084859	chr4	140812124	9	19	GLSPQLQETV	CTCTCACCTCAGCTACAAGAGACTGTGAAA
PAX3-MAML3	chr2	223096797	chr4	140812124	10	19	ARVQLQETV	CGAGTACAGCTACAAGAGACTGTGAAA
PAX3-MAML3	chr2	223096797	chr4	140812124	10	20	ARVQLQETVK	CGAGTACAGCTACAAGAGACTGTGAAAAGG
PAX3-MAML3	chr2	223096797	chr4	140812124	10	21	ARVQLQETVKR	CGAGTACAGCTACAAGAGACTGTGAAAAGGAAG
PAX3-MAML3	chr2	223096797	chr4	140812124	11	20	RVQLQETVK	GTACAGCTACAAGAGACTGTGAAAAGG
PAX3-MAML3	chr2	223096797	chr4	140812124	11	21	RVQLQETVKR	GTACAGCTACAAGAGACTGTGAAAAGGAAG
PAX3-MAML3	chr2	223096797	chr4	140812124	12	21	VQLQETVKR	CAGCTACAAGAGACTGTGAAAAGGAAG
PAX3-MAML3	chr2	223096797	chr4	140812124	5	15	AKLTEARVQL	AAGCTCACCGAGGCCCGAGTACAGCTACAA
PAX3-MAML3	chr2	223096797	chr4	140812124	6	15	KLTEARVQL	CTCACCGAGGCCCGAGTACAGCTACAA

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
PAX3-MAML3	chr2	223084859	chr4	140812124	10	25	LSPQLQETVKRKLEG	TCACCTCAGCTACAAGAGACTGTGAAAAGGAAGTTGGAAGGAGCT
PAX3-MAML3	chr2	223084859	chr4	140812124	11	26	SPQLQETVKRKLEGA	CCTCAGCTACAAGAGACTGTGAAAAGGAAGTTGGAAGGAGCTCGA
PAX3-MAML3	chr2	223096797	chr4	140812124	10	25	ARVQLQETVKRKLEG	CGAGTACAGCTACAAGAGACTGTGAAAAGGAAGTTGGAAGGAGCT
PAX3-MAML3	chr2	223096797	chr4	140812124	11	26	RVQLQETVKRKLEGA	GTACAGCTACAAGAGACTGTGAAAAGGAAGTTGGAAGGAGCTCGA
PAX3-MAML3	chr2	223096797	chr4	140812124	7	22	LTEARVQLQETVKRK	ACCGAGGCCCGAGTACAGCTACAAGAGACTGTGAAAAGGAAGTTG
PAX3-MAML3	chr2	223096797	chr4	140812124	8	23	TEARVQLQETVKRKL	GAGGCCCGAGTACAGCTACAAGAGACTGTGAAAAGGAAGTTGGAA
PAX3-MAML3	chr2	223096797	chr4	140812124	9	24	EARVQLQETVKRKLE	GCCCGAGTACAGCTACAAGAGACTGTGAAAAGGAAGTTGGAAGGA

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Information of the samples that have these potential fusion neoantigens of PAX3-MAML3

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
N/A	PAX3-MAML3	chr2	223084859	ENST00000336840	chr4	140812124	ENST00000327122	KF727276
N/A	PAX3-MAML3	chr2	223096797	ENST00000336840	chr4	140812124	ENST00000327122	KF727277

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Potential target of CAR-T therapy development for PAX3-MAML3

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 PAX3-MAML3

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 PAX3-MAML3

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	PAX3	C1847800	Waardenburg Syndrome Type 1	33	CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
Hgene	PAX3	C0079661	Klein's Syndrome	16	CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Hgene	PAX3	C3266898	Waardenburg Syndrome	12	CLINGEN;CTD_human;GENOMICS_ENGLAND
Hgene	PAX3	C1852510	Craniofacial deafness hand syndrome	5	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Hgene	PAX3	C0038219	Status Dysraphicus	4	CTD_human
Hgene	PAX3	C0080178	Spina Bifida	4	CTD_human
Hgene	PAX3	C0266508	Rachischisis	4	CTD_human
Hgene	PAX3	C0011999	Diastematomyelia	3	CTD_human
Hgene	PAX3	C0027794	Neural Tube Defects	3	CTD_human
Hgene	PAX3	C0027806	Neurenteric Cyst	3	CTD_human
Hgene	PAX3	C0080218	Tethered Cord Syndrome	3	CTD_human
Hgene	PAX3	C0152234	Iniencephaly	3	CTD_human
Hgene	PAX3	C0152426	Craniorachischisis	3	CTD_human
Hgene	PAX3	C0266453	Exencephaly	3	CTD_human
Hgene	PAX3	C0344479	Spinal Cord Myelodysplasia	3	CTD_human
Hgene	PAX3	C0599973	Waardenburg Anophthalmia Syndrome	3	ORPHANET
Hgene	PAX3	C0702169	Acrania	3	CTD_human
Hgene	PAX3	C0206655	Alveolar rhabdomyosarcoma	2	CTD_human;GENOMICS_ENGLAND;ORPHANET
Hgene	PAX3	C0011052	Prelingual Deafness	1	CTD_human
Hgene	PAX3	C0011053	Deafness	1	CTD_human
Hgene	PAX3	C0018566	Congenital Hand Deformities	1	CTD_human
Hgene	PAX3	C0086395	Hearing Loss, Extreme	1	CTD_human
Hgene	PAX3	C0205944	Sarcoma, Epithelioid	1	CTD_human
Hgene	PAX3	C0205945	Sarcoma, Spindle Cell	1	CTD_human
Hgene	PAX3	C0265541	Cranioschisis	1	CTD_human
Hgene	PAX3	C0376634	Craniofacial Abnormalities	1	CTD_human
Hgene	PAX3	C0497552	Congenital neurologic anomalies	1	CTD_human
Hgene	PAX3	C0581883	Complete Hearing Loss	1	CTD_human
Hgene	PAX3	C0751068	Deafness, Acquired	1	CTD_human
Hgene	PAX3	C1261473	Sarcoma	1	CTD_human
Hgene	PAX3	C1710096	Sinonasal undifferentiated carcinoma	1	CTD_human
Hgene	PAX3	C3665473	Bilateral Deafness	1	CTD_human
Hgene	PAX3	C4082305	Deaf Mutism	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)