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Fusion Protein:KDM6A-DMD

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: KDM6A-DMD
	FusionPDB ID: 41900
	FusionGDB2.0 ID: 41900
		Hgene	Tgene
	Gene symbol	KDM6A	DMD
	Gene ID	7403	1756
	Gene name	lysine demethylase 6A	dystrophin
	Synonyms	KABUK2\|UTX\|bA386N14.2	BMD\|CMD3B\|DXS142\|DXS164\|DXS206\|DXS230\|DXS239\|DXS268\|DXS269\|DXS270\|DXS272\|MRX85
	Cytomap	Xp11.3	Xp21.2-p21.1
	Type of gene	protein-coding	protein-coding
	Description	lysine-specific demethylase 6AbA386N14.2 (ubiquitously transcribed X chromosome tetratricopeptide repeat protein (UTX))histone demethylase UTXlysine (K)-specific demethylase 6Aubiquitously transcribed tetratricopeptide repeat protein X-linkedubiquito	dystrophin
	Modification date	20200313	20200329
	UniProtAcc	O15550 Main function of 5'-partner protein: FUNCTION: Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17851529, PubMed:17713478, PubMed:17761849). Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-27' (PubMed:17851529, PubMed:17713478, PubMed:17761849). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Demethylation of 'Lys-27' of histone H3 is concomitant with methylation of 'Lys-4' of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A (PubMed:17761849). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression (By similarity). {ECO:0000250\|UniProtKB:O70546, ECO:0000269\|PubMed:17713478, ECO:0000269\|PubMed:17761849, ECO:0000269\|PubMed:17851529, ECO:0000269\|PubMed:18003914}.	P11532 Main function of 5'-partner protein: FUNCTION: Anchors the extracellular matrix to the cytoskeleton via F-actin. Ligand for dystroglycan. Component of the dystrophin-associated glycoprotein complex which accumulates at the neuromuscular junction (NMJ) and at a variety of synapses in the peripheral and central nervous systems and has a structural function in stabilizing the sarcolemma. Also implicated in signaling events and synaptic transmission. {ECO:0000250\|UniProtKB:P11531, ECO:0000269\|PubMed:16710609}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000377967, ENST00000382899, ENST00000536777, ENST00000543216, ENST00000479423,	ENST00000445312, ENST00000288447, ENST00000361471, ENST00000378680, ENST00000378702, ENST00000378723, ENST00000343523, ENST00000357033, ENST00000359836, ENST00000378677, ENST00000378707, ENST00000474231, ENST00000541735,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	19 X 9 X 11=1881	35 X 39 X 12=16380
	# samples	20	41
	** MAII score	log2(20/1881*10)=-3.23342794374847 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(41/16380*10)=-5.32016763702292 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: KDM6A [Title/Abstract] AND DMD [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: KDM6A [Title/Abstract] AND DMD [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	KDM6A(44733233)-DMD(31676261), # samples:1 KDM6A(44833960)-DMD(31497220), # samples:1
Anticipated loss of major functional domain due to fusion event.	KDM6A-DMD 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. KDM6A-DMD 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. KDM6A-DMD 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. KDM6A-DMD 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	DMD	GO:0043043	peptide biosynthetic process	16000376

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:44733233/chrX:31676261)
- 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 KDM6A (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 DMD (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)
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000378707	DMD	chrX	31676261	-	6143	266	41	3451	1136
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000359836	DMD	chrX	31676261	-	6072	266	41	3466	1141
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000541735	DMD	chrX	31676261	-	5813	266	41	3121	1026
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000343523	DMD	chrX	31676261	-	5781	266	41	3175	1044
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000378677	DMD	chrX	31676261	-	6143	266	41	3451	1136
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000357033	DMD	chrX	31676261	-	6143	266	41	3451	1136
ENST00000377967	KDM6A	chrX	44733233	+	ENST00000474231	DMD	chrX	31676261	-	3942	266	41	3505	1154
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000378707	DMD	chrX	31676261	-	6119	242	17	3427	1136
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000359836	DMD	chrX	31676261	-	6048	242	17	3442	1141
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000541735	DMD	chrX	31676261	-	5789	242	17	3097	1026
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000343523	DMD	chrX	31676261	-	5757	242	17	3151	1044
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000378677	DMD	chrX	31676261	-	6119	242	17	3427	1136
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000357033	DMD	chrX	31676261	-	6119	242	17	3427	1136
ENST00000382899	KDM6A	chrX	44733233	+	ENST00000474231	DMD	chrX	31676261	-	3918	242	17	3481	1154
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000378707	DMD	chrX	31676261	-	6119	242	17	3427	1136
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000359836	DMD	chrX	31676261	-	6048	242	17	3442	1141
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000541735	DMD	chrX	31676261	-	5789	242	17	3097	1026
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000343523	DMD	chrX	31676261	-	5757	242	17	3151	1044
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000378677	DMD	chrX	31676261	-	6119	242	17	3427	1136
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000357033	DMD	chrX	31676261	-	6119	242	17	3427	1136
ENST00000536777	KDM6A	chrX	44733233	+	ENST00000474231	DMD	chrX	31676261	-	3918	242	17	3481	1154
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000378707	DMD	chrX	31676261	-	6102	225	0	3410	1136
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000359836	DMD	chrX	31676261	-	6031	225	0	3425	1141
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000541735	DMD	chrX	31676261	-	5772	225	0	3080	1026
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000343523	DMD	chrX	31676261	-	5740	225	0	3134	1044
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000378677	DMD	chrX	31676261	-	6102	225	0	3410	1136
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000357033	DMD	chrX	31676261	-	6102	225	0	3410	1136
ENST00000543216	KDM6A	chrX	44733233	+	ENST00000474231	DMD	chrX	31676261	-	3901	225	0	3464	1154
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000378707	DMD	chrX	31497220	-	5627	425	41	2935	964
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000359836	DMD	chrX	31497220	-	5556	425	41	2950	969
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000541735	DMD	chrX	31497220	-	5297	425	41	2605	854
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000343523	DMD	chrX	31497220	-	5265	425	41	2659	872
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000378677	DMD	chrX	31497220	-	5627	425	41	2935	964
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000357033	DMD	chrX	31497220	-	5627	425	41	2935	964
ENST00000377967	KDM6A	chrX	44833960	-	ENST00000474231	DMD	chrX	31497220	-	3426	425	41	2989	982
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000378707	DMD	chrX	31497220	-	5603	401	17	2911	964
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000359836	DMD	chrX	31497220	-	5532	401	17	2926	969
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000541735	DMD	chrX	31497220	-	5273	401	17	2581	854
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000343523	DMD	chrX	31497220	-	5241	401	17	2635	872
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000378677	DMD	chrX	31497220	-	5603	401	17	2911	964
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000357033	DMD	chrX	31497220	-	5603	401	17	2911	964
ENST00000382899	KDM6A	chrX	44833960	-	ENST00000474231	DMD	chrX	31497220	-	3402	401	17	2965	982
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000378707	DMD	chrX	31497220	-	5603	401	17	2911	964
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000359836	DMD	chrX	31497220	-	5532	401	17	2926	969
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000541735	DMD	chrX	31497220	-	5273	401	17	2581	854
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000343523	DMD	chrX	31497220	-	5241	401	17	2635	872
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000378677	DMD	chrX	31497220	-	5603	401	17	2911	964
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000357033	DMD	chrX	31497220	-	5603	401	17	2911	964
ENST00000536777	KDM6A	chrX	44833960	-	ENST00000474231	DMD	chrX	31497220	-	3402	401	17	2965	982
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000378707	DMD	chrX	31497220	-	5586	384	0	2894	964
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000359836	DMD	chrX	31497220	-	5515	384	0	2909	969
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000541735	DMD	chrX	31497220	-	5256	384	0	2564	854
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000343523	DMD	chrX	31497220	-	5224	384	0	2618	872
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000378677	DMD	chrX	31497220	-	5586	384	0	2894	964
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000357033	DMD	chrX	31497220	-	5586	384	0	2894	964
ENST00000543216	KDM6A	chrX	44833960	-	ENST00000474231	DMD	chrX	31497220	-	3385	384	0	2948	982

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
ENST00000377967	ENST00000378707	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000231611	0.99976844
ENST00000377967	ENST00000359836	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000148597	0.99985135
ENST00000377967	ENST00000541735	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000166752	0.9998332
ENST00000377967	ENST00000343523	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000218206	0.9997818
ENST00000377967	ENST00000378677	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000231611	0.99976844
ENST00000377967	ENST00000357033	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000231611	0.99976844
ENST00000377967	ENST00000474231	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.001627586	0.9983725
ENST00000382899	ENST00000378707	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000234714	0.99976534
ENST00000382899	ENST00000359836	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000150761	0.9998492
ENST00000382899	ENST00000541735	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000168727	0.9998312
ENST00000382899	ENST00000343523	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000221162	0.9997788
ENST00000382899	ENST00000378677	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000234714	0.99976534
ENST00000382899	ENST00000357033	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000234714	0.99976534
ENST00000382899	ENST00000474231	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.001665071	0.99833494
ENST00000536777	ENST00000378707	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000234714	0.99976534
ENST00000536777	ENST00000359836	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000150761	0.9998492
ENST00000536777	ENST00000541735	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000168727	0.9998312
ENST00000536777	ENST00000343523	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000221162	0.9997788
ENST00000536777	ENST00000378677	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000234714	0.99976534
ENST00000536777	ENST00000357033	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000234714	0.99976534
ENST00000536777	ENST00000474231	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.001665071	0.99833494
ENST00000543216	ENST00000378707	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000231659	0.9997683
ENST00000543216	ENST00000359836	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000148897	0.9998511
ENST00000543216	ENST00000541735	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000165871	0.99983406
ENST00000543216	ENST00000343523	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000218478	0.99978155
ENST00000543216	ENST00000378677	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000231659	0.9997683
ENST00000543216	ENST00000357033	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.000231659	0.9997683
ENST00000543216	ENST00000474231	KDM6A	chrX	44733233	+	DMD	chrX	31676261	-	0.001646496	0.9983535
ENST00000377967	ENST00000378707	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000114069	0.9998859
ENST00000377967	ENST00000359836	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000101807	0.9998982
ENST00000377967	ENST00000541735	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000150545	0.99984944
ENST00000377967	ENST00000343523	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000134496	0.99986553
ENST00000377967	ENST00000378677	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000114069	0.9998859
ENST00000377967	ENST00000357033	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000114069	0.9998859
ENST00000377967	ENST00000474231	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000805926	0.9991941
ENST00000382899	ENST00000378707	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118761	0.99988127
ENST00000382899	ENST00000359836	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000106152	0.9998938
ENST00000382899	ENST00000541735	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000157594	0.9998424
ENST00000382899	ENST00000343523	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000140533	0.99985945
ENST00000382899	ENST00000378677	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118761	0.99988127
ENST00000382899	ENST00000357033	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118761	0.99988127
ENST00000382899	ENST00000474231	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000849215	0.99915075
ENST00000536777	ENST00000378707	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118761	0.99988127
ENST00000536777	ENST00000359836	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000106152	0.9998938
ENST00000536777	ENST00000541735	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000157594	0.9998424
ENST00000536777	ENST00000343523	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000140533	0.99985945
ENST00000536777	ENST00000378677	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118761	0.99988127
ENST00000536777	ENST00000357033	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118761	0.99988127
ENST00000536777	ENST00000474231	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000849215	0.99915075
ENST00000543216	ENST00000378707	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118899	0.999881
ENST00000543216	ENST00000359836	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000106267	0.99989367
ENST00000543216	ENST00000541735	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000157901	0.99984205
ENST00000543216	ENST00000343523	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000140967	0.999859
ENST00000543216	ENST00000378677	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118899	0.999881
ENST00000543216	ENST00000357033	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000118899	0.999881
ENST00000543216	ENST00000474231	KDM6A	chrX	44833960	-	DMD	chrX	31497220	-	0.000848136	0.9991518

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 KDM6A-DMD

+/-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
KDM6A	chrX	44733233	DMD	chrX	31676261	225	75	HEDGARTKALLGKQLAKDLRQWQTNV
KDM6A	chrX	44733233	DMD	chrX	31676261	242	75	HEDGARTKALLGKQLAKDLRQWQTNV
KDM6A	chrX	44733233	DMD	chrX	31676261	266	75	HEDGARTKALLGKQLAKDLRQWQTNV
KDM6A	chrX	44833960	DMD	chrX	31497220	384	128	YQRYYSLQSDYWKAFKRELKTKEPVI
KDM6A	chrX	44833960	DMD	chrX	31497220	401	128	YQRYYSLQSDYWKAFKRELKTKEPVI
KDM6A	chrX	44833960	DMD	chrX	31497220	425	128	YQRYYSLQSDYWKAFKRELKTKEPVI

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Potential FusionNeoAntigen Information of KDM6A-DMD 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.

KDM6A-DMD_44733233_31676261.msa
KDM6A-DMD_44833960_31497220.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)
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A30:08	ALLGKQLAK	0.9853	0.7548	8	17
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B57:01	KQLAKDLRQW	0.998	0.9911	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A30:08	KALLGKQLAK	0.9936	0.7262	7	17
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B58:02	KQLAKDLRQW	0.9925	0.9819	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B58:01	KQLAKDLRQW	0.9851	0.9833	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A32:13	KQLAKDLRQW	0.8171	0.9601	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A30:08	RTKALLGKQLA	0.9935	0.675	5	16
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B14:03	TKALLGKQL	0.2614	0.7851	6	15
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B44:08	KQLAKDLRQW	0.8594	0.7872	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A30:01	ALLGKQLAK	0.9812	0.8548	8	17
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B39:02	TKALLGKQL	0.9728	0.841	6	15
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B15:09	TKALLGKQL	0.4339	0.8457	6	15
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B57:10	KQLAKDLRQW	0.998	0.9911	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B15:24	KQLAKDLRQW	0.9979	0.9775	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B57:04	KQLAKDLRQW	0.9946	0.8805	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A30:01	KALLGKQLAK	0.9932	0.8264	7	17
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B58:06	KQLAKDLRQW	0.9823	0.9701	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-A32:01	KQLAKDLRQW	0.9692	0.9573	12	22
KDM6A-DMD	chrX	44733233	chrX	31676261	266	HLA-B27:06	ARTKALLGKQL	0.9997	0.5839	4	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:01	LQSDYWKAF	0.9992	0.9332	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:25	LQSDYWKAF	0.9627	0.9458	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:11	SLQSDYWKA	0.9113	0.6139	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:38	SLQSDYWKA	0.9106	0.6355	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:60	SLQSDYWKA	0.9078	0.5239	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:24	SLQSDYWKA	0.9073	0.5887	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:67	SLQSDYWKA	0.9073	0.5887	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:30	SLQSDYWKA	0.9073	0.5887	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:27	SLQSDYWKA	0.9062	0.5529	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:16	SLQSDYWKA	0.9015	0.5494	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:21	SLQSDYWKA	0.8854	0.7271	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:03	LQSDYWKAF	0.8682	0.8608	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:13	SLQSDYWKA	0.8565	0.6494	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:29	SLQSDYWKA	0.8503	0.5939	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:20	SLQSDYWKA	0.8128	0.5916	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:18	LQSDYWKAF	0.7622	0.7758	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B47:01	LQSDYWKAF	0.6672	0.7978	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B13:01	LQSDYWKAF	0.5965	0.9852	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A30:08	KAFKRELKTK	0.9929	0.6624	12	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:07	LQSDYWKAF	0.9964	0.8313	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:04	LQSDYWKAF	0.9825	0.9641	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:21	LQSDYWKAF	0.954	0.9269	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:01	SLQSDYWKA	0.9073	0.5887	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:05	LQSDYWKAF	0.8546	0.9443	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C03:14	LQSDYWKAF	0.7145	0.9891	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C12:16	YWKAFKREL	0.3725	0.9628	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:80	YWKAFKREL	0.1613	0.9411	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:67	YWKAFKREL	0.1613	0.9411	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:29	YWKAFKREL	0.1131	0.9275	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:05	YWKAFKREL	0.0771	0.9599	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:10	YWKAFKREL	0.0744	0.9552	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:13	YWKAFKREL	0.0707	0.9292	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:46	YWKAFKREL	0.0662	0.8989	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:19	YWKAFKREL	0.0643	0.8016	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:27	YWKAFKREL	0.0432	0.95	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:27	LQSDYWKAF	0.9993	0.9464	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:125	LQSDYWKAF	0.9992	0.9332	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:34	LQSDYWKAF	0.9992	0.9332	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:33	LQSDYWKAF	0.9992	0.9332	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:135	LQSDYWKAF	0.9991	0.949	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:50	LQSDYWKAF	0.999	0.9504	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:24	LQSDYWKAF	0.9987	0.9729	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:35	LQSDYWKAF	0.9955	0.9425	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:53	LQSDYWKAF	0.9899	0.9266	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:12	LQSDYWKAF	0.9854	0.9472	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:39	LQSDYWKAF	0.9657	0.8999	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:54	LQSDYWKAF	0.8998	0.9054	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:68	LQSDYWKAF	0.894	0.7662	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A02:06	SLQSDYWKA	0.8854	0.7271	5	14
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B15:20	LQSDYWKAF	0.8378	0.9676	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C12:02	LQSDYWKAF	0.8317	0.9826	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B35:28	LQSDYWKAF	0.8113	0.9702	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B35:20	LQSDYWKAF	0.7963	0.9728	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B48:02	LQSDYWKAF	0.683	0.9628	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-B18:04	LQSDYWKAF	0.6054	0.9481	6	15
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C06:17	YWKAFKREL	0.4131	0.9871	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C06:02	YWKAFKREL	0.4131	0.9871	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C03:67	YWKAFKREL	0.2603	0.9665	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:04	YWKAFKREL	0.2169	0.9007	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:02	YWKAFKREL	0.1613	0.9411	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C14:02	YWKAFKREL	0.1429	0.952	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C14:03	YWKAFKREL	0.1429	0.952	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C06:08	YWKAFKREL	0.1215	0.984	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C07:17	YWKAFKREL	0.0736	0.9489	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-C06:06	YWKAFKREL	0.0683	0.9801	10	19
KDM6A-DMD	chrX	44833960	chrX	31497220	425	HLA-A30:01	KAFKRELKTK	0.9932	0.8051	12	22

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Potential FusionNeoAntigen Information of KDM6A-DMD in HLA II

KDM6A-DMD_44833960_31497220.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)
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-0805	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-0840	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-0840	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-0840	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1111	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1111	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1114	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1114	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1119	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1119	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1120	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1120	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1131	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1131	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1145	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1145	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1164	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1164	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1168	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1168	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1169	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1169	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1172	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1172	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1173	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1182	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1182	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1186	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1186	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1302	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1302	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1303	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1303	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1303	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-13101	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-13101	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-13101	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1310	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1310	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1310	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1312	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1312	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1316	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1316	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1321	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1321	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1323	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1323	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1329	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1329	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1333	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1333	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1333	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1334	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1334	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1336	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1336	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1339	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1339	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1341	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1341	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1349	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1349	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1363	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1363	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1366	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1366	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1366	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1373	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1373	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1374	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1374	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1382	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1382	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1386	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1386	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1388	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1388	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1388	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1390	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1390	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1390	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1395	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1395	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1395	DYWKAFKRELKTKEP	9	24
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1396	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1396	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1397	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1397	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1399	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1399	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1403	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1403	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1413	YWKAFKRELKTKEPV	10	25
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1413	WKAFKRELKTKEPVI	11	26
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1424	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1424	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1440	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1440	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1442	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1463	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1463	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1467	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1467	QSDYWKAFKRELKTK	7	22
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1477	SDYWKAFKRELKTKE	8	23
KDM6A-DMD	chrX	44833960	chrX	31497220	425	DRB1-1477	QSDYWKAFKRELKTK	7	22

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Fusion breakpoint peptide structures of KDM6A-DMD

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
5491	LQSDYWKAFKRELK	KDM6A	DMD	chrX	44833960	chrX	31497220	425

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
9425	TKALLGKQLAKDLR	KDM6A	DMD	chrX	44733233	chrX	31676261	266

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KDM6A-DMD

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	5491	LQSDYWKAFKRELK	-7.9962	-8.1096
HLA-B14:02	3BVN	5491	LQSDYWKAFKRELK	-5.70842	-6.74372
HLA-B52:01	3W39	5491	LQSDYWKAFKRELK	-6.83737	-6.95077
HLA-B52:01	3W39	5491	LQSDYWKAFKRELK	-4.4836	-5.5189
HLA-A11:01	4UQ2	5491	LQSDYWKAFKRELK	-10.0067	-10.1201
HLA-A11:01	4UQ2	5491	LQSDYWKAFKRELK	-9.03915	-10.0745
HLA-A24:02	5HGA	5491	LQSDYWKAFKRELK	-6.56204	-6.67544
HLA-A24:02	5HGA	5491	LQSDYWKAFKRELK	-5.42271	-6.45801
HLA-B44:05	3DX8	5491	LQSDYWKAFKRELK	-7.85648	-8.89178
HLA-B44:05	3DX8	5491	LQSDYWKAFKRELK	-5.3978	-5.5112
HLA-A02:01	6TDR	5491	LQSDYWKAFKRELK	-3.37154	-4.40684
HLA-B14:02	3BVN	9425	TKALLGKQLAKDLR	-5.97758	-6.09098
HLA-B14:02	3BVN	9425	TKALLGKQLAKDLR	-5.15013	-6.18543
HLA-B52:01	3W39	9425	TKALLGKQLAKDLR	-6.29935	-6.41275
HLA-B52:01	3W39	9425	TKALLGKQLAKDLR	-6.07479	-7.11009
HLA-A24:02	5HGA	9425	TKALLGKQLAKDLR	-7.25246	-8.28776
HLA-A24:02	5HGA	9425	TKALLGKQLAKDLR	-6.23064	-6.34404
HLA-B44:05	3DX8	9425	TKALLGKQLAKDLR	-4.66421	-5.69951
HLA-B44:05	3DX8	9425	TKALLGKQLAKDLR	-4.52141	-4.63481
HLA-A02:01	6TDR	9425	TKALLGKQLAKDLR	-7.72945	-7.84285

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Vaccine Design for the FusionNeoAntigens of KDM6A-DMD

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
KDM6A-DMD	chrX	44733233	chrX	31676261	12	22	KQLAKDLRQW	AAGCAGTTGGCCAAAGACCTCCGCCAGTGG
KDM6A-DMD	chrX	44733233	chrX	31676261	4	15	ARTKALLGKQL	GCCAGGACGAAGGCCCTACTGGGCAAGCAGTTG
KDM6A-DMD	chrX	44733233	chrX	31676261	5	16	RTKALLGKQLA	AGGACGAAGGCCCTACTGGGCAAGCAGTTGGCC
KDM6A-DMD	chrX	44733233	chrX	31676261	6	15	TKALLGKQL	ACGAAGGCCCTACTGGGCAAGCAGTTG
KDM6A-DMD	chrX	44733233	chrX	31676261	7	17	KALLGKQLAK	AAGGCCCTACTGGGCAAGCAGTTGGCCAAA
KDM6A-DMD	chrX	44733233	chrX	31676261	8	17	ALLGKQLAK	GCCCTACTGGGCAAGCAGTTGGCCAAA
KDM6A-DMD	chrX	44833960	chrX	31497220	10	19	YWKAFKREL	TACTGGAAGGCCTTCAAGAGGGAATTG
KDM6A-DMD	chrX	44833960	chrX	31497220	12	22	KAFKRELKTK	AAGGCCTTCAAGAGGGAATTGAAAACTAAA
KDM6A-DMD	chrX	44833960	chrX	31497220	5	14	SLQSDYWKA	AGTTTACAGTCTGACTACTGGAAGGCC
KDM6A-DMD	chrX	44833960	chrX	31497220	6	15	LQSDYWKAF	TTACAGTCTGACTACTGGAAGGCCTTC

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
KDM6A-DMD	chrX	44833960	chrX	31497220	10	25	YWKAFKRELKTKEPV	TACTGGAAGGCCTTCAAGAGGGAATTGAAAACTAAAGAACCTGTA
KDM6A-DMD	chrX	44833960	chrX	31497220	11	26	WKAFKRELKTKEPVI	TGGAAGGCCTTCAAGAGGGAATTGAAAACTAAAGAACCTGTAATC
KDM6A-DMD	chrX	44833960	chrX	31497220	7	22	QSDYWKAFKRELKTK	CAGTCTGACTACTGGAAGGCCTTCAAGAGGGAATTGAAAACTAAA
KDM6A-DMD	chrX	44833960	chrX	31497220	8	23	SDYWKAFKRELKTKE	TCTGACTACTGGAAGGCCTTCAAGAGGGAATTGAAAACTAAAGAA
KDM6A-DMD	chrX	44833960	chrX	31497220	9	24	DYWKAFKRELKTKEP	GACTACTGGAAGGCCTTCAAGAGGGAATTGAAAACTAAAGAACCT

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Information of the samples that have these potential fusion neoantigens of KDM6A-DMD

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
ACC	KDM6A-DMD	chrX	44733233	ENST00000377967	chrX	31676261	ENST00000343523	TCGA-OR-A5KV-01A
LUAD	KDM6A-DMD	chrX	44833960	ENST00000377967	chrX	31497220	ENST00000343523	TCGA-49-AARO-01A

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Potential target of CAR-T therapy development for KDM6A-DMD

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 KDM6A-DMD

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 KDM6A-DMD

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)