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Fusion Protein:PCCB-KDM4A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PCCB-KDM4A
	FusionPDB ID: 63171
	FusionGDB2.0 ID: 63171
		Hgene	Tgene
	Gene symbol	PCCB	KDM4A
	Gene ID	5096	9682
	Gene name	propionyl-CoA carboxylase subunit beta	lysine demethylase 4A
	Synonyms	-	JHDM3A\|JMJD2\|JMJD2A\|TDRD14A
	Cytomap	3q22.3	1p34.2-p34.1
	Type of gene	protein-coding	protein-coding
	Description	propionyl-CoA carboxylase beta chain, mitochondrialPCCase subunit betapropanoyl-CoA:carbon dioxide ligase subunit betapropionyl CoA carboxylase, beta polypeptidepropionyl Coenzyme A carboxylase, beta polypeptidepropionyl-CoA carboxylase beta subunit	lysine-specific demethylase 4AjmjC domain-containing histone demethylation protein 3Ajumonji C domain-containing histone demethylase 3Ajumonji domain containing 2jumonji domain containing 2Ajumonji domain-containing protein 2Alysine (K)-specific dem
	Modification date	20200313	20200313
	UniProtAcc	.	O75164 Main function of 5'-partner protein: FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code (PubMed:26741168). Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively. {ECO:0000269\|PubMed:16024779, ECO:0000269\|PubMed:16603238, ECO:0000269\|PubMed:26741168}.; FUNCTION: [Isoform 2]: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain. {ECO:0000269\|PubMed:21694756}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000474833, ENST00000251654, ENST00000462637, ENST00000466072, ENST00000468777, ENST00000469217, ENST00000471595, ENST00000482086, ENST00000483687, ENST00000490504, ENST00000478469,	ENST00000372396, ENST00000463151,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 9 X 4=288	4 X 4 X 3=48
	# samples	8	4
	** MAII score	log2(8/288*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PCCB [Title/Abstract] AND KDM4A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PCCB [Title/Abstract] AND KDM4A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PCCB(136019953)-KDM4A(44128564), # samples:1
Anticipated loss of major functional domain due to fusion event.	PCCB-KDM4A 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. PCCB-KDM4A 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. PCCB-KDM4A 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. PCCB-KDM4A 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	KDM4A	GO:0016577	histone demethylation	16024779
Tgene	KDM4A	GO:0045892	negative regulation of transcription, DNA-templated	16024779
Tgene	KDM4A	GO:0070544	histone H3-K36 demethylation	21914792

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:136019953/chr1:44128564)
- 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 PCCB (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 KDM4A (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)
ENST00000471595	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4895	984	18	3749	1243
ENST00000251654	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4947	1036	70	3801	1243
ENST00000483687	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4841	930	21	3695	1224
ENST00000490504	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4727	816	21	3581	1186
ENST00000466072	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4898	987	21	3752	1243
ENST00000482086	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4550	639	21	3404	1127
ENST00000468777	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4991	1080	21	3845	1274
ENST00000462637	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4829	918	21	3683	1220
ENST00000469217	PCCB	chr3	136019953	+	ENST00000372396	KDM4A	chr1	44128564	+	4954	1043	17	3808	1263

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
ENST00000471595	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000674837	0.99932516
ENST00000251654	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000706521	0.99929345
ENST00000483687	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.0006907	0.9993093
ENST00000490504	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000625656	0.99937433
ENST00000466072	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000680028	0.99932003
ENST00000482086	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000713133	0.99928695
ENST00000468777	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000673295	0.9993267
ENST00000462637	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000727745	0.9992723
ENST00000469217	ENST00000372396	PCCB	chr3	136019953	+	KDM4A	chr1	44128564	+	0.000677179	0.9993229

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 PCCB-KDM4A

+/-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
PCCB	chr3	136019953	KDM4A	chr1	44128564	1036	322	STKAYNMVDIIHSHVDEWNIGRLRTI
PCCB	chr3	136019953	KDM4A	chr1	44128564	1043	128	GRLVYVFSQQIIGWAQWLPLVISALW
PCCB	chr3	136019953	KDM4A	chr1	44128564	1080	132	YVFSQIRASAMSPRLVSDSWTQAIHL
PCCB	chr3	136019953	KDM4A	chr1	44128564	639	206	STKAYNMVDIIHSHVDEWNIGRLRTI
PCCB	chr3	136019953	KDM4A	chr1	44128564	816	265	STKAYNMVDIIHSHVDEWNIGRLRTI
PCCB	chr3	136019953	KDM4A	chr1	44128564	918	299	STKAYNMVDIIHSHVDEWNIGRLRTI
PCCB	chr3	136019953	KDM4A	chr1	44128564	930	303	STKAYNMVDIIHSHVDEWNIGRLRTI
PCCB	chr3	136019953	KDM4A	chr1	44128564	984	322	STKAYNMVDIIHSHVDEWNIGRLRTI
PCCB	chr3	136019953	KDM4A	chr1	44128564	987	322	STKAYNMVDIIHSHVDEWNIGRLRTI

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Potential FusionNeoAntigen Information of PCCB-KDM4A 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.

PCCB-KDM4A_136019953_44128564.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)
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B52:01	SAMSPRLV	0.9994	0.7732	8	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B58:01	FSQQIIGW	0.9978	0.9033	6	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:01	SHVDEWNI	0.9977	0.9461	12	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:02	SHVDEWNI	0.9974	0.9476	12	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:01	IHSHVDEW	0.8933	0.9571	10	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B57:01	IIHSHVDEW	0.9979	0.9816	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B58:01	IIHSHVDEW	0.9927	0.9551	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B58:02	IIHSHVDEW	0.9915	0.9416	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:16	IIHSHVDEW	0.9906	0.7434	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A02:21	MVDIIHSHV	0.9894	0.5042	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B57:03	IIHSHVDEW	0.9882	0.9857	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:17	IIHSHVDEW	0.9873	0.912	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A02:38	MVDIIHSHV	0.9834	0.5739	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B07:02	SPRLVSDSW	0.9808	0.5128	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A02:13	MVDIIHSHV	0.9714	0.5323	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A32:13	VFSQQIIGW	0.9681	0.88	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:02	NMVDIIHSH	0.9177	0.7795	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A31:08	QQIIGWAQW	0.9077	0.8082	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:01	SPRLVSDSW	0.8498	0.6662	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A32:13	IIHSHVDEW	0.827	0.9314	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A32:13	QQIIGWAQW	0.7957	0.9943	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:08	SPRLVSDSW	0.743	0.7012	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B47:01	QQIIGWAQW	0.7217	0.8375	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A24:14	VFSQQIIGW	0.6302	0.561	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B13:01	QQIIGWAQW	0.3793	0.9976	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B82:01	SPRLVSDSW	0.002	0.5574	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:01	MSPRLVSDSW	0.9998	0.9136	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B58:02	MSPRLVSDSW	0.9995	0.8186	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:01	YVFSQQIIGW	0.9992	0.9606	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B58:01	MSPRLVSDSW	0.999	0.803	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B58:01	YVFSQQIIGW	0.9956	0.9158	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:03	MSPRLVSDSW	0.9953	0.936	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B58:02	YVFSQQIIGW	0.9937	0.8368	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:03	YVFSQQIIGW	0.9567	0.9404	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A32:13	YVFSQQIIGW	0.9539	0.8711	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:01	AMSPRLVSDSW	0.9999	0.9132	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:01	SHVDEWNIGRL	0.9998	0.8977	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B39:01	SHVDEWNIGRL	0.9998	0.7231	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:02	SHVDEWNIGRL	0.9998	0.8916	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:01	FSQQIIGWAQW	0.9997	0.9865	6	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B58:01	FSQQIIGWAQW	0.9994	0.9921	6	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B58:02	FSQQIIGWAQW	0.9994	0.9928	6	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A24:20	VYVFSQQIIGW	0.998	0.62	3	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B58:01	AMSPRLVSDSW	0.9979	0.8267	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-A32:13	AMSPRLVSDSW	0.9967	0.9753	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:03	FSQQIIGWAQW	0.9939	0.9975	6	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C06:03	SAMSPRLV	0.9976	0.9899	8	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B39:05	SHVDEWNI	0.9969	0.8079	12	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C05:09	MVDIIHSHV	0.9999	0.8735	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C04:10	MVDIIHSHV	0.9998	0.6151	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C04:07	MVDIIHSHV	0.9998	0.632	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:04	RASAMSPRL	0.9996	0.9284	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C08:15	MVDIIHSHV	0.9995	0.8964	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:06	ASAMSPRLV	0.9993	0.9317	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:06	RASAMSPRL	0.9991	0.932	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:07	RASAMSPRL	0.999	0.9803	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:19	RASAMSPRL	0.999	0.9889	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C04:06	MVDIIHSHV	0.9987	0.7026	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:08	RASAMSPRL	0.9985	0.8976	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C04:06	RASAMSPRL	0.9955	0.8883	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C04:14	MVDIIHSHV	0.9846	0.737	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C02:06	RASAMSPRL	0.9792	0.9791	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C08:13	MVDIIHSHV	0.9786	0.884	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C08:04	MVDIIHSHV	0.9786	0.884	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C02:06	MVDIIHSHV	0.9782	0.9065	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C06:03	ASAMSPRLV	0.9684	0.9933	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C12:04	ASAMSPRLV	0.9678	0.9932	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C06:03	RASAMSPRL	0.9569	0.9931	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:21	NMVDIIHSH	0.934	0.7615	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C08:13	RASAMSPRL	0.9286	0.9843	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C08:04	RASAMSPRL	0.9286	0.9843	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C12:12	RASAMSPRL	0.9227	0.924	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B44:08	QQIIGWAQW	0.8693	0.9559	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C08:03	MVDIIHSHV	0.8688	0.9448	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C02:06	ASAMSPRLV	0.8666	0.9774	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C08:03	RASAMSPRL	0.8107	0.9843	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B07:12	SPRLVSDSW	0.7888	0.6507	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:31	NMVDIIHSH	0.7814	0.773	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:04	NMVDIIHSH	0.7765	0.7677	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B42:02	SPRLVSDSW	0.2197	0.5721	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B42:01	SPRLVSDSW	0.2143	0.5666	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B44:08	SQQIIGWAQW	0.9423	0.9477	7	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B39:05	SHVDEWNIGRL	0.9997	0.7096	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A24:02	VYVFSQQIIGW	0.998	0.62	3	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:05	SHVDEWNI	0.9977	0.9461	12	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C16:02	SAMSPRLV	0.997	0.9913	8	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:05	IHSHVDEW	0.8933	0.9571	10	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C05:01	MVDIIHSHV	0.9999	0.8735	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C04:03	MVDIIHSHV	0.9999	0.6759	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C18:01	MVDIIHSHV	0.9998	0.631	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C04:01	MVDIIHSHV	0.9998	0.632	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:09	RASAMSPRL	0.9996	0.9284	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:05	ASAMSPRLV	0.9995	0.8945	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C08:02	MVDIIHSHV	0.9995	0.8964	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:02	ASAMSPRLV	0.9995	0.8796	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:02	RASAMSPRL	0.999	0.9006	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C15:05	MVDIIHSHV	0.9988	0.7897	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C15:05	RASAMSPRL	0.9988	0.9103	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:04	RASAMSPRL	0.9982	0.9899	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:03	RASAMSPRL	0.9982	0.9899	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:17	RASAMSPRL	0.998	0.9797	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B57:10	IIHSHVDEW	0.9979	0.9816	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:05	RASAMSPRL	0.9975	0.9366	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B57:04	IIHSHVDEW	0.9974	0.7026	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A68:02	MVDIIHSHV	0.9955	0.5353	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C16:04	RASAMSPRL	0.9946	0.9658	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B58:06	IIHSHVDEW	0.9937	0.7698	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A69:01	MVDIIHSHV	0.9926	0.5762	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A02:06	MVDIIHSHV	0.9894	0.5042	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:13	IIHSHVDEW	0.989	0.7553	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B57:02	IIHSHVDEW	0.9887	0.8842	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B15:24	QQIIGWAQW	0.9851	0.9715	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B07:09	SPRLVSDSW	0.9833	0.5056	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:24	IIHSHVDEW	0.9828	0.9302	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B07:22	SPRLVSDSW	0.9808	0.5128	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C16:01	RASAMSPRL	0.9781	0.9789	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C16:02	ASAMSPRLV	0.9759	0.993	7	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C17:01	MVDIIHSHV	0.9657	0.7561	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C16:02	RASAMSPRL	0.965	0.9931	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A32:01	IIHSHVDEW	0.9604	0.9316	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B07:13	RASAMSPRL	0.9594	0.859	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C03:06	RASAMSPRL	0.9568	0.9905	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A32:01	QQIIGWAQW	0.9103	0.9952	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-C08:01	MVDIIHSHV	0.8688	0.9448	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:77	SPRLVSDSW	0.8498	0.6662	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:13	RASAMSPRL	0.8446	0.9174	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:23	SPRLVSDSW	0.8423	0.6228	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:17	SPRLVSDSW	0.8339	0.5516	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:30	SPRLVSDSW	0.8339	0.5516	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B15:13	QQIIGWAQW	0.8168	0.9108	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B53:02	IIHSHVDEW	0.8147	0.5076	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C08:01	RASAMSPRL	0.8107	0.9843	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-C17:01	RASAMSPRL	0.7933	0.9622	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B35:20	NMVDIIHSH	0.7571	0.8461	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:11	SPRLVSDSW	0.7336	0.6981	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:24	SPRLVSDSW	0.6871	0.6618	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B44:21	QQIIGWAQW	0.643	0.6399	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B35:28	QQIIGWAQW	0.619	0.9566	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B15:13	VFSQQIIGW	0.6133	0.8057	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B48:02	QQIIGWAQW	0.4838	0.9532	8	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B07:13	MVDIIHSHV	0.4443	0.6737	6	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A25:01	IIHSHVDEW	0.3909	0.864	9	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B18:04	NMVDIIHSH	0.0851	0.8233	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B18:07	SPRLVSDSW	0.0442	0.6867	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B18:07	NMVDIIHSH	0.0303	0.7456	5	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B15:08	SPRLVSDSW	0.0258	0.6694	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B15:11	SPRLVSDSW	0.022	0.6924	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B35:43	SPRLVSDSW	0.0216	0.6753	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B82:02	SPRLVSDSW	0.002	0.5574	11	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:10	MSPRLVSDSW	0.9998	0.9136	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:04	MSPRLVSDSW	0.9992	0.648	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:10	YVFSQQIIGW	0.9992	0.9606	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B58:06	MSPRLVSDSW	0.9988	0.7517	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:04	YVFSQQIIGW	0.9978	0.6868	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B15:24	SQQIIGWAQW	0.9955	0.9839	7	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B58:06	YVFSQQIIGW	0.9936	0.7871	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-A25:01	DIIHSHVDEW	0.9875	0.9059	8	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B15:24	YVFSQQIIGW	0.9875	0.9242	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:02	MSPRLVSDSW	0.9848	0.902	10	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B15:13	YVFSQQIIGW	0.9806	0.7139	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A32:01	YVFSQQIIGW	0.9424	0.8738	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:13	DIIHSHVDEW	0.9067	0.741	8	18
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-A25:01	YVFSQQIIGW	0.8193	0.895	4	14
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B15:24	AMSPRLVSDSW	0.9999	0.8617	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:10	AMSPRLVSDSW	0.9999	0.9132	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-B57:04	AMSPRLVSDSW	0.9998	0.6352	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B38:05	SHVDEWNIGRL	0.9998	0.8977	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:10	FSQQIIGWAQW	0.9997	0.9865	6	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B15:09	SHVDEWNIGRL	0.9994	0.5148	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:04	FSQQIIGWAQW	0.9993	0.8396	6	17
PCCB-KDM4A	chr3	136019953	chr1	44128564	1080	HLA-A32:01	AMSPRLVSDSW	0.9986	0.945	9	20
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	HLA-B39:11	SHVDEWNIGRL	0.9978	0.6474	12	23
PCCB-KDM4A	chr3	136019953	chr1	44128564	1043	HLA-B57:02	FSQQIIGWAQW	0.9894	0.9924	6	17

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Potential FusionNeoAntigen Information of PCCB-KDM4A in HLA II

PCCB-KDM4A_136019953_44128564.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)
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0401	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0407	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0407	STKAYNMVDIIHSHV	0	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0419	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0431	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0431	STKAYNMVDIIHSHV	0	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0433	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0434	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0435	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0438	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0443	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0447	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0447	STKAYNMVDIIHSHV	0	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0454	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0454	STKAYNMVDIIHSHV	0	15
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0461	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0463	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0464	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0469	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0474	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0475	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0476	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-0482	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-1001	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-1003	TKAYNMVDIIHSHVD	1	16
PCCB-KDM4A	chr3	136019953	chr1	44128564	1036	DRB1-1130	TKAYNMVDIIHSHVD	1	16

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Fusion breakpoint peptide structures of PCCB-KDM4A

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
2580	FSQQIIGWAQWLPL	PCCB	KDM4A	chr3	136019953	chr1	44128564	1043

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6054	MVDIIHSHVDEWNI	PCCB	KDM4A	chr3	136019953	chr1	44128564	1036

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
7708	RASAMSPRLVSDSW	PCCB	KDM4A	chr3	136019953	chr1	44128564	1080

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PCCB-KDM4A

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	2580	FSQQIIGWAQWLPL	-8.85616	-8.96956
HLA-B14:02	3BVN	2580	FSQQIIGWAQWLPL	-5.66423	-6.69953
HLA-B52:01	3W39	2580	FSQQIIGWAQWLPL	-6.49489	-6.60829
HLA-B52:01	3W39	2580	FSQQIIGWAQWLPL	-3.99785	-5.03315
HLA-A11:01	4UQ2	2580	FSQQIIGWAQWLPL	-4.90759	-5.94289
HLA-A24:02	5HGA	2580	FSQQIIGWAQWLPL	-7.27887	-7.39227
HLA-A24:02	5HGA	2580	FSQQIIGWAQWLPL	-7.11524	-8.15054
HLA-B27:05	6PYJ	2580	FSQQIIGWAQWLPL	-6.11615	-6.22955
HLA-B27:05	6PYJ	2580	FSQQIIGWAQWLPL	-4.78818	-5.82348
HLA-B44:05	3DX8	2580	FSQQIIGWAQWLPL	-7.22602	-7.33942
HLA-B44:05	3DX8	2580	FSQQIIGWAQWLPL	-4.86671	-5.90201
HLA-B14:02	3BVN	6054	MVDIIHSHVDEWNI	-5.6364	-5.6364
HLA-A24:02	5HGA	6054	MVDIIHSHVDEWNI	-9.18993	-9.18993
HLA-B14:02	3BVN	7708	RASAMSPRLVSDSW	-7.9962	-8.1096
HLA-B14:02	3BVN	7708	RASAMSPRLVSDSW	-5.70842	-6.74372
HLA-B52:01	3W39	7708	RASAMSPRLVSDSW	-6.83737	-6.95077
HLA-B52:01	3W39	7708	RASAMSPRLVSDSW	-4.4836	-5.5189
HLA-A11:01	4UQ2	7708	RASAMSPRLVSDSW	-10.0067	-10.1201
HLA-A11:01	4UQ2	7708	RASAMSPRLVSDSW	-9.03915	-10.0745
HLA-A24:02	5HGA	7708	RASAMSPRLVSDSW	-6.56204	-6.67544
HLA-A24:02	5HGA	7708	RASAMSPRLVSDSW	-5.42271	-6.45801
HLA-B44:05	3DX8	7708	RASAMSPRLVSDSW	-7.85648	-8.89178
HLA-B44:05	3DX8	7708	RASAMSPRLVSDSW	-5.3978	-5.5112
HLA-A02:01	6TDR	7708	RASAMSPRLVSDSW	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of PCCB-KDM4A

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
PCCB-KDM4A	chr3	136019953	chr1	44128564	10	18	IHSHVDEW	ATACACTCTCATGTTGATGAGTGG
PCCB-KDM4A	chr3	136019953	chr1	44128564	10	20	MSPRLVSDSW	ATACACTCTCATGTTGATGAGTGGAATATT
PCCB-KDM4A	chr3	136019953	chr1	44128564	11	20	SPRLVSDSW	CACTCTCATGTTGATGAGTGGAATATT
PCCB-KDM4A	chr3	136019953	chr1	44128564	12	20	SHVDEWNI	TCTCATGTTGATGAGTGGAATATT
PCCB-KDM4A	chr3	136019953	chr1	44128564	12	23	SHVDEWNIGRL	TCTCATGTTGATGAGTGGAATATTGGCCGGCTG
PCCB-KDM4A	chr3	136019953	chr1	44128564	3	14	VYVFSQQIIGW	GCCTACAACATGGTGGACATCATACACTCTCAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	4	14	YVFSQQIIGW	TACAACATGGTGGACATCATACACTCTCAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	5	14	NMVDIIHSH	AACATGGTGGACATCATACACTCTCAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	5	14	VFSQQIIGW	AACATGGTGGACATCATACACTCTCAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	6	14	FSQQIIGW	ATGGTGGACATCATACACTCTCAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	6	15	MVDIIHSHV	ATGGTGGACATCATACACTCTCATGTT
PCCB-KDM4A	chr3	136019953	chr1	44128564	6	15	RASAMSPRL	ATGGTGGACATCATACACTCTCATGTT
PCCB-KDM4A	chr3	136019953	chr1	44128564	6	17	FSQQIIGWAQW	ATGGTGGACATCATACACTCTCATGTTGATGAG
PCCB-KDM4A	chr3	136019953	chr1	44128564	7	16	ASAMSPRLV	GTGGACATCATACACTCTCATGTTGAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	7	17	SQQIIGWAQW	GTGGACATCATACACTCTCATGTTGATGAG
PCCB-KDM4A	chr3	136019953	chr1	44128564	8	16	SAMSPRLV	GACATCATACACTCTCATGTTGAT
PCCB-KDM4A	chr3	136019953	chr1	44128564	8	17	QQIIGWAQW	GACATCATACACTCTCATGTTGATGAG
PCCB-KDM4A	chr3	136019953	chr1	44128564	8	18	DIIHSHVDEW	GACATCATACACTCTCATGTTGATGAGTGG
PCCB-KDM4A	chr3	136019953	chr1	44128564	9	18	IIHSHVDEW	ATCATACACTCTCATGTTGATGAGTGG
PCCB-KDM4A	chr3	136019953	chr1	44128564	9	20	AMSPRLVSDSW	ATCATACACTCTCATGTTGATGAGTGGAATATT

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
PCCB-KDM4A	chr3	136019953	chr1	44128564	0	15	STKAYNMVDIIHSHV	TCAACCAAAGCCTACAACATGGTGGACATCATACACTCTCATGTT
PCCB-KDM4A	chr3	136019953	chr1	44128564	1	16	TKAYNMVDIIHSHVD	ACCAAAGCCTACAACATGGTGGACATCATACACTCTCATGTTGAT

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Information of the samples that have these potential fusion neoantigens of PCCB-KDM4A

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
OV	PCCB-KDM4A	chr3	136019953	ENST00000251654	chr1	44128564	ENST00000372396	TCGA-13-1403
OV	PCCB-KDM4A	chr3	136019953	ENST00000468777	chr1	44128564	ENST00000372396	TCGA-13-1403
OV	PCCB-KDM4A	chr3	136019953	ENST00000469217	chr1	44128564	ENST00000372396	TCGA-13-1403

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Potential target of CAR-T therapy development for PCCB-KDM4A

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 PCCB-KDM4A

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 PCCB-KDM4A

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)