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Fusion Protein:ATP2B4-OPTC

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ATP2B4-OPTC
	FusionPDB ID: 7872
	FusionGDB2.0 ID: 7872
		Hgene	Tgene
	Gene symbol	ATP2B4	OPTC
	Gene ID	493	26254
	Gene name	ATPase plasma membrane Ca2+ transporting 4	opticin
	Synonyms	ATP2B2\|MXRA1\|PMCA4\|PMCA4b\|PMCA4x	OPT
	Cytomap	1q32.1	1q32.1
	Type of gene	protein-coding	protein-coding
	Description	plasma membrane calcium-transporting ATPase 4ATPase, Ca++ transporting, plasma membrane 4matrix-remodeling-associated protein 1sarcolemmal calcium pump	opticinoculoglycan
	Modification date	20200327	20200313
	UniProtAcc	P23634 Main function of 5'-partner protein: FUNCTION: Calcium/calmodulin-regulated and magnesium-dependent enzyme that catalyzes the hydrolysis of ATP coupled with the transport of calcium out of the cell (PubMed:8530416). By regulating sperm cell calcium homeostasis, may play a role in sperm motility (By similarity). {ECO:0000250\|UniProtKB:Q6Q477, ECO:0000269\|PubMed:8530416}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000357681, ENST00000367218, ENST00000367219, ENST00000391954, ENST00000341360, ENST00000466407,	ENST00000367222,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 5 X 8=560	1 X 3 X 2=6
	# samples	17	3
	** MAII score	log2(17/560*10)=-1.71989208080726 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/6*10)=2.32192809488736
Fusion gene context	PubMed: ATP2B4 [Title/Abstract] AND OPTC [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ATP2B4 [Title/Abstract] AND OPTC [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ATP2B4(203596347)-OPTC(203466105), # samples:2
Anticipated loss of major functional domain due to fusion event.	ATP2B4-OPTC 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. ATP2B4-OPTC 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	ATP2B4	GO:0006874	cellular calcium ion homeostasis	19278978\|25798335
Hgene	ATP2B4	GO:0010629	negative regulation of gene expression	25147342
Hgene	ATP2B4	GO:0010751	negative regulation of nitric oxide mediated signal transduction	19278978
Hgene	ATP2B4	GO:0016525	negative regulation of angiogenesis	25147342
Hgene	ATP2B4	GO:0033138	positive regulation of peptidyl-serine phosphorylation	19278978
Hgene	ATP2B4	GO:0043537	negative regulation of blood vessel endothelial cell migration	25147342
Hgene	ATP2B4	GO:0045019	negative regulation of nitric oxide biosynthetic process	11591728\|19278978
Hgene	ATP2B4	GO:0051001	negative regulation of nitric-oxide synthase activity	11591728\|17242280\|19278978\|19287093
Hgene	ATP2B4	GO:0070885	negative regulation of calcineurin-NFAT signaling cascade	19287093\|25147342
Hgene	ATP2B4	GO:0071872	cellular response to epinephrine stimulus	19278978
Hgene	ATP2B4	GO:0098736	negative regulation of the force of heart contraction	17242280
Hgene	ATP2B4	GO:0140199	negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process	17242280
Hgene	ATP2B4	GO:1900082	negative regulation of arginine catabolic process	19278978
Hgene	ATP2B4	GO:1901660	calcium ion export	25798335
Hgene	ATP2B4	GO:1902548	negative regulation of cellular response to vascular endothelial growth factor stimulus	25147342
Hgene	ATP2B4	GO:1903078	positive regulation of protein localization to plasma membrane	15955804
Hgene	ATP2B4	GO:1903249	negative regulation of citrulline biosynthetic process	19278978
Hgene	ATP2B4	GO:2000481	positive regulation of cAMP-dependent protein kinase activity	19278978

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:203596347/chr1:203466105)
- 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 ATP2B4 (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 OPTC (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)
ENST00000357681	ATP2B4	chr1	203683405	-	ENST00000367222	OPTC	chr1	203472042	+	4040	3529	1096	3795	899
ENST00000391954	ATP2B4	chr1	203683405	-	ENST00000367222	OPTC	chr1	203472042	+	3801	3290	857	3556	899
ENST00000367218	ATP2B4	chr1	203683405	-	ENST00000367222	OPTC	chr1	203472042	+	3801	3290	857	3556	899
ENST00000367219	ATP2B4	chr1	203683405	-	ENST00000367222	OPTC	chr1	203472042	+	3765	3254	857	3520	887
ENST00000341360	ATP2B4	chr1	203683405	-	ENST00000367222	OPTC	chr1	203472042	+	3314	2803	370	3069	899

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
ENST00000357681	ENST00000367222	ATP2B4	chr1	203683405	-	OPTC	chr1	203472042	+	0.003454572	0.9965454
ENST00000391954	ENST00000367222	ATP2B4	chr1	203683405	-	OPTC	chr1	203472042	+	0.003292443	0.99670756
ENST00000367218	ENST00000367222	ATP2B4	chr1	203683405	-	OPTC	chr1	203472042	+	0.003292443	0.99670756
ENST00000367219	ENST00000367222	ATP2B4	chr1	203683405	-	OPTC	chr1	203472042	+	0.003759787	0.99624026
ENST00000341360	ENST00000367222	ATP2B4	chr1	203683405	-	OPTC	chr1	203472042	+	0.003336544	0.9966634

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 ATP2B4-OPTC

+/-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
ATP2B4	chr1	203683405	OPTC	chr1	203472042	2803	811	GPALKKADVGFAMAMEKLQFLYLSDN
ATP2B4	chr1	203683405	OPTC	chr1	203472042	3254	799	GPALKKADVGFAMAMEKLQFLYLSDN
ATP2B4	chr1	203683405	OPTC	chr1	203472042	3290	811	GPALKKADVGFAMAMEKLQFLYLSDN
ATP2B4	chr1	203683405	OPTC	chr1	203472042	3529	811	GPALKKADVGFAMAMEKLQFLYLSDN

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Potential FusionNeoAntigen Information of ATP2B4-OPTC 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.

ATP2B4-OPTC_203683405_203472042.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)
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:05	MAMEKLQF	0.9988	0.5454	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:01	MAMEKLQF	0.9963	0.877	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:03	MAMEKLQFL	0.9981	0.9052	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:01	AMAMEKLQF	0.9977	0.9111	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B14:02	MAMEKLQFL	0.9975	0.7445	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B14:01	MAMEKLQFL	0.9975	0.7445	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:01	MAMEKLQFL	0.9969	0.8835	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B52:01	MAMEKLQFL	0.994	0.916	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:05	MAMEKLQFL	0.993	0.5358	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:02	MAMEKLQFL	0.9915	0.9435	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:04	MAMEKLQFL	0.9915	0.9435	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:16	MAMEKLQFL	0.9914	0.7407	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:09	MAMEKLQFL	0.9908	0.7775	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:25	AMAMEKLQF	0.9793	0.9467	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:03	AMAMEKLQF	0.927	0.854	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A32:13	AMAMEKLQF	0.9124	0.8874	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B13:01	AMAMEKLQF	0.0874	0.96	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:01	MAMEKLQFLY	0.999	0.8653	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A02:13	AMAMEKLQFL	0.9828	0.6167	11	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A02:38	AMAMEKLQFL	0.9678	0.6319	11	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:19	FAMAMEKL	0.9999	0.9894	10	18
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:12	MAMEKLQF	0.9996	0.944	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:14	MAMEKLQF	0.9971	0.9694	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:19	MAMEKLQFL	0.9999	0.9807	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:08	MAMEKLQFL	0.9999	0.823	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C15:06	MAMEKLQFL	0.9998	0.8953	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:07	MAMEKLQFL	0.9998	0.972	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C15:04	MAMEKLQFL	0.9998	0.8835	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C04:06	MAMEKLQFL	0.9995	0.8964	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C08:04	MAMEKLQFL	0.999	0.9642	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C08:13	MAMEKLQFL	0.999	0.9642	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C04:14	MAMEKLQFL	0.9989	0.8782	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C06:03	MAMEKLQFL	0.9985	0.9923	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:04	MAMEKLQFL	0.9985	0.992	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:12	MAMEKLQFL	0.9984	0.9375	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B42:02	MAMEKLQFL	0.9983	0.8748	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:07	AMAMEKLQF	0.9977	0.7382	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:14	MAMEKLQFL	0.9974	0.9722	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:05	MAMEKLQFL	0.9967	0.9579	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C01:30	MAMEKLQFL	0.996	0.9596	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C01:17	MAMEKLQFL	0.9959	0.9565	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:10	MAMEKLQFL	0.9953	0.9712	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C02:06	MAMEKLQFL	0.9948	0.9517	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C08:03	MAMEKLQFL	0.9946	0.9883	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:16	MAMEKLQFL	0.994	0.9735	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B51:07	MAMEKLQFL	0.9939	0.9071	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:13	MAMEKLQFL	0.9926	0.9074	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:12	MAMEKLQFL	0.9915	0.9435	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:80	MAMEKLQFL	0.9903	0.9523	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:67	MAMEKLQFL	0.9903	0.9523	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B14:03	MAMEKLQFL	0.9893	0.7627	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:27	MAMEKLQFL	0.989	0.9561	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:29	MAMEKLQFL	0.9875	0.9059	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:19	MAMEKLQFL	0.9831	0.6893	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:95	MAMEKLQFL	0.9792	0.6507	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B39:10	MAMEKLQFL	0.9416	0.9319	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:05	AMAMEKLQF	0.936	0.8563	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:04	AMAMEKLQF	0.9335	0.9377	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C05:09	KADVGFAMAM	0.9999	0.9426	5	15
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C08:15	KADVGFAMAM	0.9998	0.9758	5	15
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:31	MAMEKLQFLY	0.9992	0.8305	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:02	MAMEKLQF	1	0.972	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C16:04	MAMEKLQF	0.9999	0.9841	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:04	FAMAMEKL	0.9999	0.9864	10	18
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:03	FAMAMEKL	0.9999	0.9864	10	18
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:05	FAMAMEKL	0.9998	0.9091	10	18
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:02	MAMEKLQF	0.9998	0.9774	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:17	FAMAMEKL	0.9997	0.9648	10	18
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:03	MAMEKLQF	0.9997	0.9798	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C16:01	MAMEKLQF	0.9995	0.9651	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:11	MAMEKLQF	0.9994	0.9421	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:30	MAMEKLQF	0.9989	0.7904	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:17	MAMEKLQF	0.9989	0.7904	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C16:02	MAMEKLQF	0.9984	0.9772	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:18	MAMEKLQF	0.9963	0.877	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:24	MAMEKLQF	0.9944	0.8779	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:12	MAMEKLQF	0.9918	0.9449	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B18:07	MAMEKLQF	0.9453	0.7759	12	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:67	MAMEKLQFL	0.9998	0.9663	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C15:09	MAMEKLQFL	0.9998	0.8835	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:04	MAMEKLQFL	0.9998	0.9779	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:03	MAMEKLQFL	0.9998	0.9779	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:17	MAMEKLQFL	0.9997	0.962	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:05	MAMEKLQFL	0.9997	0.8766	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C15:02	MAMEKLQFL	0.9996	0.8631	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C15:05	MAMEKLQFL	0.9996	0.9117	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C16:04	MAMEKLQFL	0.9995	0.983	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C04:04	MAMEKLQFL	0.9995	0.8984	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:02	MAMEKLQFL	0.9995	0.9711	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:06	MAMEKLQFL	0.9991	0.9789	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:03	MAMEKLQFL	0.9985	0.9796	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C06:06	MAMEKLQFL	0.9984	0.9873	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:13	MAMEKLQFL	0.9983	0.9116	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C16:02	MAMEKLQFL	0.9982	0.9851	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:04	MAMEKLQFL	0.9982	0.9215	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C06:02	MAMEKLQFL	0.9981	0.9915	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C06:17	MAMEKLQFL	0.9981	0.9915	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:27	AMAMEKLQF	0.9979	0.9261	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:135	AMAMEKLQF	0.9978	0.9093	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C16:01	MAMEKLQFL	0.9978	0.9745	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:33	AMAMEKLQF	0.9977	0.9111	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:34	AMAMEKLQF	0.9977	0.9111	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:125	AMAMEKLQF	0.9977	0.9111	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C04:03	MAMEKLQFL	0.9972	0.8429	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:50	AMAMEKLQF	0.9972	0.9335	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:35	AMAMEKLQF	0.9971	0.9139	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:18	MAMEKLQFL	0.9969	0.8835	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:24	AMAMEKLQF	0.9963	0.9189	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C01:02	MAMEKLQFL	0.9957	0.9533	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C01:03	MAMEKLQFL	0.9956	0.9381	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:12	AMAMEKLQF	0.9953	0.7607	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:53	AMAMEKLQF	0.9953	0.8942	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C08:01	MAMEKLQFL	0.9946	0.9883	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B78:02	MAMEKLQFL	0.9945	0.5182	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C18:01	MAMEKLQFL	0.9936	0.8369	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:17	MAMEKLQFL	0.9932	0.7657	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:30	MAMEKLQFL	0.9932	0.7657	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C02:02	MAMEKLQFL	0.9928	0.972	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C02:10	MAMEKLQFL	0.9928	0.972	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C12:02	MAMEKLQFL	0.9922	0.9769	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:09	MAMEKLQFL	0.9915	0.9435	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:02	MAMEKLQFL	0.9903	0.9523	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:17	MAMEKLQFL	0.9894	0.9655	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A68:02	MAMEKLQFL	0.9894	0.6766	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B08:12	MAMEKLQFL	0.988	0.9646	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C06:08	MAMEKLQFL	0.9869	0.9812	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A69:01	MAMEKLQFL	0.9842	0.502	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:22	MAMEKLQFL	0.983	0.7637	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C07:01	MAMEKLQFL	0.9801	0.6363	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:39	AMAMEKLQF	0.9794	0.8981	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:68	AMAMEKLQF	0.9756	0.6279	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:54	AMAMEKLQF	0.9732	0.8704	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A32:01	AMAMEKLQF	0.965	0.9194	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C17:01	MAMEKLQFL	0.9552	0.8758	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:20	AMAMEKLQF	0.9388	0.9075	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:28	AMAMEKLQF	0.9121	0.9124	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B07:13	MAMEKLQFL	0.8826	0.7844	12	21
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:73	AMAMEKLQF	0.8768	0.9249	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:30	AMAMEKLQF	0.8234	0.966	11	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C05:01	KADVGFAMAM	0.9999	0.9426	5	15
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C03:02	FAMAMEKLQF	0.9999	0.9761	10	20
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-C08:02	KADVGFAMAM	0.9998	0.9758	5	15
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B57:04	MAMEKLQFLY	0.9995	0.653	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:11	MAMEKLQFLY	0.9993	0.8988	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:23	MAMEKLQFLY	0.999	0.8811	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:77	MAMEKLQFLY	0.999	0.8653	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:11	MAMEKLQFLY	0.9989	0.8342	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B15:08	MAMEKLQFLY	0.9988	0.8322	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:43	MAMEKLQFLY	0.9985	0.839	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:30	MAMEKLQFLY	0.9976	0.7287	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:24	MAMEKLQFLY	0.9976	0.8314	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-B35:17	MAMEKLQFLY	0.9976	0.7287	12	22
ATP2B4-OPTC	chr1	203683405	chr1	203472042	2803	HLA-A02:03	AMAMEKLQFL	0.9949	0.5356	11	21

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Potential FusionNeoAntigen Information of ATP2B4-OPTC in HLA II

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)

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Fusion breakpoint peptide structures of ATP2B4-OPTC

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
128	ADVGFAMAMEKLQF	ATP2B4	OPTC	chr1	203683405	chr1	203472042	2803

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATP2B4-OPTC

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	128	ADVGFAMAMEKLQF	-7.15543	-7.26883
HLA-B14:02	3BVN	128	ADVGFAMAMEKLQF	-4.77435	-5.80965
HLA-B52:01	3W39	128	ADVGFAMAMEKLQF	-6.80875	-6.92215
HLA-B52:01	3W39	128	ADVGFAMAMEKLQF	-4.20386	-5.23916
HLA-A11:01	4UQ2	128	ADVGFAMAMEKLQF	-7.5194	-8.5547
HLA-A11:01	4UQ2	128	ADVGFAMAMEKLQF	-6.9601	-7.0735
HLA-A24:02	5HGA	128	ADVGFAMAMEKLQF	-7.52403	-7.63743
HLA-A24:02	5HGA	128	ADVGFAMAMEKLQF	-5.82433	-6.85963
HLA-B27:05	6PYJ	128	ADVGFAMAMEKLQF	-3.28285	-4.31815
HLA-B44:05	3DX8	128	ADVGFAMAMEKLQF	-5.91172	-6.94702
HLA-B44:05	3DX8	128	ADVGFAMAMEKLQF	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of ATP2B4-OPTC

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
ATP2B4-OPTC	chr1	203683405	chr1	203472042	10	18	FAMAMEKL	TTTGCCATGGCAATGGAGAAGCTG
ATP2B4-OPTC	chr1	203683405	chr1	203472042	10	20	FAMAMEKLQF	TTTGCCATGGCAATGGAGAAGCTGCAGTTC
ATP2B4-OPTC	chr1	203683405	chr1	203472042	11	20	AMAMEKLQF	GCCATGGCAATGGAGAAGCTGCAGTTC
ATP2B4-OPTC	chr1	203683405	chr1	203472042	11	21	AMAMEKLQFL	GCCATGGCAATGGAGAAGCTGCAGTTCCTT
ATP2B4-OPTC	chr1	203683405	chr1	203472042	12	20	MAMEKLQF	ATGGCAATGGAGAAGCTGCAGTTC
ATP2B4-OPTC	chr1	203683405	chr1	203472042	12	21	MAMEKLQFL	ATGGCAATGGAGAAGCTGCAGTTCCTT
ATP2B4-OPTC	chr1	203683405	chr1	203472042	12	22	MAMEKLQFLY	ATGGCAATGGAGAAGCTGCAGTTCCTTTAC
ATP2B4-OPTC	chr1	203683405	chr1	203472042	5	15	KADVGFAMAM	AAAGCGGATGTTGGTTTTGCCATGGCAATG

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

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Information of the samples that have these potential fusion neoantigens of ATP2B4-OPTC

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
SARC	ATP2B4-OPTC	chr1	203683405	ENST00000341360	chr1	203472042	ENST00000367222	TCGA-DX-AB32-01A

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Potential target of CAR-T therapy development for ATP2B4-OPTC

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

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000341360

151_171

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000341360

357_376

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000341360

410_427

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000341360

93_113

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000357681

151_171

802

1206.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000357681

357_376

802

1206.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000357681

410_427

802

1206.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000357681

93_113

802

1206.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367218

151_171

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367218

357_376

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367218

410_427

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367218

93_113

802

1171.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367219

151_171

790

1159.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367219

357_376

790

1159.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367219

410_427

790

1159.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000367219

93_113

790

1159.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000391954

151_171

802

1135.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000391954

357_376

802

1135.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000391954

410_427

802

1135.0

Transmembrane

Helical

Hgene

ATP2B4

chr1:203683405

chr1:203472042

ENST00000391954

93_113

802

1135.0

Transmembrane

Helical

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 ATP2B4-OPTC

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 ATP2B4-OPTC

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)