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Fusion Protein:ARHGEF7-ATP11A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ARHGEF7-ATP11A
	FusionPDB ID: 6340
	FusionGDB2.0 ID: 6340
		Hgene	Tgene
	Gene symbol	ARHGEF7	ATP11A
	Gene ID	8874	23250
	Gene name	Rho guanine nucleotide exchange factor 7	ATPase phospholipid transporting 11A
	Synonyms	BETA-PIX\|COOL-1\|COOL1\|Nbla10314\|P50\|P50BP\|P85\|P85COOL1\|P85SPR\|PAK3\|PIXB	ATPIH\|ATPIS
	Cytomap	13q34	13q34
	Type of gene	protein-coding	protein-coding
	Description	rho guanine nucleotide exchange factor 7PAK-interacting exchange factor betaRho guanine nucleotide exchange factor (GEF) 7SH3 domain-containing proline-rich protein	probable phospholipid-transporting ATPase IHATPase, class VI, type 11AP4-ATPase flippase complex alpha subunit ATP11Aphospholipid-translocating ATPasepotential phospholipid-transporting ATPase IH
	Modification date	20200327	20200313
	UniProtAcc	Q14155 Main function of 5'-partner protein: FUNCTION: Acts as a RAC1 guanine nucleotide exchange factor (GEF) and can induce membrane ruffling. Functions in cell migration, attachment and cell spreading. Promotes targeting of RAC1 to focal adhesions (By similarity). May function as a positive regulator of apoptosis. Downstream of NMDA receptors and CaMKK-CaMK1 signaling cascade, promotes the formation of spines and synapses in hippocampal neurons. {ECO:0000250, ECO:0000269\|PubMed:18184567, ECO:0000269\|PubMed:18716323, ECO:0000269\|PubMed:19041750}.	Q6ZP68 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000483189, ENST00000218789, ENST00000317133, ENST00000370623, ENST00000375723, ENST00000375736, ENST00000375737, ENST00000375739, ENST00000375741, ENST00000426073, ENST00000478679, ENST00000544132,	ENST00000283558, ENST00000375630, ENST00000375645, ENST00000487903, ENST00000419448,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	25 X 17 X 12=5100	14 X 15 X 4=840
	# samples	26	12
	** MAII score	log2(26/5100*10)=-4.29391371871777 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(12/840*10)=-2.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ARHGEF7 [Title/Abstract] AND ATP11A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ARHGEF7 [Title/Abstract] AND ATP11A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ARHGEF7(111920017)-ATP11A(113459271), # samples:2
Anticipated loss of major functional domain due to fusion event.	ARHGEF7-ATP11A 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. ARHGEF7-ATP11A 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. ARHGEF7-ATP11A 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. ARHGEF7-ATP11A 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. ARHGEF7-ATP11A seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. ARHGEF7-ATP11A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. ARHGEF7-ATP11A seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	ARHGEF7	GO:0043547	positive regulation of GTPase activity	21048939

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr13:111920017/chr13:113459271)
- 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 ARHGEF7 (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 ATP11A (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)

ENST00000544132

ARHGEF7

chr13

111920017

ENST00000283558

ATP11A

chr13

113459271

4150

907

664

4149

1162

ENST00000544132

ARHGEF7

chr13

111920017

ENST00000375630

ATP11A

chr13

113459271

9425

907

664

4320

1218

ENST00000544132

ARHGEF7

chr13

111920017

ENST00000487903

ATP11A

chr13

113459271

9515

907

664

4149

1161

ENST00000544132

ARHGEF7

chr13

111920017

ENST00000375645

ATP11A

chr13

113459271

9452

907

664

4149

1161

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
ENST00000544132	ENST00000283558	ARHGEF7	chr13	111920017	+	ATP11A	chr13	113459271	+	0.000695323	0.99930465
ENST00000544132	ENST00000375630	ARHGEF7	chr13	111920017	+	ATP11A	chr13	113459271	+	0.000200739	0.9997993
ENST00000544132	ENST00000487903	ARHGEF7	chr13	111920017	+	ATP11A	chr13	113459271	+	0.000183799	0.99981624
ENST00000544132	ENST00000375645	ARHGEF7	chr13	111920017	+	ATP11A	chr13	113459271	+	0.000173134	0.99982685

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 ARHGEF7-ATP11A

+/-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
ARHGEF7	chr13	111920017	ATP11A	chr13	113459271	907	80	CQSPFCSECPHGTQYTFWNFIPKNLF

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Potential FusionNeoAntigen Information of ARHGEF7-ATP11A 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.

ARHGEF7-ATP11A_111920017_113459271.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)
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B52:01	TQYTFWNF	0.8482	0.8874	12	20
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:03	SECPHGTQY	0.9993	0.6537	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:01	CPHGTQYTF	0.9972	0.6226	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:08	CPHGTQYTF	0.9954	0.6239	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:01	SECPHGTQY	0.9935	0.6687	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:02	CPHGTQYTF	0.9869	0.6619	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:03	CPHGTQYTF	0.984	0.6533	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:01	SECPHGTQY	0.9401	0.651	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B13:02	TQYTFWNFI	0.8892	0.6894	12	21
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-A32:13	GTQYTFWNF	0.8544	0.9545	11	20
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:02	CPHGTQYTF	0.8272	0.7019	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:04	CPHGTQYTF	0.8272	0.7019	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B45:01	SECPHGTQY	0.6609	0.6514	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:03	SECPHGTQY	0.2882	0.5071	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B52:01	TQYTFWNFI	0.1753	0.8692	12	21
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:03	CSECPHGTQY	0.5193	0.7371	5	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:03	SECPHGTQYTF	0.9999	0.6506	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:08	SECPHGTQYTF	0.9978	0.5418	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:01	SECPHGTQYTF	0.9947	0.5115	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:01	SECPHGTQYTF	0.9877	0.6116	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:01	FCSECPHGTQY	0.8218	0.8529	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:31	CPHGTQYTF	0.9971	0.6101	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:21	CPHGTQYTF	0.9863	0.6129	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:12	CPHGTQYTF	0.8272	0.7019	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:05	SECPHGTQY	0.777	0.5055	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:31	SECPHGTQY	0.6447	0.5077	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B51:07	CPHGTQYTF	0.5642	0.5908	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B42:02	CPHGTQYTF	0.521	0.5511	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B39:10	CPHGTQYTF	0.4222	0.872	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B42:01	CPHGTQYTF	0.3864	0.546	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B51:07	TQYTFWNFI	0.1477	0.7627	12	21
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:04	TQYTFWNF	0.9183	0.83	12	20
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:26	SECPHGTQY	0.9993	0.6537	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:07	SECPHGTQY	0.9993	0.6537	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:13	SECPHGTQY	0.9993	0.6537	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:77	CPHGTQYTF	0.9972	0.6226	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:23	CPHGTQYTF	0.9971	0.5983	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:20	CPHGTQYTF	0.9964	0.7127	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:04	SECPHGTQY	0.9951	0.6853	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:07	SECPHGTQY	0.9938	0.6283	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:05	SECPHGTQY	0.9935	0.6687	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:08	SECPHGTQY	0.9924	0.5692	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:11	CPHGTQYTF	0.9872	0.6126	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:24	CPHGTQYTF	0.9864	0.6917	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:06	SECPHGTQY	0.9833	0.6519	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:13	CPHGTQYTF	0.9795	0.6667	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:03	SECPHGTQY	0.9784	0.6581	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-A32:01	GTQYTFWNF	0.9497	0.9191	11	20
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:11	SECPHGTQY	0.9487	0.5081	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:125	SECPHGTQY	0.9401	0.651	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:33	SECPHGTQY	0.9401	0.651	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:34	SECPHGTQY	0.9401	0.651	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:27	SECPHGTQY	0.9313	0.6837	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:135	SECPHGTQY	0.9259	0.6982	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:50	SECPHGTQY	0.9219	0.5577	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:12	SECPHGTQY	0.8346	0.6704	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:09	CPHGTQYTF	0.8272	0.7019	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:20	SECPHGTQY	0.7814	0.5656	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:28	SECPHGTQY	0.7522	0.5793	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:04	CPHGTQYTF	0.7001	0.7835	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:53	SECPHGTQY	0.6475	0.6404	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:20	SECPHGTQY	0.6348	0.5936	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B67:01	CPHGTQYTF	0.5693	0.7306	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B78:02	CPHGTQYTF	0.5425	0.5029	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:07	CPHGTQYTF	0.4515	0.7056	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B48:02	SECPHGTQY	0.3539	0.5361	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:54	SECPHGTQY	0.2527	0.5949	6	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:43	CPHGTQYTF	0.1647	0.5738	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:08	CPHGTQYTF	0.1589	0.5713	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:11	CPHGTQYTF	0.1501	0.5617	8	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:43	ECPHGTQYTF	0.8139	0.5332	7	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:24	ECPHGTQYTF	0.7807	0.5179	7	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:26	CSECPHGTQY	0.5193	0.7371	5	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:07	CSECPHGTQY	0.5193	0.7371	5	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:13	CSECPHGTQY	0.5193	0.7371	5	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:07	ECPHGTQYTF	0.4503	0.5659	7	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:13	SECPHGTQYTF	0.9999	0.6506	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:07	SECPHGTQYTF	0.9999	0.6506	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B44:26	SECPHGTQYTF	0.9999	0.6506	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:11	SECPHGTQYTF	0.9992	0.6064	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:53	SECPHGTQYTF	0.9991	0.6498	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:54	SECPHGTQYTF	0.9972	0.6088	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B15:53	FCSECPHGTQY	0.9949	0.7282	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:77	SECPHGTQYTF	0.9947	0.5115	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:23	SECPHGTQYTF	0.9929	0.5152	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:05	SECPHGTQYTF	0.9877	0.6116	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:08	SECPHGTQYTF	0.9872	0.5346	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B48:02	SECPHGTQYTF	0.9855	0.5041	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B35:24	SECPHGTQYTF	0.9854	0.6655	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:04	SECPHGTQYTF	0.9852	0.6248	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:03	SECPHGTQYTF	0.9845	0.6034	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B67:01	SECPHGTQYTF	0.9658	0.6493	6	17
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B48:02	FCSECPHGTQY	0.9406	0.6978	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:04	FCSECPHGTQY	0.94	0.8658	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:11	FCSECPHGTQY	0.9373	0.8252	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:05	FCSECPHGTQY	0.8218	0.8529	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:08	FCSECPHGTQY	0.814	0.8074	4	15
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	907	HLA-B18:06	FCSECPHGTQY	0.7735	0.8633	4	15

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Potential FusionNeoAntigen Information of ARHGEF7-ATP11A 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 ARHGEF7-ATP11A

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
8499	SECPHGTQYTFWNF	ARHGEF7	ATP11A	chr13	111920017	chr13	113459271	907

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARHGEF7-ATP11A

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	8499	SECPHGTQYTFWNF	-5.34942	-6.38472
HLA-B14:02	3BVN	8499	SECPHGTQYTFWNF	-5.0153	-5.1287
HLA-B52:01	3W39	8499	SECPHGTQYTFWNF	-7.47358	-7.58698
HLA-B52:01	3W39	8499	SECPHGTQYTFWNF	-4.5023	-5.5376
HLA-A11:01	4UQ2	8499	SECPHGTQYTFWNF	-7.49832	-7.61172
HLA-A24:02	5HGA	8499	SECPHGTQYTFWNF	-8.30687	-8.42027
HLA-A24:02	5HGA	8499	SECPHGTQYTFWNF	-5.37786	-6.41316
HLA-B27:05	6PYJ	8499	SECPHGTQYTFWNF	-6.81213	-7.84743
HLA-B44:05	3DX8	8499	SECPHGTQYTFWNF	-9.00919	-9.12259
HLA-B44:05	3DX8	8499	SECPHGTQYTFWNF	-3.81824	-4.85354

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Vaccine Design for the FusionNeoAntigens of ARHGEF7-ATP11A

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
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	11	20	GTQYTFWNF	ACACAGTACACATTTTGGAACTTTATA
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	12	20	TQYTFWNF	CAGTACACATTTTGGAACTTTATA
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	12	21	TQYTFWNFI	CAGTACACATTTTGGAACTTTATACCC
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	4	15	FCSECPHGTQY	TGCAGTGAATGTCCTCACGGAACACAGTACACA
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	5	15	CSECPHGTQY	AGTGAATGTCCTCACGGAACACAGTACACA
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	6	15	SECPHGTQY	GAATGTCCTCACGGAACACAGTACACA
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	6	17	SECPHGTQYTF	GAATGTCCTCACGGAACACAGTACACATTTTGG
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	7	17	ECPHGTQYTF	TGTCCTCACGGAACACAGTACACATTTTGG
ARHGEF7-ATP11A	chr13	111920017	chr13	113459271	8	17	CPHGTQYTF	CCTCACGGAACACAGTACACATTTTGG

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 ARHGEF7-ATP11A

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
LUAD	ARHGEF7-ATP11A	chr13	111920017	ENST00000544132	chr13	113459271	ENST00000283558	TCGA-O1-A52J-01A

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Potential target of CAR-T therapy development for ARHGEF7-ATP11A

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

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

1001_1023

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

1030_1050

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

1069_1093

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

297_318

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

350_372

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

62_82

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

882_902

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

89_110

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

915_934

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000283558

965_986

1135.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

1001_1023

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

1030_1050

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

1069_1093

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

297_318

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

350_372

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

62_82

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

882_902

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

89_110

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

915_934

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000375645

965_986

2857.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

1001_1023

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

1030_1050

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

1069_1093

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

297_318

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

350_372

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

62_82

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

882_902

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

89_110

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

915_934

2878.0

Transmembrane

Helical

Tgene

ATP11A

chr13:111920017

chr13:113459271

ENST00000487903

965_986

2878.0

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
ARHGEF7	chr13	111920017	ENST00000544132	ATP11A	chr13	113459271	ENST00000283558
ARHGEF7	chr13	111920017	ENST00000544132	ATP11A	chr13	113459271	ENST00000375630
ARHGEF7	chr13	111920017	ENST00000544132	ATP11A	chr13	113459271	ENST00000375645

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Related Drugs to ARHGEF7-ATP11A

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 ARHGEF7-ATP11A

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)