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Fusion Protein:SLC22A23-FOXP4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SLC22A23-FOXP4
	FusionPDB ID: 82458
	FusionGDB2.0 ID: 82458
		Hgene	Tgene
	Gene symbol	SLC22A23	FOXP4
	Gene ID	63027	116113
	Gene name	solute carrier family 22 member 23	forkhead box P4
	Synonyms	C6orf85	hFKHLA
	Cytomap	6p25.2	6p21.1
	Type of gene	protein-coding	protein-coding
	Description	solute carrier family 22 member 23ion transporter protein	forkhead box protein P4fork head-related protein like Awinged-helix repressor FOXP4
	Modification date	20200313	20200313
	UniProtAcc	.	Q8IVH2 Main function of 5'-partner protein: FUNCTION: Transcriptional repressor that represses lung-specific expression. {ECO:0000250}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000380298, ENST00000406686, ENST00000436008, ENST00000380302, ENST00000433689, ENST00000490273,	ENST00000307972, ENST00000373057, ENST00000373060, ENST00000373063, ENST00000409208,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 5 X 9=540	5 X 6 X 4=120
	# samples	14	6
	** MAII score	log2(14/540*10)=-1.94753258010586 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/120*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SLC22A23 [Title/Abstract] AND FOXP4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SLC22A23 [Title/Abstract] AND FOXP4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SLC22A23(3456140)-FOXP4(41545724), # samples:1
Anticipated loss of major functional domain due to fusion event.	SLC22A23-FOXP4 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. SLC22A23-FOXP4 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:3456140/chr6:41545724)
- 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 SLC22A23 (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 FOXP4 (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)
ENST00000436008	SLC22A23	chr6	3456140	-	ENST00000373060	FOXP4	chr6	41545724	+	6403	1117	307	2955	882
ENST00000436008	SLC22A23	chr6	3456140	-	ENST00000373063	FOXP4	chr6	41545724	+	6365	1117	307	2916	869
ENST00000436008	SLC22A23	chr6	3456140	-	ENST00000409208	FOXP4	chr6	41545724	+	3943	1117	307	2919	870
ENST00000436008	SLC22A23	chr6	3456140	-	ENST00000373057	FOXP4	chr6	41545724	+	3977	1117	307	2949	880
ENST00000436008	SLC22A23	chr6	3456140	-	ENST00000307972	FOXP4	chr6	41545724	+	4646	1117	307	2955	882
ENST00000406686	SLC22A23	chr6	3456140	-	ENST00000373060	FOXP4	chr6	41545724	+	5940	654	0	2492	830
ENST00000406686	SLC22A23	chr6	3456140	-	ENST00000373063	FOXP4	chr6	41545724	+	5902	654	0	2453	817
ENST00000406686	SLC22A23	chr6	3456140	-	ENST00000409208	FOXP4	chr6	41545724	+	3480	654	0	2456	818
ENST00000406686	SLC22A23	chr6	3456140	-	ENST00000373057	FOXP4	chr6	41545724	+	3514	654	0	2486	828
ENST00000406686	SLC22A23	chr6	3456140	-	ENST00000307972	FOXP4	chr6	41545724	+	4183	654	0	2492	830
ENST00000380298	SLC22A23	chr6	3456140	-	ENST00000373060	FOXP4	chr6	41545724	+	5940	654	0	2492	830
ENST00000380298	SLC22A23	chr6	3456140	-	ENST00000373063	FOXP4	chr6	41545724	+	5902	654	0	2453	817
ENST00000380298	SLC22A23	chr6	3456140	-	ENST00000409208	FOXP4	chr6	41545724	+	3480	654	0	2456	818
ENST00000380298	SLC22A23	chr6	3456140	-	ENST00000373057	FOXP4	chr6	41545724	+	3514	654	0	2486	828
ENST00000380298	SLC22A23	chr6	3456140	-	ENST00000307972	FOXP4	chr6	41545724	+	4183	654	0	2492	830

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
ENST00000436008	ENST00000373060	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.018746123	0.98125386
ENST00000436008	ENST00000373063	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.018386856	0.98161316
ENST00000436008	ENST00000409208	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.052142903	0.9478571
ENST00000436008	ENST00000373057	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.046982415	0.95301765
ENST00000436008	ENST00000307972	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.04155933	0.95844066
ENST00000406686	ENST00000373060	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.01753779	0.98246217
ENST00000406686	ENST00000373063	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.017014826	0.9829852
ENST00000406686	ENST00000409208	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.055613503	0.9443864
ENST00000406686	ENST00000373057	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.050419804	0.94958025
ENST00000406686	ENST00000307972	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.041234367	0.9587657
ENST00000380298	ENST00000373060	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.01753779	0.98246217
ENST00000380298	ENST00000373063	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.017014826	0.9829852
ENST00000380298	ENST00000409208	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.055613503	0.9443864
ENST00000380298	ENST00000373057	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.050419804	0.94958025
ENST00000380298	ENST00000307972	SLC22A23	chr6	3456140	-	FOXP4	chr6	41545724	+	0.041234367	0.9587657

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 SLC22A23-FOXP4

+/-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
SLC22A23	chr6	3456140	FOXP4	chr6	41545724	1117	270	GIRAGLVQNVVSKALQVARQFLLQQA
SLC22A23	chr6	3456140	FOXP4	chr6	41545724	654	218	GIRAGLVQNVVSKALQVARQFLLQQA

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Potential FusionNeoAntigen Information of SLC22A23-FOXP4 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.

SLC22A23-FOXP4_3456140_41545724.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)
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:01	KALQVARQF	0.9991	0.9075	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B58:02	KALQVARQF	0.997	0.8425	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:01	VQNVVSKAL	0.9964	0.6901	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:03	KALQVARQF	0.9954	0.9228	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:17	KALQVARQF	0.9918	0.7913	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:16	KALQVARQF	0.9903	0.6579	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B58:01	KALQVARQF	0.9888	0.81	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A31:08	KALQVARQF	0.9868	0.5755	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:03	KALQVARQF	0.9748	0.662	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A74:03	VSKALQVAR	0.9652	0.7094	10	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A74:11	VSKALQVAR	0.9652	0.7094	10	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A74:09	VSKALQVAR	0.9652	0.7094	10	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:01	VQNVVSKAL	0.928	0.8203	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B14:01	VQNVVSKAL	0.9277	0.8281	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B14:02	VQNVVSKAL	0.9277	0.8281	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A31:02	VSKALQVAR	0.9253	0.7474	10	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A32:13	KALQVARQF	0.8708	0.9257	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:13	VQNVVSKAL	0.7997	0.8552	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:03	VQNVVSKAL	0.7888	0.642	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B13:02	VQNVVSKAL	0.6376	0.6804	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B13:01	VQNVVSKAL	0.5624	0.9309	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B52:01	KALQVARQF	0.1751	0.9138	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B13:01	KALQVARQF	0.1246	0.9092	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B52:01	VQNVVSKAL	0.046	0.9396	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A31:02	VVSKALQVAR	0.8897	0.7609	9	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:01	VSKALQVARQF	0.9999	0.8744	10	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:03	VSKALQVARQF	0.9995	0.9222	10	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A68:24	NVVSKALQVAR	0.9958	0.679	8	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A68:03	NVVSKALQVAR	0.9941	0.6593	8	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A68:05	NVVSKALQVAR	0.969	0.6624	8	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A33:05	NVVSKALQVAR	0.9487	0.5435	8	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A33:01	NVVSKALQVAR	0.9487	0.5435	8	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:06	NVVSKALQV	0.9988	0.7322	8	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:04	KALQVARQF	0.9773	0.831	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:04	VQNVVSKAL	0.9768	0.7672	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:08	KALQVARQF	0.9751	0.7791	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A31:01	VSKALQVAR	0.9736	0.6936	10	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:07	VQNVVSKAL	0.9731	0.5583	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:19	KALQVARQF	0.9726	0.9679	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C07:95	KALQVARQF	0.9556	0.7068	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C02:06	NVVSKALQV	0.9435	0.8605	8	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:06	KALQVARQF	0.9408	0.8194	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:09	VQNVVSKAL	0.9371	0.6222	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:07	KALQVARQF	0.9292	0.8951	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:08	VQNVVSKAL	0.9143	0.8573	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:14	KALQVARQF	0.8185	0.9478	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B14:03	VQNVVSKAL	0.6679	0.8342	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C12:12	KALQVARQF	0.4343	0.9642	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C02:06	KALQVARQF	0.3884	0.904	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:05	VQNVVSKAL	0.2829	0.589	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C12:04	KALQVARQF	0.2773	0.9894	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C06:03	KALQVARQF	0.2675	0.9897	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A31:01	VVSKALQVAR	0.9461	0.7055	9	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A68:01	NVVSKALQVAR	0.9958	0.679	8	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:10	KALQVARQF	0.9991	0.9075	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:02	NVVSKALQV	0.9988	0.6568	8	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:05	NVVSKALQV	0.9988	0.7804	8	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B58:06	KALQVARQF	0.9968	0.7803	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:135	VQNVVSKAL	0.9965	0.6876	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:125	VQNVVSKAL	0.9964	0.6901	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:34	VQNVVSKAL	0.9964	0.6901	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:33	VQNVVSKAL	0.9964	0.6901	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:27	VQNVVSKAL	0.9962	0.7344	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:24	VQNVVSKAL	0.9956	0.7588	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:50	VQNVVSKAL	0.9934	0.8169	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A32:01	KALQVARQF	0.9885	0.9283	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:04	KALQVARQF	0.9825	0.6933	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:09	KALQVARQF	0.9773	0.831	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:02	KALQVARQF	0.9754	0.9471	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:35	VQNVVSKAL	0.9721	0.7423	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-A74:01	VSKALQVAR	0.9652	0.7094	10	19
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:13	KALQVARQF	0.9652	0.5546	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:03	KALQVARQF	0.9638	0.9657	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:04	KALQVARQF	0.9638	0.9657	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:73	VQNVVSKAL	0.9451	0.8593	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:02	VQNVVSKAL	0.9368	0.8535	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:05	KALQVARQF	0.9333	0.847	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:53	VQNVVSKAL	0.9319	0.6589	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:31	VQNVVSKAL	0.9259	0.8206	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C03:17	KALQVARQF	0.9033	0.9428	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:30	VQNVVSKAL	0.8816	0.7779	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B35:28	KALQVARQF	0.8665	0.7591	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:24	KALQVARQF	0.8662	0.7823	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:02	KALQVARQF	0.8603	0.8986	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B39:11	VQNVVSKAL	0.853	0.7848	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:54	VQNVVSKAL	0.8399	0.6228	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:05	KALQVARQF	0.8294	0.8555	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:12	VQNVVSKAL	0.8247	0.7296	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C15:02	KALQVARQF	0.8204	0.7941	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C16:01	KALQVARQF	0.8019	0.9756	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C16:04	KALQVARQF	0.7617	0.9818	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C16:02	KALQVARQF	0.7223	0.9858	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B48:02	VQNVVSKAL	0.5846	0.6532	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C06:08	KALQVARQF	0.5748	0.9796	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C02:10	KALQVARQF	0.4723	0.9233	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C02:02	KALQVARQF	0.4723	0.9233	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:09	VQNVVSKAL	0.4197	0.6604	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C12:03	KALQVARQF	0.394	0.9825	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-C12:02	KALQVARQF	0.3589	0.9573	12	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B35:28	VQNVVSKAL	0.2586	0.6916	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:20	VQNVVSKAL	0.2565	0.6751	6	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B15:68	SKALQVARQF	0.9819	0.5014	11	21
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	HLA-B57:10	VSKALQVARQF	0.9999	0.8744	10	21

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Potential FusionNeoAntigen Information of SLC22A23-FOXP4 in HLA II

SLC22A23-FOXP4_3456140_41545724.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)
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0201	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0201	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0201	GIRAGLVQNVVSKAL	0	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0202	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0202	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0204	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0204	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0205	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0205	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0210	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0210	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0211	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0211	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0212	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0212	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0213	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0213	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0214	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0214	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0215	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0215	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0217	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0217	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0218	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0218	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0219	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0219	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0220	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0220	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0222	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0222	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0223	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0223	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0224	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0224	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0224	GIRAGLVQNVVSKAL	0	15
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0225	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0225	IRAGLVQNVVSKALQ	1	16
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0301	RAGLVQNVVSKALQV	2	17
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	654	DRB3-0301	IRAGLVQNVVSKALQ	1	16

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Fusion breakpoint peptide structures of SLC22A23-FOXP4

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
10213	VQNVVSKALQVARQ	SLC22A23	FOXP4	chr6	3456140	chr6	41545724	654

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SLC22A23-FOXP4

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	10213	VQNVVSKALQVARQ	-7.15543	-7.26883
HLA-B14:02	3BVN	10213	VQNVVSKALQVARQ	-4.77435	-5.80965
HLA-B52:01	3W39	10213	VQNVVSKALQVARQ	-6.80875	-6.92215
HLA-B52:01	3W39	10213	VQNVVSKALQVARQ	-4.20386	-5.23916
HLA-A11:01	4UQ2	10213	VQNVVSKALQVARQ	-7.5194	-8.5547
HLA-A11:01	4UQ2	10213	VQNVVSKALQVARQ	-6.9601	-7.0735
HLA-A24:02	5HGA	10213	VQNVVSKALQVARQ	-7.52403	-7.63743
HLA-A24:02	5HGA	10213	VQNVVSKALQVARQ	-5.82433	-6.85963
HLA-B27:05	6PYJ	10213	VQNVVSKALQVARQ	-3.28285	-4.31815
HLA-B44:05	3DX8	10213	VQNVVSKALQVARQ	-5.91172	-6.94702
HLA-B44:05	3DX8	10213	VQNVVSKALQVARQ	-4.24346	-4.35686
HLA-B35:01	1A1N	10213	VQNVVSKALQVARQ	-5.9251	-6.0385
HLA-B35:01	1A1N	10213	VQNVVSKALQVARQ	-4.80237	-5.83767

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Vaccine Design for the FusionNeoAntigens of SLC22A23-FOXP4

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
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	10	19	VSKALQVAR	GTCAGCAAGGCTCTCCAAGTGGCCCGG
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	10	21	VSKALQVARQF	GTCAGCAAGGCTCTCCAAGTGGCCCGGCAGTTC
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	11	21	SKALQVARQF	AGCAAGGCTCTCCAAGTGGCCCGGCAGTTC
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	12	21	KALQVARQF	AAGGCTCTCCAAGTGGCCCGGCAGTTC
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	6	15	VQNVVSKAL	GTCCAGAACGTGGTCAGCAAGGCTCTC
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	8	17	NVVSKALQV	AACGTGGTCAGCAAGGCTCTCCAAGTG
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	8	19	NVVSKALQVAR	AACGTGGTCAGCAAGGCTCTCCAAGTGGCCCGG
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	9	19	VVSKALQVAR	GTGGTCAGCAAGGCTCTCCAAGTGGCCCGG

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
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	0	15	GIRAGLVQNVVSKAL	GGCATCCGCGCCGGCCTCGTCCAGAACGTGGTCAGCAAGGCTCTC
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	1	16	IRAGLVQNVVSKALQ	ATCCGCGCCGGCCTCGTCCAGAACGTGGTCAGCAAGGCTCTCCAA
SLC22A23-FOXP4	chr6	3456140	chr6	41545724	2	17	RAGLVQNVVSKALQV	CGCGCCGGCCTCGTCCAGAACGTGGTCAGCAAGGCTCTCCAAGTG

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Information of the samples that have these potential fusion neoantigens of SLC22A23-FOXP4

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
STAD	SLC22A23-FOXP4	chr6	3456140	ENST00000380298	chr6	41545724	ENST00000307972	TCGA-BR-A4PD-01A

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Potential target of CAR-T therapy development for SLC22A23-FOXP4

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 SLC22A23-FOXP4

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 SLC22A23-FOXP4

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)