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Fusion Protein:FOXN3-CDKL1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FOXN3-CDKL1
	FusionPDB ID: 31138
	FusionGDB2.0 ID: 31138
		Hgene	Tgene
	Gene symbol	FOXN3	CDKL1
	Gene ID	1112	8814
	Gene name	forkhead box N3	cyclin dependent kinase like 1
	Synonyms	C14orf116\|CHES1\|PRO1635	KKIALRE\|P42
	Cytomap	14q31.3-q32.11	14q21.3
	Type of gene	protein-coding	protein-coding
	Description	forkhead box protein N3checkpoint suppressor 1	cyclin-dependent kinase-like 1cyclin-dependent kinase-like 1 (CDC2-related kinase)protein kinase p42 KKIALREserine/threonine protein kinase KKIALRE
	Modification date	20200313	20200313
	UniProtAcc	O00409 Main function of 5'-partner protein: FUNCTION: Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints). {ECO:0000269\|PubMed:16102918}.	Q00532 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000261302, ENST00000345097, ENST00000555353, ENST00000557258, ENST00000555658,	ENST00000216378, ENST00000356146, ENST00000395834,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	21 X 18 X 8=3024	4 X 4 X 3=48
	# samples	22	6
	** MAII score	log2(22/3024*10)=-3.78088271069641 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/48*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: FOXN3 [Title/Abstract] AND CDKL1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: FOXN3 [Title/Abstract] AND CDKL1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FOXN3(89878278)-CDKL1(50796899), # samples:3
Anticipated loss of major functional domain due to fusion event.	FOXN3-CDKL1 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. FOXN3-CDKL1 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. FOXN3-CDKL1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. FOXN3-CDKL1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. FOXN3-CDKL1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. FOXN3-CDKL1 seems lost the major protein functional domain in Tgene partner, which is a kinase 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	FOXN3	GO:0045892	negative regulation of transcription, DNA-templated	16102918

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr14:89878278/chr14:50796899)
- 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 FOXN3 (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 CDKL1 (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)
ENST00000261302	FOXN3	chr14	89878278	-	ENST00000395834	CDKL1	chr14	50796899	-	1149	559	16	666	216
ENST00000557258	FOXN3	chr14	89878278	-	ENST00000395834	CDKL1	chr14	50796899	-	1389	799	256	906	216
ENST00000261302	FOXN3	chr14	89878277	-	ENST00000395834	CDKL1	chr14	50796899	-	1149	559	16	666	216
ENST00000557258	FOXN3	chr14	89878277	-	ENST00000395834	CDKL1	chr14	50796899	-	1389	799	256	906	216

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
ENST00000261302	ENST00000395834	FOXN3	chr14	89878278	-	CDKL1	chr14	50796899	-	0.003143925	0.9968561
ENST00000557258	ENST00000395834	FOXN3	chr14	89878278	-	CDKL1	chr14	50796899	-	0.003089158	0.99691087
ENST00000261302	ENST00000395834	FOXN3	chr14	89878277	-	CDKL1	chr14	50796899	-	0.003143925	0.9968561
ENST00000557258	ENST00000395834	FOXN3	chr14	89878277	-	CDKL1	chr14	50796899	-	0.003089158	0.99691087

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 FOXN3-CDKL1

+/-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
FOXN3	chr14	89878277	CDKL1	chr14	50796899	559	181	NKCFKKVDKERSQLQYLPQLTGSSIL
FOXN3	chr14	89878277	CDKL1	chr14	50796899	799	181	NKCFKKVDKERSQLQYLPQLTGSSIL
FOXN3	chr14	89878278	CDKL1	chr14	50796899	559	181	NKCFKKVDKERSQLQYLPQLTGSSIL
FOXN3	chr14	89878278	CDKL1	chr14	50796899	799	181	NKCFKKVDKERSQLQYLPQLTGSSIL

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Potential FusionNeoAntigen Information of FOXN3-CDKL1 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.

FOXN3-CDKL1_89878277_50796899.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)
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B14:02	ERSQLQYL	0.9981	0.5528	9	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B14:01	ERSQLQYL	0.9981	0.5528	9	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:03	KERSQLQY	0.9207	0.6373	8	16
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B48:01	SQLQYLPQL	0.9934	0.7864	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B27:07	SQLQYLPQL	0.9889	0.655	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B13:01	KERSQLQYL	0.9856	0.8598	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:24	SQLQYLPQL	0.971	0.8008	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:06	SQLQYLPQL	0.9657	0.8912	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B14:01	SQLQYLPQL	0.9622	0.9672	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B14:02	SQLQYLPQL	0.9622	0.9672	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:21	SQLQYLPQL	0.895	0.7731	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B13:02	SQLQYLPQL	0.884	0.8211	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:30	SQLQYLPQL	0.8828	0.6622	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:24	SQLQYLPQL	0.8828	0.6622	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:67	SQLQYLPQL	0.8828	0.6622	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:60	SQLQYLPQL	0.8818	0.625	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B44:03	KERSQLQYL	0.865	0.892	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:11	SQLQYLPQL	0.8613	0.6861	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:01	SQLQYLPQL	0.8585	0.9869	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:22	SQLQYLPQL	0.8508	0.663	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B40:05	SQLQYLPQL	0.8316	0.5231	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:38	SQLQYLPQL	0.8287	0.7866	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:04	SQLQYLPQL	0.8187	0.7463	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B13:01	SQLQYLPQL	0.8042	0.9925	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:17	SQLQYLPQL	0.786	0.5781	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:13	SQLQYLPQL	0.7706	0.9908	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B38:01	SQLQYLPQL	0.7572	0.9931	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B47:01	SQLQYLPQL	0.7529	0.8093	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B38:02	SQLQYLPQL	0.7425	0.9942	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:29	SQLQYLPQL	0.7395	0.6618	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:16	SQLQYLPQL	0.7325	0.6456	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:20	SQLQYLPQL	0.7263	0.6728	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:27	SQLQYLPQL	0.7006	0.73	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:13	SQLQYLPQL	0.6505	0.8097	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:35	SQLQYLPQL	0.6443	0.686	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:25	SQLQYLPQL	0.5987	0.9709	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:03	SQLQYLPQL	0.5776	0.9211	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A32:13	SQLQYLPQL	0.525	0.9229	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:10	SQLQYLPQL	0.5228	0.8481	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:13	KERSQLQYL	0.462	0.8135	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B41:01	KERSQLQYL	0.4457	0.7177	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A24:14	SQLQYLPQL	0.408	0.618	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:37	SQLQYLPQL	0.3498	0.8787	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:18	DKERSQLQY	0.2205	0.7648	7	16
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:19	SQLQYLPQL	0.1726	0.5958	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B50:01	KERSQLQYL	0.1543	0.6189	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B52:01	SQLQYLPQL	0.0704	0.9902	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B07:10	SQLQYLPQL	0.0574	0.534	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B48:01	RSQLQYLPQL	0.825	0.7329	10	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B13:02	RSQLQYLPQL	0.4595	0.8269	10	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:12	ERSQLQYL	0.9981	0.7836	9	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B14:03	ERSQLQYL	0.8878	0.6758	9	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C05:09	KVDKERSQL	1	0.9211	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:07	KVDKERSQL	0.9999	0.836	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:15	KVDKERSQL	0.9999	0.9598	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:10	KVDKERSQL	0.9999	0.8327	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C03:07	KVDKERSQL	0.9986	0.9722	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C15:06	KVDKERSQL	0.9969	0.9184	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:06	KVDKERSQL	0.9907	0.9046	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:14	KVDKERSQL	0.9772	0.8945	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B73:01	ERSQLQYLP	0.9763	0.6227	9	18
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:04	KVDKERSQL	0.9653	0.9518	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:13	KVDKERSQL	0.9653	0.9518	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:05	SQLQYLPQL	0.8868	0.651	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:01	SQLQYLPQL	0.8828	0.6622	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:05	SQLQYLPQL	0.8822	0.9831	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:07	SQLQYLPQL	0.8789	0.7166	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:08	KVDKERSQL	0.8699	0.7244	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:13	SQLQYLPQL	0.8693	0.9725	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:09	SQLQYLPQL	0.8686	0.8538	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:29	SQLQYLPQL	0.8628	0.9732	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:67	SQLQYLPQL	0.8627	0.9834	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:80	SQLQYLPQL	0.8627	0.9834	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:10	SQLQYLPQL	0.8578	0.9887	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:12	SQLQYLPQL	0.8578	0.9879	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:02	SQLQYLPQL	0.8569	0.5183	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:04	SQLQYLPQL	0.8305	0.9666	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:03	KVDKERSQL	0.8039	0.9774	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B48:03	SQLQYLPQL	0.8016	0.6983	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:46	SQLQYLPQL	0.7869	0.9622	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:27	SQLQYLPQL	0.7788	0.9797	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:07	SQLQYLPQL	0.776	0.8789	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:05	SQLQYLPQL	0.7555	0.985	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C02:06	SQLQYLPQL	0.6893	0.9788	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:08	SQLQYLPQL	0.6585	0.9694	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:07	KVDKERSQL	0.6544	0.5736	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B44:10	SQLQYLPQL	0.6322	0.7451	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B14:03	SQLQYLPQL	0.4933	0.9168	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:08	KERSQLQYL	0.4738	0.5904	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C12:16	SQLQYLPQL	0.4693	0.9787	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:05	SQLQYLPQL	0.3031	0.9412	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B51:07	SQLQYLPQL	0.0579	0.9578	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:15	FKKVDKERSQL	0.9996	0.9669	3	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:31	ERSQLQYL	0.9982	0.7747	9	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:53	KERSQLQY	0.9812	0.7746	8	16
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:54	KERSQLQY	0.9548	0.7493	8	16
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C05:01	KVDKERSQL	1	0.9211	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C01:03	KVDKERSQL	0.9999	0.8996	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:02	KVDKERSQL	0.9999	0.9598	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:01	KVDKERSQL	0.9999	0.836	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C18:01	KVDKERSQL	0.9999	0.8434	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:03	KVDKERSQL	0.9999	0.8516	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B40:04	KERSQLQYL	0.9966	0.6438	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C15:05	KVDKERSQL	0.9955	0.8997	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B27:06	SQLQYLPQL	0.9912	0.8492	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B27:09	SQLQYLPQL	0.987	0.8479	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B07:13	KVDKERSQL	0.9851	0.7499	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C17:01	SQLQYLPQL	0.9744	0.9818	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:04	KVDKERSQL	0.9678	0.9147	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C03:06	KVDKERSQL	0.9364	0.985	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C04:04	SQLQYLPQL	0.93	0.9625	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:24	SQLQYLPQL	0.9292	0.9733	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:02	SQLQYLPQL	0.9158	0.9909	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:50	SQLQYLPQL	0.9112	0.9562	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:14	SQLQYLPQL	0.9005	0.7517	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C06:06	SQLQYLPQL	0.9	0.9922	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:06	SQLQYLPQL	0.895	0.7731	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:31	SQLQYLPQL	0.8782	0.9871	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B44:26	KERSQLQYL	0.865	0.892	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B44:13	KERSQLQYL	0.865	0.892	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B44:07	KERSQLQYL	0.865	0.892	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:02	SQLQYLPQL	0.8627	0.9834	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B40:49	SQLQYLPQL	0.8544	0.6716	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:04	SQLQYLPQL	0.8519	0.9713	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C06:08	SQLQYLPQL	0.827	0.9948	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:73	SQLQYLPQL	0.8235	0.9784	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C07:17	SQLQYLPQL	0.8229	0.9855	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A32:01	SQLQYLPQL	0.8192	0.9487	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:35	SQLQYLPQL	0.8163	0.9301	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B40:21	SQLQYLPQL	0.8072	0.7483	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C17:01	KVDKERSQL	0.8056	0.9199	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:01	KVDKERSQL	0.8039	0.9774	5	14
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A02:03	SQLQYLPQL	0.8034	0.7937	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B40:12	SQLQYLPQL	0.8016	0.6983	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:54	SQLQYLPQL	0.7598	0.9456	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B38:05	SQLQYLPQL	0.7572	0.9931	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:53	SQLQYLPQL	0.7383	0.9427	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C03:67	SQLQYLPQL	0.7358	0.9899	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:30	SQLQYLPQL	0.7221	0.9788	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B18:04	DKERSQLQY	0.7175	0.9138	7	16
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:68	SQLQYLPQL	0.703	0.863	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:11	SQLQYLPQL	0.6315	0.9628	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:39	SQLQYLPQL	0.6052	0.939	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B48:02	SQLQYLPQL	0.4929	0.9599	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B39:02	KERSQLQYL	0.4861	0.8122	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B35:13	SQLQYLPQL	0.4744	0.9454	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B18:06	DKERSQLQY	0.4706	0.8933	7	16
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:54	KERSQLQYL	0.4383	0.7515	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:09	SQLQYLPQL	0.4162	0.893	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B35:28	SQLQYLPQL	0.2974	0.9621	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:20	SQLQYLPQL	0.285	0.9598	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B48:02	KERSQLQYL	0.2804	0.8299	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B15:53	KERSQLQYL	0.2391	0.7676	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-A30:04	SQLQYLPQL	0.227	0.5319	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B50:04	KERSQLQYL	0.1543	0.6189	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B50:05	KERSQLQYL	0.1543	0.6189	8	17
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-B07:13	SQLQYLPQL	0.1259	0.8373	11	20
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	HLA-C08:02	FKKVDKERSQL	0.9996	0.9669	3	14

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Potential FusionNeoAntigen Information of FOXN3-CDKL1 in HLA II

FOXN3-CDKL1_89878277_50796899.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)
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0802	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0809	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0813	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0815	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0821	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0824	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-0830	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1101	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1105	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1108	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1109	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1110	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1111	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1112	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1115	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1119	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1124	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1127	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1128	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1129	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1131	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1132	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1133	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1137	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1139	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1145	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1149	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1151	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1153	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1161	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1162	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1164	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1166	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1169	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1172	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1173	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1174	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1175	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1180	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1181	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1182	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1187	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1190	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1191	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1193	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1194	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1195	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1196	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1204	RSQLQYLPQLTGSSI	10	25
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1204	ERSQLQYLPQLTGSS	9	24
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1209	RSQLQYLPQLTGSSI	10	25
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1209	ERSQLQYLPQLTGSS	9	24
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1219	ERSQLQYLPQLTGSS	9	24
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1219	RSQLQYLPQLTGSSI	10	25
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1220	ERSQLQYLPQLTGSS	9	24
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1305	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1307	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1314	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1326	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1337	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1347	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1349	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1350	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1355	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1356	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1360	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1362	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1363	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1382	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1385	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1386	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1402	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1403	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1409	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1414	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1419	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1422	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1424	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1425	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1427	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1430	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1436	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1440	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1441	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1442	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1444	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1451	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1453	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1467	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1477	NKCFKKVDKERSQLQ	0	15
FOXN3-CDKL1	chr14	89878277	chr14	50796899	559	DRB1-1494	NKCFKKVDKERSQLQ	0	15

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Fusion breakpoint peptide structures of FOXN3-CDKL1

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
9853	VDKERSQLQYLPQL	FOXN3	CDKL1	chr14	89878277	chr14	50796899	559

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FOXN3-CDKL1

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-B52:01	3W39	9853	VDKERSQLQYLPQL	-6.05118	-6.05118
HLA-B44:05	3DX8	9853	VDKERSQLQYLPQL	-6.0991	-6.0991

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Vaccine Design for the FusionNeoAntigens of FOXN3-CDKL1

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
FOXN3-CDKL1	chr14	89878277	chr14	50796899	10	20	RSQLQYLPQL	AGGAGTCAGTTGCAGTACCTACCCCAGCTA
FOXN3-CDKL1	chr14	89878277	chr14	50796899	11	20	SQLQYLPQL	AGTCAGTTGCAGTACCTACCCCAGCTA
FOXN3-CDKL1	chr14	89878277	chr14	50796899	3	14	FKKVDKERSQL	TTTAAGAAAGTGGACAAAGAGAGGAGTCAGTTG
FOXN3-CDKL1	chr14	89878277	chr14	50796899	5	14	KVDKERSQL	AAAGTGGACAAAGAGAGGAGTCAGTTG
FOXN3-CDKL1	chr14	89878277	chr14	50796899	7	16	DKERSQLQY	GACAAAGAGAGGAGTCAGTTGCAGTAC
FOXN3-CDKL1	chr14	89878277	chr14	50796899	8	16	KERSQLQY	AAAGAGAGGAGTCAGTTGCAGTAC
FOXN3-CDKL1	chr14	89878277	chr14	50796899	8	17	KERSQLQYL	AAAGAGAGGAGTCAGTTGCAGTACCTA
FOXN3-CDKL1	chr14	89878277	chr14	50796899	9	17	ERSQLQYL	GAGAGGAGTCAGTTGCAGTACCTA
FOXN3-CDKL1	chr14	89878277	chr14	50796899	9	18	ERSQLQYLP	GAGAGGAGTCAGTTGCAGTACCTACCC

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
FOXN3-CDKL1	chr14	89878277	chr14	50796899	0	15	NKCFKKVDKERSQLQ	AATAAGTGTTTTAAGAAAGTGGACAAAGAGAGGAGTCAGTTGCAG
FOXN3-CDKL1	chr14	89878277	chr14	50796899	10	25	RSQLQYLPQLTGSSI	AGGAGTCAGTTGCAGTACCTACCCCAGCTAACTGGCAGCAGCATC
FOXN3-CDKL1	chr14	89878277	chr14	50796899	9	24	ERSQLQYLPQLTGSS	GAGAGGAGTCAGTTGCAGTACCTACCCCAGCTAACTGGCAGCAGC

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Information of the samples that have these potential fusion neoantigens of FOXN3-CDKL1

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
COAD	FOXN3-CDKL1	chr14	89878277	ENST00000261302	chr14	50796899	ENST00000395834	TCGA-A6-5667

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Potential target of CAR-T therapy development for FOXN3-CDKL1

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 FOXN3-CDKL1

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 FOXN3-CDKL1

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)