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Fusion Protein:FOXP4-CCND3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FOXP4-CCND3
	FusionPDB ID: 31237
	FusionGDB2.0 ID: 31237
		Hgene	Tgene
	Gene symbol	FOXP4	CCND3
	Gene ID	116113	896
	Gene name	forkhead box P4	cyclin D3
	Synonyms	hFKHLA	-
	Cytomap	6p21.1	6p21.1
	Type of gene	protein-coding	protein-coding
	Description	forkhead box protein P4fork head-related protein like Awinged-helix repressor FOXP4	G1/S-specific cyclin-D3D3-type cyclin
	Modification date	20200313	20200313
	UniProtAcc	Q8IVH2 Main function of 5'-partner protein: FUNCTION: Transcriptional repressor that represses lung-specific expression. {ECO:0000250}.	P30281 Main function of 5'-partner protein: FUNCTION: Regulatory component of the cyclin D3-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition. Phosphorylation of RB1 allows dissociation of the transcription factor E2F from the RB/E2F complex and the subsequent transcription of E2F target genes which are responsible for the progression through the G(1) phase. Hypophosphorylates RB1 in early G(1) phase. Cyclin D-CDK4 complexes are major integrators of various mitogenenic and antimitogenic signals. Also substrate for SMAD3, phosphorylating SMAD3 in a cell-cycle-dependent manner and repressing its transcriptional activity. Component of the ternary complex, cyclin D3/CDK4/CDKN1B, required for nuclear translocation and activity of the cyclin D-CDK4 complex. {ECO:0000269\|PubMed:15358120}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000307972, ENST00000373057, ENST00000373060, ENST00000373063, ENST00000409208,	ENST00000372987, ENST00000372988, ENST00000372991, ENST00000414200, ENST00000415497, ENST00000510503, ENST00000511642, ENST00000511686,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 7 X 4=196	9 X 3 X 7=189
	# samples	10	11
	** MAII score	log2(10/196*10)=-0.970853654340483 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/189*10)=-0.780882710696413 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: FOXP4 [Title/Abstract] AND CCND3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: FOXP4 [Title/Abstract] AND CCND3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FOXP4(41545819)-CCND3(41908323), # samples:3
Anticipated loss of major functional domain due to fusion event.	FOXP4-CCND3 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. FOXP4-CCND3 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. FOXP4-CCND3 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. FOXP4-CCND3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	CCND3	GO:0001934	positive regulation of protein phosphorylation	8114739
Tgene	CCND3	GO:0045737	positive regulation of cyclin-dependent protein serine/threonine kinase activity	8114739

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:41545819/chr6:41908323)
- 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 FOXP4 (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 CCND3 (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)
ENST00000373060	FOXP4	chr6	41545819	+	ENST00000511642	CCND3	chr6	41905132	-	2229	758	458	1222	254
ENST00000373063	FOXP4	chr6	41545819	+	ENST00000511642	CCND3	chr6	41905132	-	2229	758	458	1222	254
ENST00000409208	FOXP4	chr6	41545819	+	ENST00000511642	CCND3	chr6	41905132	-	2082	611	311	1075	254
ENST00000373057	FOXP4	chr6	41545819	+	ENST00000511642	CCND3	chr6	41905132	-	2007	536	236	1000	254
ENST00000307972	FOXP4	chr6	41545819	+	ENST00000511642	CCND3	chr6	41905132	-	1783	312	12	776	254
ENST00000373060	FOXP4	chr6	41552629	+	ENST00000511642	CCND3	chr6	41905132	-	2352	881	458	1345	295
ENST00000373063	FOXP4	chr6	41552629	+	ENST00000511642	CCND3	chr6	41905132	-	2352	881	458	1345	295
ENST00000409208	FOXP4	chr6	41552629	+	ENST00000511642	CCND3	chr6	41905132	-	2205	734	311	1198	295
ENST00000373057	FOXP4	chr6	41552629	+	ENST00000511642	CCND3	chr6	41905132	-	2130	659	236	1123	295
ENST00000307972	FOXP4	chr6	41552629	+	ENST00000511642	CCND3	chr6	41905132	-	1906	435	12	899	295
ENST00000373060	FOXP4	chr6	41533702	+	ENST00000511642	CCND3	chr6	41905132	-	2133	662	458	1126	222
ENST00000373063	FOXP4	chr6	41533702	+	ENST00000511642	CCND3	chr6	41905132	-	2133	662	458	1126	222
ENST00000409208	FOXP4	chr6	41533702	+	ENST00000511642	CCND3	chr6	41905132	-	1986	515	311	979	222
ENST00000373057	FOXP4	chr6	41533702	+	ENST00000511642	CCND3	chr6	41905132	-	1911	440	236	904	222
ENST00000307972	FOXP4	chr6	41533702	+	ENST00000511642	CCND3	chr6	41905132	-	1687	216	12	680	222

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
ENST00000373060	ENST00000511642	FOXP4	chr6	41545819	+	CCND3	chr6	41905132	-	0.06072927	0.93927073
ENST00000373063	ENST00000511642	FOXP4	chr6	41545819	+	CCND3	chr6	41905132	-	0.06072927	0.93927073
ENST00000409208	ENST00000511642	FOXP4	chr6	41545819	+	CCND3	chr6	41905132	-	0.07020636	0.9297937
ENST00000373057	ENST00000511642	FOXP4	chr6	41545819	+	CCND3	chr6	41905132	-	0.06819085	0.9318091
ENST00000307972	ENST00000511642	FOXP4	chr6	41545819	+	CCND3	chr6	41905132	-	0.08464635	0.9153536
ENST00000373060	ENST00000511642	FOXP4	chr6	41552629	+	CCND3	chr6	41905132	-	0.020734834	0.9792652
ENST00000373063	ENST00000511642	FOXP4	chr6	41552629	+	CCND3	chr6	41905132	-	0.020734834	0.9792652
ENST00000409208	ENST00000511642	FOXP4	chr6	41552629	+	CCND3	chr6	41905132	-	0.024059348	0.97594064
ENST00000373057	ENST00000511642	FOXP4	chr6	41552629	+	CCND3	chr6	41905132	-	0.023294637	0.9767054
ENST00000307972	ENST00000511642	FOXP4	chr6	41552629	+	CCND3	chr6	41905132	-	0.027771987	0.97222805
ENST00000373060	ENST00000511642	FOXP4	chr6	41533702	+	CCND3	chr6	41905132	-	0.05818045	0.94181955
ENST00000373063	ENST00000511642	FOXP4	chr6	41533702	+	CCND3	chr6	41905132	-	0.05818045	0.94181955
ENST00000409208	ENST00000511642	FOXP4	chr6	41533702	+	CCND3	chr6	41905132	-	0.08776937	0.9122306
ENST00000373057	ENST00000511642	FOXP4	chr6	41533702	+	CCND3	chr6	41905132	-	0.08296455	0.9170355
ENST00000307972	ENST00000511642	FOXP4	chr6	41533702	+	CCND3	chr6	41905132	-	0.07358518	0.9264148

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 FOXP4-CCND3

+/-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
FOXP4	chr6	41533702	CCND3	chr6	41905132	216	67	EMSPAELLHFQQQQDWEVLVLGKLKW
FOXP4	chr6	41533702	CCND3	chr6	41905132	440	67	EMSPAELLHFQQQQDWEVLVLGKLKW
FOXP4	chr6	41533702	CCND3	chr6	41905132	515	67	EMSPAELLHFQQQQDWEVLVLGKLKW
FOXP4	chr6	41533702	CCND3	chr6	41905132	662	67	EMSPAELLHFQQQQDWEVLVLGKLKW
FOXP4	chr6	41545819	CCND3	chr6	41905132	312	99	PGNNDSKQSASAVQDWEVLVLGKLKW
FOXP4	chr6	41545819	CCND3	chr6	41905132	536	99	PGNNDSKQSASAVQDWEVLVLGKLKW
FOXP4	chr6	41545819	CCND3	chr6	41905132	611	99	PGNNDSKQSASAVQDWEVLVLGKLKW
FOXP4	chr6	41545819	CCND3	chr6	41905132	758	99	PGNNDSKQSASAVQDWEVLVLGKLKW
FOXP4	chr6	41552629	CCND3	chr6	41905132	435	138	QLQALLQQQQALMLQQDWEVLVLGKL
FOXP4	chr6	41552629	CCND3	chr6	41905132	659	138	QLQALLQQQQALMLQQDWEVLVLGKL
FOXP4	chr6	41552629	CCND3	chr6	41905132	734	138	QLQALLQQQQALMLQQDWEVLVLGKL
FOXP4	chr6	41552629	CCND3	chr6	41905132	881	138	QLQALLQQQQALMLQQDWEVLVLGKL

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Potential FusionNeoAntigen Information of FOXP4-CCND3 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.

FOXP4-CCND3_41533702_41905132.msa
FOXP4-CCND3_41545819_41905132.msa
FOXP4-CCND3_41552629_41905132.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)
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:13	QQQDWEVL	0.9124	0.9913	11	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:21	FQQQQDWEV	0.9578	0.8225	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:30	FQQQQDWEV	0.9461	0.7504	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:24	FQQQQDWEV	0.9461	0.7504	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:67	FQQQQDWEV	0.9461	0.7504	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:60	FQQQQDWEV	0.9455	0.7681	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B48:01	QQQQDWEVL	0.9389	0.8115	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:01	QQQQDWEVL	0.9341	0.9704	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:22	FQQQQDWEV	0.9102	0.7815	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:21	QQQDWEVLV	0.8893	0.8353	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:13	QQQQDWEVL	0.8882	0.9903	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:60	QQQDWEVLV	0.8802	0.7417	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:29	FQQQQDWEV	0.8801	0.7527	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:30	QQQDWEVLV	0.8731	0.7594	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:24	QQQDWEVLV	0.8731	0.7594	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:67	QQQDWEVLV	0.8731	0.7594	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:04	FQQQQDWEV	0.8549	0.8944	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:20	FQQQQDWEV	0.8532	0.7563	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B38:01	QQQQDWEVL	0.849	0.9886	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B38:02	QQQQDWEVL	0.8429	0.9896	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:02	QQQDWEVLV	0.8147	0.9737	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:16	FQQQQDWEV	0.7681	0.7096	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:27	FQQQQDWEV	0.7353	0.7183	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:29	QQQDWEVLV	0.7289	0.7615	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:01	QQQDWEVLV	0.711	0.9968	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:20	QQQDWEVLV	0.7005	0.7654	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:02	FQQQQDWEV	0.64	0.9832	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B38:01	LHFQQQQDW	0.5848	0.9968	7	16
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B38:02	LHFQQQQDW	0.5367	0.9975	7	16
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:16	QQQDWEVLV	0.53	0.626	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:01	FQQQQDWEV	0.485	0.9976	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:01	QQQQDWEVL	0.4844	0.9961	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B15:18	LHFQQQQDW	0.4766	0.9515	7	16
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:19	FQQQQDWEV	0.3885	0.6974	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:19	QQQDWEVLV	0.3585	0.6094	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:13	FQQQQDWEV	0.3052	0.9951	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B52:01	QQQDWEVLV	0.1103	0.9922	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B48:01	QQQDWEVLVL	0.9137	0.9113	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:13	QQQDWEVLVL	0.8183	0.9948	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:02	QQQDWEVLVL	0.6239	0.9631	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B13:01	QQQDWEVLVL	0.5702	0.9976	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:01	FQQQQDWEV	0.9461	0.7504	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:05	FQQQQDWEV	0.93	0.7578	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:05	QQQDWEVLV	0.924	0.7643	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:02	FQQQQDWEV	0.9158	0.6865	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:01	QQQDWEVLV	0.8731	0.7594	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:05	QQQQDWEVL	0.8671	0.9684	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:08	QQQQDWEVL	0.8638	0.9765	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B48:03	QQQQDWEVL	0.7565	0.7082	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:08	FQQQQDWEV	0.3723	0.9735	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:05	FQQQQDWEV	0.2638	0.9887	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B48:03	FQQQQDWEV	0.2595	0.7969	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:08	QQQDWEVLVL	0.8336	0.9891	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B48:03	QQQDWEVLVL	0.7864	0.8336	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B48:03	FQQQQDWEVL	0.616	0.6386	9	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:06	FQQQQDWEV	0.9578	0.8225	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:14	FQQQQDWEV	0.9576	0.7963	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:02	QQQQDWEVL	0.9413	0.9905	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:31	QQQQDWEVL	0.9384	0.97	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:14	QQQDWEVLV	0.8925	0.8214	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-A02:06	QQQDWEVLV	0.8893	0.8353	11	20
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B38:05	QQQQDWEVL	0.849	0.9886	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:11	QQQQDWEVL	0.8273	0.9479	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B15:73	QQQQDWEVL	0.7759	0.8493	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:12	QQQQDWEVL	0.7565	0.7082	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B15:30	QQQQDWEVL	0.7335	0.9631	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:49	QQQQDWEVL	0.64	0.6718	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:21	QQQQDWEVL	0.6032	0.7925	10	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B38:05	LHFQQQQDW	0.5848	0.9968	7	16
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:21	FQQQQDWEV	0.3941	0.8343	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:11	FQQQQDWEV	0.3685	0.9484	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:02	FQQQQDWEV	0.3348	0.9951	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:12	FQQQQDWEV	0.2595	0.7969	9	18
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B15:73	QQQDWEVLVL	0.9321	0.9794	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B15:30	QQQDWEVLVL	0.9137	0.9881	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B39:02	QQQDWEVLVL	0.9041	0.9948	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:12	QQQDWEVLVL	0.7864	0.8336	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:49	QQQDWEVLVL	0.6834	0.811	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:21	QQQDWEVLVL	0.6552	0.8869	11	21
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:12	FQQQQDWEVL	0.616	0.6386	9	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:21	FQQQQDWEVL	0.5405	0.7059	9	19
FOXP4-CCND3	chr6	41533702	chr6	41905132	216	HLA-B40:21	QQQQDWEVLVL	0.9257	0.8834	10	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:01	QSASAVQDW	0.9968	0.9898	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:01	QSASAVQDW	0.9942	0.9945	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:16	QSASAVQDW	0.9914	0.9665	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:17	QSASAVQDW	0.99	0.9673	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:02	QSASAVQDW	0.9877	0.9792	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:21	AVQDWEVLV	0.9862	0.8318	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:38	AVQDWEVLV	0.983	0.8077	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B48:01	VQDWEVLVL	0.9822	0.967	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:60	AVQDWEVLV	0.9803	0.7528	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:30	AVQDWEVLV	0.9799	0.7483	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:24	AVQDWEVLV	0.9799	0.7483	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:67	AVQDWEVLV	0.9799	0.7483	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:03	SAVQDWEVL	0.9789	0.9522	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:11	AVQDWEVLV	0.978	0.7563	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:22	AVQDWEVLV	0.9684	0.7366	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:35	AVQDWEVLV	0.9583	0.7583	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:27	AVQDWEVLV	0.9509	0.7998	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:04	AVQDWEVLV	0.942	0.9111	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:02	SAVQDWEVL	0.9387	0.9851	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:04	SAVQDWEVL	0.9387	0.9851	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:16	AVQDWEVLV	0.9386	0.635	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:29	AVQDWEVLV	0.938	0.7497	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:13	AVQDWEVLV	0.9275	0.8478	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:03	QSASAVQDW	0.92	0.9953	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:20	AVQDWEVLV	0.9146	0.7546	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:01	VQDWEVLVL	0.8737	0.9779	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B53:01	QSASAVQDW	0.8332	0.6421	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:13	VQDWEVLVL	0.7954	0.9935	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B13:02	VQDWEVLVL	0.7665	0.9524	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B38:01	VQDWEVLVL	0.7295	0.9929	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B38:02	VQDWEVLVL	0.7066	0.9932	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:19	AVQDWEVLV	0.6907	0.6457	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B13:01	VQDWEVLVL	0.6865	0.9967	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:10	VQDWEVLVL	0.6449	0.8993	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:37	VQDWEVLVL	0.5722	0.9066	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A32:13	QSASAVQDW	0.5602	0.948	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B13:02	AVQDWEVLV	0.4981	0.9875	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B52:01	VQDWEVLVL	0.1939	0.9959	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:01	KQSASAVQDW	0.9795	0.9863	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:02	KQSASAVQDW	0.9406	0.9578	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:01	KQSASAVQDW	0.9189	0.9711	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:03	KQSASAVQDW	0.8323	0.9877	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A32:13	KQSASAVQDW	0.5992	0.949	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:01	SKQSASAVQDW	0.9997	0.9679	5	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:01	SKQSASAVQDW	0.9948	0.9311	5	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C05:09	VQDWEVLVL	0.9998	0.9906	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:10	VQDWEVLVL	0.9998	0.974	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:07	VQDWEVLVL	0.9998	0.982	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:15	VQDWEVLVL	0.9997	0.9942	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:19	SAVQDWEVL	0.999	0.9931	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:08	SAVQDWEVL	0.9989	0.9779	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:06	VQDWEVLVL	0.9828	0.9886	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:01	AVQDWEVLV	0.9799	0.7483	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:13	SAVQDWEVL	0.9773	0.9808	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:04	SAVQDWEVL	0.9773	0.9808	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:05	AVQDWEVLV	0.9772	0.7212	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:14	VQDWEVLVL	0.9696	0.9888	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:12	SAVQDWEVL	0.9387	0.9851	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:13	VQDWEVLVL	0.929	0.9908	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:04	VQDWEVLVL	0.929	0.9908	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:03	VQDWEVLVL	0.9279	0.9962	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C07:13	VQDWEVLVL	0.9137	0.9712	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C07:29	VQDWEVLVL	0.9136	0.9729	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:03	SAVQDWEVL	0.8963	0.9918	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:09	VQDWEVLVL	0.8603	0.9493	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:07	VQDWEVLVL	0.859	0.8076	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:08	VQDWEVLVL	0.8115	0.9873	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B48:03	VQDWEVLVL	0.7971	0.8582	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:05	VQDWEVLVL	0.7257	0.9752	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C02:06	VQDWEVLVL	0.7132	0.9769	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B44:08	QSASAVQDW	0.4322	0.6671	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B44:08	KQSASAVQDW	0.6615	0.7416	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:01	VQDWEVLVL	0.9998	0.982	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:03	VQDWEVLVL	0.9998	0.9839	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C01:03	VQDWEVLVL	0.9998	0.9798	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C05:01	VQDWEVLVL	0.9998	0.9906	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C18:01	VQDWEVLVL	0.9998	0.9797	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:02	VQDWEVLVL	0.9997	0.9942	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:03	SAVQDWEVL	0.9992	0.9943	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:04	SAVQDWEVL	0.9992	0.9943	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:04	QSASAVQDW	0.9972	0.7363	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C15:02	AVQDWEVLV	0.9969	0.9717	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B40:40	VQDWEVLVL	0.9945	0.5291	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:10	QSASAVQDW	0.9942	0.9945	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:06	QSASAVQDW	0.9869	0.9753	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:14	AVQDWEVLV	0.9863	0.8152	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:06	AVQDWEVLV	0.9862	0.8318	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C04:04	VQDWEVLVL	0.9815	0.9894	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:02	QSASAVQDW	0.9742	0.9236	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:13	SAVQDWEVL	0.9731	0.9554	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:06	SAVQDWEVL	0.9672	0.9951	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:22	SAVQDWEVL	0.9406	0.8357	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:09	SAVQDWEVL	0.9387	0.9851	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:67	VQDWEVLVL	0.9364	0.992	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:01	VQDWEVLVL	0.9279	0.9962	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C17:01	VQDWEVLVL	0.9142	0.9854	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:02	VQDWEVLVL	0.9087	0.9937	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:31	VQDWEVLVL	0.9041	0.9774	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C08:01	SAVQDWEVL	0.8963	0.9918	10	19
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A02:14	VQDWEVLVL	0.8794	0.8455	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C07:04	VQDWEVLVL	0.8573	0.9737	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-C03:06	VQDWEVLVL	0.8298	0.994	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B40:12	VQDWEVLVL	0.7971	0.8582	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B40:49	VQDWEVLVL	0.7798	0.8517	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B39:11	VQDWEVLVL	0.773	0.9622	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A69:01	AVQDWEVLV	0.7636	0.8721	11	20
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B38:05	VQDWEVLVL	0.7295	0.9929	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B40:21	VQDWEVLVL	0.7084	0.9197	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:73	VQDWEVLVL	0.6303	0.9893	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B35:13	VQDWEVLVL	0.564	0.9397	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:09	VQDWEVLVL	0.5605	0.9815	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:30	VQDWEVLVL	0.5443	0.9822	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A25:01	QSASAVQDW	0.3306	0.8029	7	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B48:05	VQDWEVLVL	0.1134	0.6461	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B07:13	VQDWEVLVL	0.0579	0.9038	12	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B15:24	KQSASAVQDW	0.9966	0.931	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:04	KQSASAVQDW	0.9824	0.7352	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:10	KQSASAVQDW	0.9795	0.9863	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B58:06	KQSASAVQDW	0.9106	0.93	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:02	KQSASAVQDW	0.863	0.9321	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-A32:01	KQSASAVQDW	0.8538	0.9347	6	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B40:21	AVQDWEVLVL	0.3873	0.9603	11	21
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:10	SKQSASAVQDW	0.9997	0.9679	5	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:04	SKQSASAVQDW	0.9987	0.7953	5	16
FOXP4-CCND3	chr6	41545819	chr6	41905132	312	HLA-B57:02	SKQSASAVQDW	0.9945	0.9402	5	16
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B58:01	QALMLQQDW	0.996	0.9865	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:30	LMLQQDWEV	0.994	0.694	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:60	LMLQQDWEV	0.994	0.7205	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B57:01	QALMLQQDW	0.994	0.9924	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:24	LMLQQDWEV	0.994	0.694	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:67	LMLQQDWEV	0.994	0.694	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:11	LMLQQDWEV	0.9937	0.6954	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:21	LMLQQDWEV	0.9929	0.7862	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:22	LMLQQDWEV	0.99	0.7766	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B58:02	QALMLQQDW	0.9883	0.982	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:16	LMLQQDWEV	0.9877	0.685	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:27	LMLQQDWEV	0.9803	0.6484	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:38	LMLQQDWEV	0.9785	0.5533	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:13	LMLQQDWEV	0.976	0.7105	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:04	LMLQQDWEV	0.9755	0.8943	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:35	LMLQQDWEV	0.9753	0.6994	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:29	LMLQQDWEV	0.9673	0.6959	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:20	LMLQQDWEV	0.9611	0.7052	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B48:01	LQQQQALML	0.9517	0.8191	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:19	LMLQQDWEV	0.9436	0.7212	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B57:03	QALMLQQDW	0.9115	0.9961	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B53:01	QALMLQQDW	0.9094	0.8496	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:17	LMLQQDWEV	0.9079	0.8927	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B39:13	LQQQQALML	0.5724	0.9912	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B13:02	LQQQQALML	0.5176	0.8121	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B13:01	LQQQQALML	0.468	0.9969	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B52:01	LQQQQALML	0.0623	0.9923	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:11	MLQQDWEVLV	0.9963	0.7751	12	22
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:16	ALMLQQDWEV	0.9903	0.6343	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:27	ALMLQQDWEV	0.9895	0.6664	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:22	ALMLQQDWEV	0.9893	0.7864	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:11	ALMLQQDWEV	0.9861	0.6947	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:30	ALMLQQDWEV	0.9859	0.6911	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:67	ALMLQQDWEV	0.9859	0.6911	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:24	ALMLQQDWEV	0.9859	0.6911	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:60	ALMLQQDWEV	0.9857	0.7374	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:19	MLQQDWEVLV	0.9669	0.7491	12	22
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:19	ALMLQQDWEV	0.9484	0.663	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:29	ALMLQQDWEV	0.8856	0.6947	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:35	ALMLQQDWEV	0.8834	0.6915	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:20	ALMLQQDWEV	0.8761	0.7011	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:01	LMLQQDWEV	0.994	0.694	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:07	LMLQQDWEV	0.9938	0.752	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:02	LMLQQDWEV	0.9904	0.7164	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B44:06	QALMLQQDW	0.6918	0.5748	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B48:03	LQQQQALML	0.6299	0.7759	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B39:08	LQQQQALML	0.5386	0.9847	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:01	ALMLQQDWEV	0.9859	0.6911	10	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B44:08	QQALMLQQDW	0.8402	0.8059	8	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B57:04	QALMLQQDW	0.9944	0.7293	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B57:10	QALMLQQDW	0.994	0.9924	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:06	LMLQQDWEV	0.9929	0.7862	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-A02:14	LMLQQDWEV	0.9928	0.7757	11	20
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B58:06	QALMLQQDW	0.9808	0.9718	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B57:02	QALMLQQDW	0.9762	0.9724	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B15:13	QALMLQQDW	0.9403	0.9739	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B15:73	LQQQQALML	0.8729	0.9701	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B53:02	QALMLQQDW	0.8358	0.866	9	18
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B15:30	LQQQQALML	0.745	0.9643	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B39:02	LQQQQALML	0.7032	0.991	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B40:12	LQQQQALML	0.6299	0.7759	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B40:21	LQQQQALML	0.5005	0.819	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B40:49	LQQQQALML	0.4897	0.747	5	14
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B40:21	MLQQDWEVL	0.2085	0.6892	12	21
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	HLA-B15:24	QQALMLQQDW	0.9843	0.9729	8	18

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Potential FusionNeoAntigen Information of FOXP4-CCND3 in HLA II

FOXP4-CCND3_41552629_41905132.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)
FOXP4-CCND3	chr6	41552629	chr6	41905132	435	DRB1-0102	QALLQQQQALMLQQD	2	17

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Fusion breakpoint peptide structures of FOXP4-CCND3

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
4540	KQSASAVQDWEVLV	FOXP4	CCND3	chr6	41545819	chr6	41905132	312

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
5221	LLHFQQQQDWEVLV	FOXP4	CCND3	chr6	41533702	chr6	41905132	216

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
7518	QQQQALMLQQDWEV	FOXP4	CCND3	chr6	41552629	chr6	41905132	435

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FOXP4-CCND3

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	4540	KQSASAVQDWEVLV	-6.77781	-6.89121
HLA-B14:02	3BVN	4540	KQSASAVQDWEVLV	-3.08719	-4.12249
HLA-B52:01	3W39	4540	KQSASAVQDWEVLV	-6.66315	-6.77655
HLA-B52:01	3W39	4540	KQSASAVQDWEVLV	-2.65785	-3.69315
HLA-A24:02	5HGA	4540	KQSASAVQDWEVLV	-7.20627	-7.31967
HLA-A24:02	5HGA	4540	KQSASAVQDWEVLV	-6.50211	-7.53741
HLA-B44:05	3DX8	4540	KQSASAVQDWEVLV	-7.75024	-7.86364
HLA-B44:05	3DX8	4540	KQSASAVQDWEVLV	-6.53073	-7.56603
HLA-A02:01	6TDR	4540	KQSASAVQDWEVLV	-4.4528	-5.4881
HLA-B14:02	3BVN	5221	LLHFQQQQDWEVLV	-7.9962	-8.1096
HLA-B14:02	3BVN	5221	LLHFQQQQDWEVLV	-5.70842	-6.74372
HLA-B52:01	3W39	5221	LLHFQQQQDWEVLV	-6.83737	-6.95077
HLA-B52:01	3W39	5221	LLHFQQQQDWEVLV	-4.4836	-5.5189
HLA-A11:01	4UQ2	5221	LLHFQQQQDWEVLV	-10.0067	-10.1201
HLA-A11:01	4UQ2	5221	LLHFQQQQDWEVLV	-9.03915	-10.0745
HLA-A24:02	5HGA	5221	LLHFQQQQDWEVLV	-6.56204	-6.67544
HLA-A24:02	5HGA	5221	LLHFQQQQDWEVLV	-5.42271	-6.45801
HLA-B44:05	3DX8	5221	LLHFQQQQDWEVLV	-7.85648	-8.89178
HLA-B44:05	3DX8	5221	LLHFQQQQDWEVLV	-5.3978	-5.5112
HLA-A02:01	6TDR	5221	LLHFQQQQDWEVLV	-3.37154	-4.40684
HLA-B14:02	3BVN	7518	QQQQALMLQQDWEV	-6.81784	-6.93724
HLA-B14:02	3BVN	7518	QQQQALMLQQDWEV	-5.72956	-6.77086
HLA-B52:01	3W39	7518	QQQQALMLQQDWEV	-7.39683	-7.51623
HLA-B52:01	3W39	7518	QQQQALMLQQDWEV	-6.35068	-7.39198
HLA-A11:01	4UQ2	7518	QQQQALMLQQDWEV	-2.93775	-3.05715
HLA-A24:02	5HGA	7518	QQQQALMLQQDWEV	-8.28894	-8.40834
HLA-A24:02	5HGA	7518	QQQQALMLQQDWEV	-6.60463	-7.64593
HLA-B44:05	3DX8	7518	QQQQALMLQQDWEV	-6.05305	-6.17245
HLA-B44:05	3DX8	7518	QQQQALMLQQDWEV	-2.83839	-3.87969
HLA-A02:01	6TDR	7518	QQQQALMLQQDWEV	-7.33893	-7.45833

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Vaccine Design for the FusionNeoAntigens of FOXP4-CCND3

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
FOXP4-CCND3	chr6	41533702	chr6	41905132	10	19	QQQQDWEVL	CAGCAACAGGACTGGGAGGTGCTGGTC
FOXP4-CCND3	chr6	41533702	chr6	41905132	10	21	QQQQDWEVLVL	CAGCAACAGGACTGGGAGGTGCTGGTCCTAGGG
FOXP4-CCND3	chr6	41533702	chr6	41905132	11	19	QQQDWEVL	CAACAGGACTGGGAGGTGCTGGTC
FOXP4-CCND3	chr6	41533702	chr6	41905132	11	20	QQQDWEVLV	CAACAGGACTGGGAGGTGCTGGTCCTA
FOXP4-CCND3	chr6	41533702	chr6	41905132	11	21	QQQDWEVLVL	CAACAGGACTGGGAGGTGCTGGTCCTAGGG
FOXP4-CCND3	chr6	41533702	chr6	41905132	7	16	LHFQQQQDW	CACTTCCAGCAGCAACAGGACTGGGAG
FOXP4-CCND3	chr6	41533702	chr6	41905132	9	18	FQQQQDWEV	CAGCAGCAACAGGACTGGGAGGTGCTG
FOXP4-CCND3	chr6	41533702	chr6	41905132	9	19	FQQQQDWEVL	CAGCAGCAACAGGACTGGGAGGTGCTGGTC
FOXP4-CCND3	chr6	41545819	chr6	41905132	10	19	SAVQDWEVL	GCTGTGCAGGACTGGGAGGTGCTGGTC
FOXP4-CCND3	chr6	41545819	chr6	41905132	11	20	AVQDWEVLV	GTGCAGGACTGGGAGGTGCTGGTCCTA
FOXP4-CCND3	chr6	41545819	chr6	41905132	11	21	AVQDWEVLVL	GTGCAGGACTGGGAGGTGCTGGTCCTAGGG
FOXP4-CCND3	chr6	41545819	chr6	41905132	12	21	VQDWEVLVL	CAGGACTGGGAGGTGCTGGTCCTAGGG
FOXP4-CCND3	chr6	41545819	chr6	41905132	5	16	SKQSASAVQDW	AAACAGTCTGCCTCTGCTGTGCAGGACTGGGAG
FOXP4-CCND3	chr6	41545819	chr6	41905132	6	16	KQSASAVQDW	CAGTCTGCCTCTGCTGTGCAGGACTGGGAG
FOXP4-CCND3	chr6	41545819	chr6	41905132	7	16	QSASAVQDW	TCTGCCTCTGCTGTGCAGGACTGGGAG
FOXP4-CCND3	chr6	41552629	chr6	41905132	10	20	ALMLQQDWEV	CTCCAGCAGGACTGGGAGGTGCTGGTCCTA
FOXP4-CCND3	chr6	41552629	chr6	41905132	11	20	LMLQQDWEV	CAGCAGGACTGGGAGGTGCTGGTCCTA
FOXP4-CCND3	chr6	41552629	chr6	41905132	12	21	MLQQDWEVL	CAGGACTGGGAGGTGCTGGTCCTAGGG
FOXP4-CCND3	chr6	41552629	chr6	41905132	12	22	MLQQDWEVLV	CAGGACTGGGAGGTGCTGGTCCTAGGGAAG
FOXP4-CCND3	chr6	41552629	chr6	41905132	5	14	LQQQQALML	CAGCAAGCCCTCATGCTCCAGCAGGAC
FOXP4-CCND3	chr6	41552629	chr6	41905132	8	18	QQALMLQQDW	CTCATGCTCCAGCAGGACTGGGAGGTGCTG
FOXP4-CCND3	chr6	41552629	chr6	41905132	9	18	QALMLQQDW	ATGCTCCAGCAGGACTGGGAGGTGCTG

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
FOXP4-CCND3	chr6	41552629	chr6	41905132	2	17	QALLQQQQALMLQQD	CTCCAGCAGCAGCAAGCCCTCATGCTCCAGCAGGACTGGGAGGTG

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Information of the samples that have these potential fusion neoantigens of FOXP4-CCND3

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
LUSC	FOXP4-CCND3	chr6	41533702	ENST00000307972	chr6	41905132	ENST00000511642	TCGA-46-3769
LUSC	FOXP4-CCND3	chr6	41545819	ENST00000307972	chr6	41905132	ENST00000511642	TCGA-46-3769
LUSC	FOXP4-CCND3	chr6	41552629	ENST00000307972	chr6	41905132	ENST00000511642	TCGA-46-3769

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Potential target of CAR-T therapy development for FOXP4-CCND3

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 FOXP4-CCND3

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 FOXP4-CCND3

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)