Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:YTHDC2-CTNND1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: YTHDC2-CTNND1
	FusionPDB ID: 100091
	FusionGDB2.0 ID: 100091
		Hgene	Tgene
	Gene symbol	YTHDC2	CTNND1
	Gene ID	64848	100528016
	Gene name	YTH domain containing 2	TMX2-CTNND1 readthrough (NMD candidate)
	Synonyms	CAHL\|hYTHDC2	CAS\|CTNND1\|p120(cas)\|p120(ctn)
	Cytomap	5q22.2	11q12.1
	Type of gene	protein-coding	ncRNA
	Description	3'-5' RNA helicase YTHDC2CsA-associated helicase-like proteinprobable ATP-dependent RNA helicase YTHDC2	Cadherin-associated Src substrateCatenin delta-1TMX2-CTNND1 readthrough (non-protein coding)p120 catenin
	Modification date	20200313	20200313
	UniProtAcc	.	O60716 Main function of 5'-partner protein: FUNCTION: Key regulator of cell-cell adhesion that associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability (PubMed:14610055, PubMed:20371349). Beside cell-cell adhesion, regulates gene transcription through several transcription factors including ZBTB33/Kaiso2 and GLIS2, and the activity of Rho family GTPases and downstream cytoskeletal dynamics (PubMed:10207085, PubMed:20371349). Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors (PubMed:17344476). {ECO:0000269\|PubMed:10207085, ECO:0000269\|PubMed:14610055, ECO:0000269\|PubMed:17344476, ECO:0000269\|PubMed:20371349}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000161863, ENST00000515883,	ENST00000358694, ENST00000399050, ENST00000415361, ENST00000426142, ENST00000525902, ENST00000526357, ENST00000526772, ENST00000526938, ENST00000527467, ENST00000528232, ENST00000528621, ENST00000529526, ENST00000529873, ENST00000529986, ENST00000530748, ENST00000531014, ENST00000532245, ENST00000532463, ENST00000532649, ENST00000532787, ENST00000532844, ENST00000533667, ENST00000534579, ENST00000360682, ENST00000361332, ENST00000361391, ENST00000361796, ENST00000399039, ENST00000428599, ENST00000524630, ENST00000529919, ENST00000530094,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 4 X 3=48	17 X 21 X 10=3570
	# samples	4	25
	** MAII score	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(25/3570*10)=-3.83592407425437 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: YTHDC2 [Title/Abstract] AND CTNND1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: YTHDC2 [Title/Abstract] AND CTNND1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	YTHDC2(112851059)-CTNND1(57569205), # samples:1
Anticipated loss of major functional domain due to fusion event.	YTHDC2-CTNND1 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. YTHDC2-CTNND1 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. YTHDC2-CTNND1 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. YTHDC2-CTNND1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	YTHDC2	GO:0034612	response to tumor necrosis factor	21559518
Hgene	YTHDC2	GO:0070555	response to interleukin-1	21559518

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:112851059/chr11:57569205)
- 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 YTHDC2 (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 CTNND1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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)
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000524630	CTNND1	chr11	57569205	+	5575	491	174	2336	720
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000529919	CTNND1	chr11	57569205	+	3984	491	174	2351	725
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000399039	CTNND1	chr11	57569205	+	4392	491	174	2351	725
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000360682	CTNND1	chr11	57569205	+	5250	491	174	2378	734
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000361796	CTNND1	chr11	57569205	+	5208	491	174	2336	720
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000361391	CTNND1	chr11	57569205	+	5231	491	174	2360	728
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000530094	CTNND1	chr11	57569205	+	5294	491	174	2423	749
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000428599	CTNND1	chr11	57569205	+	5207	491	174	2336	720
ENST00000161863	YTHDC2	chr5	112851059	+	ENST00000361332	CTNND1	chr11	57569205	+	5294	491	174	2423	749
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000524630	CTNND1	chr11	57569205	+	5549	465	148	2310	720
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000529919	CTNND1	chr11	57569205	+	3958	465	148	2325	725
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000399039	CTNND1	chr11	57569205	+	4366	465	148	2325	725
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000360682	CTNND1	chr11	57569205	+	5224	465	148	2352	734
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000361796	CTNND1	chr11	57569205	+	5182	465	148	2310	720
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000361391	CTNND1	chr11	57569205	+	5205	465	148	2334	728
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000530094	CTNND1	chr11	57569205	+	5268	465	148	2397	749
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000428599	CTNND1	chr11	57569205	+	5181	465	148	2310	720
ENST00000515883	YTHDC2	chr5	112851059	+	ENST00000361332	CTNND1	chr11	57569205	+	5268	465	148	2397	749

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
ENST00000161863	ENST00000524630	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.00171871	0.99828136
ENST00000161863	ENST00000529919	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.005537252	0.9944628
ENST00000161863	ENST00000399039	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.00304772	0.9969523
ENST00000161863	ENST00000360682	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001919016	0.99808097
ENST00000161863	ENST00000361796	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001842101	0.9981579
ENST00000161863	ENST00000361391	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001795144	0.9982048
ENST00000161863	ENST00000530094	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001930347	0.9980697
ENST00000161863	ENST00000428599	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001840406	0.9981596
ENST00000161863	ENST00000361332	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001930347	0.9980697
ENST00000515883	ENST00000524630	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001715683	0.9982843
ENST00000515883	ENST00000529919	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.00550902	0.994491
ENST00000515883	ENST00000399039	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.003036563	0.99696344
ENST00000515883	ENST00000360682	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001921232	0.9980788
ENST00000515883	ENST00000361796	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001842383	0.99815756
ENST00000515883	ENST00000361391	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001798711	0.99820125
ENST00000515883	ENST00000530094	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001933162	0.99806684
ENST00000515883	ENST00000428599	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001840682	0.99815935
ENST00000515883	ENST00000361332	YTHDC2	chr5	112851059	+	CTNND1	chr11	57569205	+	0.001933162	0.99806684

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

Top

Fusion Protein Breakpoint Sequences for YTHDC2-CTNND1

+/-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
YTHDC2	chr5	112851059	CTNND1	chr11	57569205	465	106	LSQSLGLVSKSKGSYEDMIGEEVPSD
YTHDC2	chr5	112851059	CTNND1	chr11	57569205	491	106	LSQSLGLVSKSKGSYEDMIGEEVPSD

Top

Potential FusionNeoAntigen Information of YTHDC2-CTNND1 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.

YTHDC2-CTNND1_112851059_57569205.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)
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:01	LVSKSKGSY	0.9898	0.6973	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:25	LVSKSKGSY	0.9456	0.7298	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:02	LVSKSKGSY	0.8343	0.7423	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:01	GLVSKSKGSY	0.9978	0.6962	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:25	GLVSKSKGSY	0.922	0.7481	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:135	LVSKSKGSY	0.9903	0.6958	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:33	LVSKSKGSY	0.9898	0.6973	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:125	LVSKSKGSY	0.9898	0.6973	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:34	LVSKSKGSY	0.9898	0.6973	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:27	LVSKSKGSY	0.9897	0.6542	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:50	LVSKSKGSY	0.9843	0.8938	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:11	LVSKSKGSY	0.9738	0.6176	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:08	LVSKSKGSY	0.973	0.616	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:35	LVSKSKGSY	0.9729	0.6508	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B35:43	LVSKSKGSY	0.9483	0.6063	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:12	LVSKSKGSY	0.943	0.7186	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:39	LVSKSKGSY	0.9409	0.5817	6	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:34	GLVSKSKGSY	0.9978	0.6962	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:135	GLVSKSKGSY	0.9978	0.7036	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:125	GLVSKSKGSY	0.9978	0.6962	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:33	GLVSKSKGSY	0.9978	0.6962	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:27	GLVSKSKGSY	0.9976	0.7072	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:50	GLVSKSKGSY	0.9963	0.8863	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:35	GLVSKSKGSY	0.9939	0.7118	5	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	HLA-B15:39	GLVSKSKGSY	0.9327	0.5576	5	15

Top

Potential FusionNeoAntigen Information of YTHDC2-CTNND1 in HLA II

YTHDC2-CTNND1_112851059_57569205.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)
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0101	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0101	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0101	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0105	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0105	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0105	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0107	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0107	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0107	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0109	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0109	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0111	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0111	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0111	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0113	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0113	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0113	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0115	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0115	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0117	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0117	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0117	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0119	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0119	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0119	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0121	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0121	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0121	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0125	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0125	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0125	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0127	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0127	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0127	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0129	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0129	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0129	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0131	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0131	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0131	KSKGSYEDMIGEEVP	9	24
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0804	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0820	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0831	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-0831	LSQSLGLVSKSKGSY	0	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1001	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1003	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1102	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1102	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1103	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1103	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1104	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1106	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1116	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1116	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1121	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1121	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1125	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1135	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1136	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1136	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1138	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1142	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1143	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1144	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1146	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1147	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1148	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1148	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1150	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1150	LSQSLGLVSKSKGSY	0	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1154	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1155	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1155	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1156	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1156	LSQSLGLVSKSKGSY	0	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1158	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1159	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1159	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1159	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1160	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1163	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1163	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1165	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1165	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1170	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1170	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1176	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1176	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1177	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1178	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1183	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1185	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1185	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1188	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1188	LSQSLGLVSKSKGSY	0	15
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1301	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1301	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1304	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1304	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1308	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1308	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1311	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1315	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1315	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1317	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1317	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1318	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1319	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1319	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1320	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1320	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1322	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1322	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1324	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1324	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1327	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1327	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1332	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1332	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1335	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1335	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1342	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1343	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1343	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1343	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1348	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1348	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1351	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1351	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1352	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1352	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1353	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1353	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1354	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1354	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1357	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1357	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1359	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1359	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1364	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1364	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1368	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1368	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1369	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1369	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1370	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1370	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1371	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1371	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1372	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1372	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1375	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1375	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1375	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1376	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1376	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1378	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1378	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1379	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1379	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1380	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1380	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1383	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1383	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1384	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1384	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1387	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1387	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1391	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1391	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1392	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1392	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1393	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1393	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1398	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1398	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1415	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1416	QSLGLVSKSKGSYED	2	17
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1416	SLGLVSKSKGSYEDM	3	18
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1484	SQSLGLVSKSKGSYE	1	16
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1527	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1527	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1534	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1534	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1601	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1601	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1602	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1602	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1603	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1603	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1604	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1605	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1607	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1608	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1608	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1609	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1610	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1611	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1611	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1612	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1612	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1614	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1614	SKGSYEDMIGEEVPS	10	25
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1616	KGSYEDMIGEEVPSD	11	26
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	491	DRB1-1616	SKGSYEDMIGEEVPS	10	25

Top

Fusion breakpoint peptide structures of YTHDC2-CTNND1

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
5796	LVSKSKGSYEDMIG	YTHDC2	CTNND1	chr5	112851059	chr11	57569205	491

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of YTHDC2-CTNND1

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-B53:01	1A1O	5796	LVSKSKGSYEDMIG	-2.521	-3.5563
HLA-B51:01	1E28	5796	LVSKSKGSYEDMIG	-1.92936	-2.96466
HLA-B57:03	2BVO	5796	LVSKSKGSYEDMIG	-3.93412	-4.04752
HLA-A03:01	2XPG	5796	LVSKSKGSYEDMIG	-4.06211	-4.17551
HLA-B14:02	3BVN	5796	LVSKSKGSYEDMIG	-5.90915	-6.02255
HLA-B14:02	3BVN	5796	LVSKSKGSYEDMIG	-3.14094	-4.17624
HLA-B27:09	3CZF	5796	LVSKSKGSYEDMIG	10001	10000
HLA-B44:03	3DX7	5796	LVSKSKGSYEDMIG	-0.694336	-1.72964
HLA-B52:01	3W39	5796	LVSKSKGSYEDMIG	-5.17909	-5.29249
HLA-B52:01	3W39	5796	LVSKSKGSYEDMIG	-3.78069	-4.81599
HLA-B18:01	4JQV	5796	LVSKSKGSYEDMIG	-3.7903	-4.8256
HLA-B18:01	4JQV	5796	LVSKSKGSYEDMIG	-2.32734	-2.44074
HLA-A11:01	4UQ2	5796	LVSKSKGSYEDMIG	-9.23212	-9.34552
HLA-A11:01	4UQ2	5796	LVSKSKGSYEDMIG	-8.48766	-9.52296
HLA-A24:02	5HGA	5796	LVSKSKGSYEDMIG	-7.36197	-7.47537
HLA-A24:02	5HGA	5796	LVSKSKGSYEDMIG	-3.3994	-4.4347
HLA-B57:01	5VUD	5796	LVSKSKGSYEDMIG	-2.43326	-3.46856
HLA-B27:05	6PYJ	5796	LVSKSKGSYEDMIG	-4.63681	-4.75021
HLA-B27:05	6PYJ	5796	LVSKSKGSYEDMIG	-2.95711	-3.99241
HLA-B27:03	6PZ5	5796	LVSKSKGSYEDMIG	-1.99721	-3.03251
HLA-B27:03	6PZ5	5796	LVSKSKGSYEDMIG	-1.21669	-1.33009
HLA-B44:05	3DX8	5796	LVSKSKGSYEDMIG	-4.55876	-4.67216
HLA-B44:05	3DX8	5796	LVSKSKGSYEDMIG	-4.48915	-5.52445
HLA-B07:02	5EO0	5796	LVSKSKGSYEDMIG	-1.42589	-2.46119
HLA-A02:01	6TDR	5796	LVSKSKGSYEDMIG	-2.39029	-3.42559

Top

Vaccine Design for the FusionNeoAntigens of YTHDC2-CTNND1

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
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	5	15	GLVSKSKGSY	TGGTTTGGTCTCTAAAAGTAAAGGGAGCTA
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	6	15	LVSKSKGSY	TTTGGTCTCTAAAAGTAAAGGGAGCTA

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
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	0	15	LSQSLGLVSKSKGSY	ACTCAGTCAGTCTCTTGGTTTGGTCTCTAAAAGTAAAGGGAGCTA
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	1	16	SQSLGLVSKSKGSYE	CAGTCAGTCTCTTGGTTTGGTCTCTAAAAGTAAAGGGAGCTATGA
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	10	25	SKGSYEDMIGEEVPS	AAGTAAAGGGAGCTATGAAGACATGATTGGTGAGGAGGTGCCATC
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	11	26	KGSYEDMIGEEVPSD	TAAAGGGAGCTATGAAGACATGATTGGTGAGGAGGTGCCATCGGA
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	2	17	QSLGLVSKSKGSYED	TCAGTCTCTTGGTTTGGTCTCTAAAAGTAAAGGGAGCTATGAAGA
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	3	18	SLGLVSKSKGSYEDM	GTCTCTTGGTTTGGTCTCTAAAAGTAAAGGGAGCTATGAAGACAT
YTHDC2-CTNND1	chr5	112851059	chr11	57569205	9	24	KSKGSYEDMIGEEVP	TAAAAGTAAAGGGAGCTATGAAGACATGATTGGTGAGGAGGTGCC

Top

Information of the samples that have these potential fusion neoantigens of YTHDC2-CTNND1

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
Non-Cancer	YTHDC2-CTNND1	chr5	112851059	ENST00000161863	chr11	57569205	ENST00000360682	TCGA-BR-6564-11A

Top

Potential target of CAR-T therapy development for YTHDC2-CTNND1

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

Top

Related Drugs to YTHDC2-CTNND1

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to YTHDC2-CTNND1

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)