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Fusion Protein:MLYCD-NKAIN4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MLYCD-NKAIN4
	FusionPDB ID: 54365
	FusionGDB2.0 ID: 54365
		Hgene	Tgene
	Gene symbol	MLYCD	NKAIN4
	Gene ID	23417	128414
	Gene name	malonyl-CoA decarboxylase	sodium/potassium transporting ATPase interacting 4
	Synonyms	MCD	C20orf58\|FAM77A\|bA261N11.2
	Cytomap	16q23.3	20q13.33
	Type of gene	protein-coding	protein-coding
	Description	malonyl-CoA decarboxylase, mitochondrialmalonyl coenzyme A decarboxylase	sodium/potassium-transporting ATPase subunit beta-1-interacting protein 4Na(+)/K(+)-transporting ATPase subunit beta-1-interacting protein 4Na+/K+ transporting ATPase interacting 4
	Modification date	20200313	20200313
	UniProtAcc	O95822 Main function of 5'-partner protein: FUNCTION: Catalyzes the conversion of malonyl-CoA to acetyl-CoA. In the fatty acid biosynthesis MCD selectively removes malonyl-CoA and thus assures that methyl-malonyl-CoA is the only chain elongating substrate for fatty acid synthase and that fatty acids with multiple methyl side chains are produced. In peroxisomes it may be involved in degrading intraperoxisomal malonyl-CoA, which is generated by the peroxisomal beta-oxidation of odd chain-length dicarboxylic fatty acids. Plays a role in the metabolic balance between glucose and lipid oxidation in muscle independent of alterations in insulin signaling. May play a role in controlling the extent of ischemic injury by promoting glucose oxidation. {ECO:0000269\|PubMed:10455107, ECO:0000269\|PubMed:15003260, ECO:0000269\|PubMed:18314420, ECO:0000269\|PubMed:23482565}.	Q8IVV8 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262430,	ENST00000370307, ENST00000466885, ENST00000370313, ENST00000370316,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 3=27	5 X 5 X 3=75
	# samples	3	5
	** MAII score	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: MLYCD [Title/Abstract] AND NKAIN4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: MLYCD [Title/Abstract] AND NKAIN4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MLYCD(83933151)-NKAIN4(61880247), # samples:1
Anticipated loss of major functional domain due to fusion event.	MLYCD-NKAIN4 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. MLYCD-NKAIN4 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	MLYCD	GO:0006085	acetyl-CoA biosynthetic process	9869665\|10417274\|10455107
Hgene	MLYCD	GO:0006633	fatty acid biosynthetic process	15003260
Hgene	MLYCD	GO:2001294	malonyl-CoA catabolic process	10417274\|10455107\|15003260

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:83933151/chr20:61880247)
- 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 MLYCD (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 NKAIN4 (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)

ENST00000262430

MLYCD

chr16

83933151

ENST00000370313

NKAIN4

chr20

61880247

1189

126

555

1016

153

ENST00000262430

MLYCD

chr16

83933151

ENST00000370316

NKAIN4

chr20

61880247

1274

126

560

174

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
ENST00000262430	ENST00000370313	MLYCD	chr16	83933151	+	NKAIN4	chr20	61880247	-	0.882747	0.117253006
ENST00000262430	ENST00000370316	MLYCD	chr16	83933151	+	NKAIN4	chr20	61880247	-	0.86131376	0.13868618

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 MLYCD-NKAIN4

+/-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
MLYCD	chr16	83933151	NKAIN4	chr20	61880247	126	30	AQALKLVEGPDVRYTLWAAVWVTWNV

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Potential FusionNeoAntigen Information of MLYCD-NKAIN4 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.

MLYCD-NKAIN4_83933151_61880247.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)
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B18:01	VEGPDVRY	0.9962	0.8871	6	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:02	GPDVRYTL	0.5885	0.9139	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:04	GPDVRYTL	0.5885	0.9139	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:07	VRYTLWAAV	0.9997	0.8498	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:04	VRYTLWAAV	0.9993	0.8051	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:23	RYTLWAAVW	0.9935	0.8259	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:20	RYTLWAAVW	0.9881	0.8882	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:25	RYTLWAAVW	0.9877	0.8899	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:15	RYTLWAAVW	0.9867	0.8924	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:31	RYTLWAAVW	0.9865	0.9021	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:17	RYTLWAAVW	0.9753	0.837	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:10	RYTLWAAVW	0.97	0.7514	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A23:05	RYTLWAAVW	0.9696	0.769	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A23:04	RYTLWAAVW	0.9576	0.8221	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A31:08	RYTLWAAVW	0.9508	0.9533	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:08	LVEGPDVRY	0.8486	0.8056	5	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:02	LVEGPDVRY	0.8267	0.9018	5	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:14	RYTLWAAVW	0.6557	0.7836	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:01	KLVEGPDVRY	0.9995	0.8818	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:02	VRYTLWAAVW	0.9995	0.6148	11	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:25	KLVEGPDVRY	0.9857	0.92	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:02	VEGPDVRYTLW	0.9997	0.6901	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:03	VEGPDVRYTLW	0.9996	0.9355	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:05	VEGPDVRYTLW	0.9976	0.8334	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B07:12	GPDVRYTL	0.9991	0.6301	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B73:01	VRYTLWAA	0.9988	0.922	11	19
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B39:10	GPDVRYTL	0.8541	0.7957	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:12	GPDVRYTL	0.5885	0.9139	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:14	VRYTLWAAV	0.9993	0.8213	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B73:01	VRYTLWAAV	0.9955	0.9416	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:02	RYTLWAAVW	0.9881	0.8882	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A23:01	RYTLWAAVW	0.9688	0.7662	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:17	EGPDVRYTL	0.9313	0.9533	7	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:30	EGPDVRYTL	0.8854	0.965	7	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:05	LVEGPDVRY	0.8667	0.7936	5	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:31	LVEGPDVRY	0.7793	0.8021	5	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C07:29	EGPDVRYTL	0.4728	0.9472	7	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:07	KLVEGPDVRY	0.9982	0.5437	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:17	VEGPDVRYTL	0.9929	0.9534	6	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:30	VEGPDVRYTL	0.9868	0.9635	6	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:04	KLVEGPDVRY	0.9579	0.9137	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:05	KLVEGPDVRY	0.8851	0.8455	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:04	VEGPDVRYTLW	0.9998	0.5037	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:08	VEGPDVRYTLW	0.9997	0.789	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B18:05	VEGPDVRY	0.9962	0.8871	6	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B18:11	VEGPDVRY	0.9901	0.8341	6	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B67:01	GPDVRYTL	0.8224	0.5865	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:09	GPDVRYTL	0.5885	0.9139	8	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:09	VRYTLWAAV	0.9996	0.7758	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:06	VRYTLWAAV	0.9996	0.8642	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:10	VRYTLWAAV	0.9992	0.8653	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B27:08	VRYTLWAAV	0.9992	0.7403	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-A24:03	RYTLWAAVW	0.9935	0.8259	12	21
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:02	EGPDVRYTL	0.9579	0.9538	7	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:03	EGPDVRYTL	0.9519	0.937	7	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C06:08	VRYTLWAAV	0.8944	0.9941	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:20	LVEGPDVRY	0.88	0.8595	5	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:20	LVEGPDVRY	0.7646	0.8717	5	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C06:02	VRYTLWAAV	0.0291	0.9962	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C06:17	VRYTLWAAV	0.0291	0.9962	11	20
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:27	KLVEGPDVRY	0.9996	0.8927	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:135	KLVEGPDVRY	0.9995	0.9166	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:33	KLVEGPDVRY	0.9995	0.8818	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:125	KLVEGPDVRY	0.9995	0.8818	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:34	KLVEGPDVRY	0.9995	0.8818	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:12	KLVEGPDVRY	0.9993	0.8345	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:50	KLVEGPDVRY	0.9992	0.8936	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:24	KLVEGPDVRY	0.9982	0.9358	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:35	KLVEGPDVRY	0.9982	0.8617	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-C01:02	VEGPDVRYTL	0.9943	0.9524	6	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B40:04	VEGPDVRYTL	0.9901	0.6864	6	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:39	KLVEGPDVRY	0.9866	0.823	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B15:20	KLVEGPDVRY	0.8959	0.9037	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B35:28	KLVEGPDVRY	0.8549	0.9011	4	14
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B41:03	VEGPDVRYTL	0.6639	0.5924	6	16
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:21	VEGPDVRYTLW	0.9999	0.527	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:22	VEGPDVRYTLW	0.9997	0.6901	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:13	VEGPDVRYTLW	0.9996	0.9355	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:26	VEGPDVRYTLW	0.9996	0.9355	6	17
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	126	HLA-B44:07	VEGPDVRYTLW	0.9996	0.9355	6	17

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Potential FusionNeoAntigen Information of MLYCD-NKAIN4 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of MLYCD-NKAIN4

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
9885	VEGPDVRYTLWAAV	MLYCD	NKAIN4	chr16	83933151	chr20	61880247	126

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MLYCD-NKAIN4

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	9885	VEGPDVRYTLWAAV	-7.54146	-7.65486
HLA-B14:02	3BVN	9885	VEGPDVRYTLWAAV	-5.05101	-6.08631
HLA-B52:01	3W39	9885	VEGPDVRYTLWAAV	-7.48565	-7.59905
HLA-B52:01	3W39	9885	VEGPDVRYTLWAAV	-5.61839	-6.65369
HLA-A11:01	4UQ2	9885	VEGPDVRYTLWAAV	-5.36758	-5.48098
HLA-A11:01	4UQ2	9885	VEGPDVRYTLWAAV	-2.41377	-3.44907
HLA-A24:02	5HGA	9885	VEGPDVRYTLWAAV	-8.3266	-8.44
HLA-A24:02	5HGA	9885	VEGPDVRYTLWAAV	-5.24481	-6.28011
HLA-B44:05	3DX8	9885	VEGPDVRYTLWAAV	-4.07996	-5.11526
HLA-B44:05	3DX8	9885	VEGPDVRYTLWAAV	-3.86967	-3.98307

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Vaccine Design for the FusionNeoAntigens of MLYCD-NKAIN4

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
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	11	19	VRYTLWAA	GTCCGGTACACGCTGTGGGCAGCC
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	11	20	VRYTLWAAV	GTCCGGTACACGCTGTGGGCAGCCGTC
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	11	21	VRYTLWAAVW	GTCCGGTACACGCTGTGGGCAGCCGTCTGG
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	12	21	RYTLWAAVW	CGGTACACGCTGTGGGCAGCCGTCTGG
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	4	14	KLVEGPDVRY	AAGCTGGTGGAGGGGCCGGACGTCCGGTAC
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	5	14	LVEGPDVRY	CTGGTGGAGGGGCCGGACGTCCGGTAC
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	6	14	VEGPDVRY	GTGGAGGGGCCGGACGTCCGGTAC
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	6	16	VEGPDVRYTL	GTGGAGGGGCCGGACGTCCGGTACACGCTG
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	6	17	VEGPDVRYTLW	GTGGAGGGGCCGGACGTCCGGTACACGCTGTGG
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	7	16	EGPDVRYTL	GAGGGGCCGGACGTCCGGTACACGCTG
MLYCD-NKAIN4	chr16	83933151	chr20	61880247	8	16	GPDVRYTL	GGGCCGGACGTCCGGTACACGCTG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of MLYCD-NKAIN4

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
LGG	MLYCD-NKAIN4	chr16	83933151	ENST00000262430	chr20	61880247	ENST00000370316	TCGA-TQ-A7RO

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Potential target of CAR-T therapy development for MLYCD-NKAIN4

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

NKAIN4

chr16:83933151

chr20:61880247

ENST00000370316

151_171

209.0

Transmembrane

Helical

Tgene

NKAIN4

chr16:83933151

chr20:61880247

ENST00000370316

62_82

209.0

Transmembrane

Helical

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to MLYCD-NKAIN4

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 MLYCD-NKAIN4

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)