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Fusion Protein:SMYD3-ZMYM4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SMYD3-ZMYM4
	FusionPDB ID: 84388
	FusionGDB2.0 ID: 84388
		Hgene	Tgene
	Gene symbol	SMYD3	ZMYM4
	Gene ID	64754	9202
	Gene name	SET and MYND domain containing 3	zinc finger MYM-type containing 4
	Synonyms	KMT3E\|ZMYND1\|ZNFN3A1\|bA74P14.1	CDIR\|MYM\|ZNF198L3\|ZNF262
	Cytomap	1q44	1p34.3
	Type of gene	protein-coding	protein-coding
	Description	histone-lysine N-methyltransferase SMYD3SET and MYND domain-containing protein 3bA74P14.1 (novel protein)zinc finger MYND domain-containing protein 1zinc finger protein, subfamily 3A (MYND domain containing), 1zinc finger, MYND domain containing 1	zinc finger MYM-type protein 4cell death inhibiting RNAzinc finger protein 262zinc finger, MYM-type 4
	Modification date	20200320	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000388985, ENST00000403792, ENST00000490107, ENST00000541742, ENST00000366517,	ENST00000482131, ENST00000314607, ENST00000373297,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	22 X 13 X 10=2860	13 X 13 X 7=1183
	# samples	24	14
	** MAII score	log2(24/2860*10)=-3.57490883605723 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1183*10)=-3.07895134139482 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SMYD3 [Title/Abstract] AND ZMYM4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SMYD3 [Title/Abstract] AND ZMYM4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ZMYM4(35827390)-SMYD3(246093239), # samples:3 SMYD3(246490503)-ZMYM4(35835630), # samples:3
Anticipated loss of major functional domain due to fusion event.	SMYD3-ZMYM4 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. SMYD3-ZMYM4 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. SMYD3-ZMYM4 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. SMYD3-ZMYM4 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. ZMYM4-SMYD3 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. ZMYM4-SMYD3 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. SMYD3-ZMYM4 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. SMYD3-ZMYM4 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. SMYD3-ZMYM4 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.

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

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

Partner

Gene

GO ID

GO term

PubMed ID

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:35827390/chr1:246093239)
- 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 SMYD3 (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 ZMYM4 (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)
ENST00000490107	SMYD3	chr1	246490503	-	ENST00000373297	ZMYM4	chr1	35835630	+	6377	571	16	4110	1364
ENST00000490107	SMYD3	chr1	246490503	-	ENST00000314607	ZMYM4	chr1	35835630	+	6645	571	16	4377	1453
ENST00000388985	SMYD3	chr1	246490503	-	ENST00000373297	ZMYM4	chr1	35835630	+	6337	531	0	4070	1356
ENST00000388985	SMYD3	chr1	246490503	-	ENST00000314607	ZMYM4	chr1	35835630	+	6605	531	0	4337	1445
ENST00000403792	SMYD3	chr1	246490503	-	ENST00000373297	ZMYM4	chr1	35835630	+	6432	626	50	4165	1371
ENST00000403792	SMYD3	chr1	246490503	-	ENST00000314607	ZMYM4	chr1	35835630	+	6700	626	50	4432	1460

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
ENST00000490107	ENST00000373297	SMYD3	chr1	246490503	-	ZMYM4	chr1	35835630	+	8.21E-05	0.99991786
ENST00000490107	ENST00000314607	SMYD3	chr1	246490503	-	ZMYM4	chr1	35835630	+	6.26E-05	0.9999373
ENST00000388985	ENST00000373297	SMYD3	chr1	246490503	-	ZMYM4	chr1	35835630	+	7.77E-05	0.9999223
ENST00000388985	ENST00000314607	SMYD3	chr1	246490503	-	ZMYM4	chr1	35835630	+	5.95E-05	0.9999405
ENST00000403792	ENST00000373297	SMYD3	chr1	246490503	-	ZMYM4	chr1	35835630	+	8.77E-05	0.99991226
ENST00000403792	ENST00000314607	SMYD3	chr1	246490503	-	ZMYM4	chr1	35835630	+	6.67E-05	0.99993324

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 SMYD3-ZMYM4

+/-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
SMYD3	chr1	246490503	ZMYM4	chr1	35835630	531	176	QLPPAFDLFEAFAKEYSHGQQQKTQE
SMYD3	chr1	246490503	ZMYM4	chr1	35835630	571	184	QLPPAFDLFEAFAKEYSHGQQQKTQE
SMYD3	chr1	246490503	ZMYM4	chr1	35835630	626	191	QLPPAFDLFEAFAKEYSHGQQQKTQE

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Potential FusionNeoAntigen Information of SMYD3-ZMYM4 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.

SMYD3-ZMYM4_246490503_35835630.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)
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:01	FEAFAKEY	0.9992	0.967	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B44:03	FEAFAKEY	0.9976	0.9779	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B15:02	DLFEAFAKEY	0.988	0.8953	6	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B15:21	LFEAFAKEY	0.9478	0.9283	7	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B15:21	DLFEAFAKEY	0.9885	0.8681	6	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B15:31	DLFEAFAKEY	0.979	0.8	6	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:07	FEAFAKEY	0.9994	0.9437	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:08	FEAFAKEY	0.9993	0.9331	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:04	FEAFAKEY	0.9992	0.9724	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:05	FEAFAKEY	0.9992	0.967	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:06	FEAFAKEY	0.9991	0.9737	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:03	FEAFAKEY	0.9988	0.964	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:11	FEAFAKEY	0.9979	0.9309	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B44:07	FEAFAKEY	0.9976	0.9779	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B44:13	FEAFAKEY	0.9976	0.9779	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B44:26	FEAFAKEY	0.9976	0.9779	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B35:20	FEAFAKEY	0.9909	0.9591	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B15:53	FEAFAKEY	0.9896	0.9185	8	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-C14:03	LFEAFAKEY	0.3638	0.9684	7	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-C14:02	LFEAFAKEY	0.3638	0.9684	7	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:07	EAFAKEYSH	0.1677	0.8603	9	18
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-A25:01	DLFEAFAKEY	0.9955	0.8064	6	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B35:20	DLFEAFAKEY	0.9818	0.8836	6	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	HLA-B18:04	DLFEAFAKEY	0.9039	0.9118	6	16

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Potential FusionNeoAntigen Information of SMYD3-ZMYM4 in HLA II

SMYD3-ZMYM4_246490503_35835630.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)
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1105	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1119	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1131	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1132	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1145	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1169	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1169	AFDLFEAFAKEYSHG	4	19
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1182	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1182	AFDLFEAFAKEYSHG	4	19
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1382	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB1-1424	FDLFEAFAKEYSHGQ	5	20
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0101	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0101	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0102	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0102	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0102	QLPPAFDLFEAFAKE	0	15
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0103	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0103	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0103	QLPPAFDLFEAFAKE	0	15
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0103	PAFDLFEAFAKEYSH	3	18
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0104	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0104	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0104	QLPPAFDLFEAFAKE	0	15
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0105	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0105	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0108N	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0108N	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0108N	QLPPAFDLFEAFAKE	0	15
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0111	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0111	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0111	QLPPAFDLFEAFAKE	0	15
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0113	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0113	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0114	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0114	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0203	PPAFDLFEAFAKEYS	2	17
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0203	LPPAFDLFEAFAKEY	1	16
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0203	QLPPAFDLFEAFAKE	0	15
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	531	DRB5-0203	PAFDLFEAFAKEYSH	3	18

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Fusion breakpoint peptide structures of SMYD3-ZMYM4

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
1207	DLFEAFAKEYSHGQ	SMYD3	ZMYM4	chr1	246490503	chr1	35835630	531

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SMYD3-ZMYM4

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	1207	DLFEAFAKEYSHGQ	-7.15543	-7.26883
HLA-B14:02	3BVN	1207	DLFEAFAKEYSHGQ	-4.77435	-5.80965
HLA-B52:01	3W39	1207	DLFEAFAKEYSHGQ	-6.80875	-6.92215
HLA-B52:01	3W39	1207	DLFEAFAKEYSHGQ	-4.20386	-5.23916
HLA-A11:01	4UQ2	1207	DLFEAFAKEYSHGQ	-7.5194	-8.5547
HLA-A11:01	4UQ2	1207	DLFEAFAKEYSHGQ	-6.9601	-7.0735
HLA-A24:02	5HGA	1207	DLFEAFAKEYSHGQ	-7.52403	-7.63743
HLA-A24:02	5HGA	1207	DLFEAFAKEYSHGQ	-5.82433	-6.85963
HLA-B27:05	6PYJ	1207	DLFEAFAKEYSHGQ	-3.28285	-4.31815
HLA-B44:05	3DX8	1207	DLFEAFAKEYSHGQ	-5.91172	-6.94702
HLA-B44:05	3DX8	1207	DLFEAFAKEYSHGQ	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of SMYD3-ZMYM4

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
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	6	16	DLFEAFAKEY	CTTTTTGAAGCCTTTGCAAAAGAGTATAGT
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	7	16	LFEAFAKEY	TTTGAAGCCTTTGCAAAAGAGTATAGT
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	8	16	FEAFAKEY	GAAGCCTTTGCAAAAGAGTATAGT
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	9	18	EAFAKEYSH	GCCTTTGCAAAAGAGTATAGTCATGGC

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
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	0	15	QLPPAFDLFEAFAKE	CTGCCACCTGCCTTTGACCTTTTTGAAGCCTTTGCAAAAGAGTAT
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	1	16	LPPAFDLFEAFAKEY	CCACCTGCCTTTGACCTTTTTGAAGCCTTTGCAAAAGAGTATAGT
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	2	17	PPAFDLFEAFAKEYS	CCTGCCTTTGACCTTTTTGAAGCCTTTGCAAAAGAGTATAGTCAT
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	3	18	PAFDLFEAFAKEYSH	GCCTTTGACCTTTTTGAAGCCTTTGCAAAAGAGTATAGTCATGGC
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	4	19	AFDLFEAFAKEYSHG	TTTGACCTTTTTGAAGCCTTTGCAAAAGAGTATAGTCATGGCCAA
SMYD3-ZMYM4	chr1	246490503	chr1	35835630	5	20	FDLFEAFAKEYSHGQ	GACCTTTTTGAAGCCTTTGCAAAAGAGTATAGTCATGGCCAACAG

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Information of the samples that have these potential fusion neoantigens of SMYD3-ZMYM4

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
SKCM	SMYD3-ZMYM4	chr1	246490503	ENST00000388985	chr1	35835630	ENST00000314607	TCGA-DA-A1I7-06A

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Potential target of CAR-T therapy development for SMYD3-ZMYM4

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 SMYD3-ZMYM4

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 SMYD3-ZMYM4

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)