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Fusion Protein:SYNPO2-METTL14

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SYNPO2-METTL14
	FusionPDB ID: 88473
	FusionGDB2.0 ID: 88473
		Hgene	Tgene
	Gene symbol	SYNPO2	METTL14
	Gene ID	171024	57721
	Gene name	synaptopodin 2	methyltransferase like 14
	Synonyms	-	hMETTL14
	Cytomap	4q26	4q26
	Type of gene	protein-coding	protein-coding
	Description	synaptopodin-2genethonin-2myopodin	N6-adenosine-methyltransferase non-catalytic subunitN6-adenosine-methyltransferase subunit METTL14methyltransferase-like protein 14
	Modification date	20200313	20200313
	UniProtAcc	.	Q9HCE5 Main function of 5'-partner protein: FUNCTION: The METTL3-METTL14 heterodimer forms a N6-methyltransferase complex that methylates adenosine residues at the N(6) position of some mRNAs and regulates the circadian clock, differentiation of embryonic stem cells and cortical neurogenesis (PubMed:24316715, PubMed:24407421, PubMed:25719671, PubMed:29348140, PubMed:27373337, PubMed:27281194). In the heterodimer formed with METTL3, METTL14 constitutes the RNA-binding scaffold that recognizes the substrate rather than the catalytic core (PubMed:27627798, PubMed:27373337, PubMed:27281194, PubMed:29348140). N6-methyladenosine (m6A), which takes place at the 5'-[AG]GAC-3' consensus sites of some mRNAs, plays a role in mRNA stability and processing (PubMed:24316715, PubMed:24407421, PubMed:25719671). M6A acts as a key regulator of mRNA stability by promoting mRNA destabilization and degradation (By similarity). In embryonic stem cells (ESCs), m6A methylation of mRNAs encoding key naive pluripotency-promoting transcripts results in transcript destabilization (By similarity). M6A regulates spermatogonial differentiation and meiosis and is essential for male fertility and spermatogenesis (By similarity). M6A also regulates cortical neurogenesis: m6A methylation of transcripts related to transcription factors, neural stem cells, the cell cycle and neuronal differentiation during brain development promotes their destabilization and decay, promoting differentiation of radial glial cells (By similarity). {ECO:0000250\|UniProtKB:Q3UIK4, ECO:0000269\|PubMed:24316715, ECO:0000269\|PubMed:24407421, ECO:0000269\|PubMed:25719671, ECO:0000269\|PubMed:27281194, ECO:0000269\|PubMed:27373337, ECO:0000269\|PubMed:27627798, ECO:0000269\|PubMed:29348140}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000307142, ENST00000429713, ENST00000434046, ENST00000448416,	ENST00000388822, ENST00000506780,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 5 X 5=175	3 X 3 X 3=27
	# samples	9	3
	** MAII score	log2(9/175*10)=-0.959358015502654 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: SYNPO2 [Title/Abstract] AND METTL14 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SYNPO2 [Title/Abstract] AND METTL14 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SYNPO2(119810296)-METTL14(119621705), # samples:3
Anticipated loss of major functional domain due to fusion event.	SYNPO2-METTL14 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. SYNPO2-METTL14 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. SYNPO2-METTL14 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. SYNPO2-METTL14 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	METTL14	GO:0080009	mRNA methylation	27281194\|27373337\|27627798

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr4:119810296/chr4:119621705)
- 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 SYNPO2 (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 METTL14 (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)
ENST00000307142	SYNPO2	chr4	119810296	+	ENST00000388822	METTL14	chr4	119621705	+	6158	301	196	1026	276
ENST00000307142	SYNPO2	chr4	119810296	+	ENST00000506780	METTL14	chr4	119621705	+	1328	301	196	1026	276
ENST00000448416	SYNPO2	chr4	119810296	+	ENST00000388822	METTL14	chr4	119621705	+	6145	288	183	1013	276
ENST00000448416	SYNPO2	chr4	119810296	+	ENST00000506780	METTL14	chr4	119621705	+	1315	288	183	1013	276
ENST00000429713	SYNPO2	chr4	119810296	+	ENST00000388822	METTL14	chr4	119621705	+	6144	287	182	1012	276
ENST00000429713	SYNPO2	chr4	119810296	+	ENST00000506780	METTL14	chr4	119621705	+	1314	287	182	1012	276
ENST00000434046	SYNPO2	chr4	119810296	+	ENST00000388822	METTL14	chr4	119621705	+	5962	105	0	830	276
ENST00000434046	SYNPO2	chr4	119810296	+	ENST00000506780	METTL14	chr4	119621705	+	1132	105	0	830	276

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
ENST00000307142	ENST00000388822	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.011250936	0.988749
ENST00000307142	ENST00000506780	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.07369269	0.9263074
ENST00000448416	ENST00000388822	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.011186198	0.9888138
ENST00000448416	ENST00000506780	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.06742911	0.93257093
ENST00000429713	ENST00000388822	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.011176919	0.98882306
ENST00000429713	ENST00000506780	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.06619741	0.93380255
ENST00000434046	ENST00000388822	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.010507747	0.9894923
ENST00000434046	ENST00000506780	SYNPO2	chr4	119810296	+	METTL14	chr4	119621705	+	0.04907688	0.9509231

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 SYNPO2-METTL14

+/-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
SYNPO2	chr4	119810296	METTL14	chr4	119621705	105	35	GGKEQKQPLQVAKIMKLEIDEIAAPR
SYNPO2	chr4	119810296	METTL14	chr4	119621705	287	35	GGKEQKQPLQVAKIMKLEIDEIAAPR
SYNPO2	chr4	119810296	METTL14	chr4	119621705	288	35	GGKEQKQPLQVAKIMKLEIDEIAAPR
SYNPO2	chr4	119810296	METTL14	chr4	119621705	301	35	GGKEQKQPLQVAKIMKLEIDEIAAPR

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Potential FusionNeoAntigen Information of SYNPO2-METTL14 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.

SYNPO2-METTL14_119810296_119621705.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)
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B51:01	QPLQVAKI	0.9916	0.5146	6	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B51:02	QPLQVAKI	0.9732	0.5689	6	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:01	QPLQVAKIM	0.963	0.8911	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B52:01	VAKIMKLEI	0.9366	0.9553	10	19
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:08	QPLQVAKIM	0.9252	0.795	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:03	QPLQVAKIM	0.9236	0.8602	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:05	QPLQVAKIM	0.9223	0.7266	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B08:01	LQVAKIMKL	0.8719	0.6395	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B14:02	LQVAKIMKL	0.8349	0.7264	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B14:01	LQVAKIMKL	0.8349	0.7264	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B53:01	QPLQVAKIM	0.8235	0.6615	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B08:09	LQVAKIMKL	0.798	0.6358	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:03	LQVAKIMKL	0.7575	0.5928	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B48:01	KQPLQVAKI	0.7354	0.5522	5	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B13:02	LQVAKIMKL	0.7321	0.5943	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B13:01	LQVAKIMKL	0.6831	0.9219	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:04	QPLQVAKIM	0.6357	0.9666	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:02	QPLQVAKIM	0.6357	0.9666	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B39:13	LQVAKIMKL	0.6174	0.8578	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B13:02	KQPLQVAKI	0.6	0.7266	5	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B13:01	KQPLQVAKI	0.3732	0.9358	5	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B81:01	QPLQVAKIM	0.1937	0.7141	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B82:01	QPLQVAKIM	0.1568	0.6427	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B52:01	LQVAKIMKL	0.088	0.8777	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B52:01	KQPLQVAKI	0.0329	0.9664	5	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:04	LQVAKIMKL	0.9851	0.6577	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-C06:03	LQVAKIMKL	0.9642	0.986	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-C02:06	LQVAKIMKL	0.8721	0.9512	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B39:12	LQVAKIMKL	0.7973	0.8434	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B42:02	QPLQVAKIM	0.6965	0.7768	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B56:04	QPLQVAKIM	0.6742	0.6594	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:12	QPLQVAKIM	0.6357	0.9666	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B42:01	QPLQVAKIM	0.62	0.7604	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B14:03	LQVAKIMKL	0.4638	0.7482	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B39:10	QPLQVAKIM	0.4362	0.9348	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B42:01	QPLQVAKIMKL	0.9609	0.7922	6	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B51:09	QPLQVAKI	0.971	0.5584	6	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B51:21	QPLQVAKI	0.9616	0.5123	6	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:24	LQVAKIMKL	0.9951	0.7216	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:50	LQVAKIMKL	0.9899	0.8072	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:35	LQVAKIMKL	0.9803	0.6254	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:77	QPLQVAKIM	0.963	0.8911	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:23	QPLQVAKIM	0.9616	0.9119	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:73	LQVAKIMKL	0.9613	0.7706	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-C07:04	LQVAKIMKL	0.9463	0.9176	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-C06:08	LQVAKIMKL	0.9461	0.9817	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:17	QPLQVAKIM	0.9315	0.8157	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:30	QPLQVAKIM	0.9315	0.8157	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:11	QPLQVAKIM	0.9061	0.925	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:24	QPLQVAKIM	0.8868	0.8859	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B08:18	LQVAKIMKL	0.8719	0.6395	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:73	KQPLQVAKI	0.8528	0.8775	5	14
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:53	LQVAKIMKL	0.8323	0.6284	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:30	LQVAKIMKL	0.8312	0.7953	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B39:02	LQVAKIMKL	0.8269	0.856	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B15:54	LQVAKIMKL	0.8042	0.5777	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B56:05	QPLQVAKIM	0.7898	0.6343	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B53:02	QPLQVAKIM	0.7484	0.6288	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:22	QPLQVAKIM	0.7342	0.6611	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B08:12	LQVAKIMKL	0.7201	0.7577	8	17
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B55:04	QPLQVAKIM	0.7062	0.5704	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B56:02	QPLQVAKIM	0.6742	0.6594	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:09	QPLQVAKIM	0.6357	0.9666	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B51:06	QPLQVAKIM	0.5969	0.5901	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B67:01	QPLQVAKIM	0.4518	0.9207	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B82:02	QPLQVAKIM	0.1568	0.6427	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B18:07	QPLQVAKIM	0.1361	0.8377	6	15
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	HLA-B35:43	QPLQVAKIM	0.0618	0.8118	6	15

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Potential FusionNeoAntigen Information of SYNPO2-METTL14 in HLA II

SYNPO2-METTL14_119810296_119621705.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)
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-0422	AKIMKLEIDEIAAPR	11	26
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1117	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1152	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1377	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1401	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1401	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1404	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1404	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1404	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1405	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1408	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1411	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1418	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1423	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1426	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1426	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1428	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1428	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1428	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1431	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1431	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1432	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1432	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1435	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1435	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1435	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1438	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1443	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1445	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1450	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1450	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1454	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1454	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1455	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1456	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1458	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1458	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1459	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1460	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1460	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1461	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1461	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1461	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1462	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1464	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1465	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1470	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1471	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1471	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1471	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1472	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1475	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1475	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1482	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1486	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1486	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1487	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1487	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1488	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1488	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1490	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1490	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1491	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1496	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1497	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1497	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1499	QPLQVAKIMKLEIDE	6	21
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1499	PLQVAKIMKLEIDEI	7	22
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB1-1499	KQPLQVAKIMKLEID	5	20
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0101	VAKIMKLEIDEIAAP	10	25
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0101	QVAKIMKLEIDEIAA	9	24
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0101	AKIMKLEIDEIAAPR	11	26
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0103	VAKIMKLEIDEIAAP	10	25
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0103	QVAKIMKLEIDEIAA	9	24
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0103	AKIMKLEIDEIAAPR	11	26
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0104	VAKIMKLEIDEIAAP	10	25
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0104	AKIMKLEIDEIAAPR	11	26
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0104	QVAKIMKLEIDEIAA	9	24
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0106	VAKIMKLEIDEIAAP	10	25
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0106	QVAKIMKLEIDEIAA	9	24
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0106	AKIMKLEIDEIAAPR	11	26
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0107	VAKIMKLEIDEIAAP	10	25
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0107	QVAKIMKLEIDEIAA	9	24
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0107	AKIMKLEIDEIAAPR	11	26
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0108	VAKIMKLEIDEIAAP	10	25
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0108	QVAKIMKLEIDEIAA	9	24
SYNPO2-METTL14	chr4	119810296	chr4	119621705	301	DRB4-0108	AKIMKLEIDEIAAPR	11	26

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Fusion breakpoint peptide structures of SYNPO2-METTL14

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
7461	QPLQVAKIMKLEID	SYNPO2	METTL14	chr4	119810296	chr4	119621705	301

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SYNPO2-METTL14

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	7461	QPLQVAKIMKLEID	-5.49577	-5.60917
HLA-B14:02	3BVN	7461	QPLQVAKIMKLEID	-4.37152	-5.40682
HLA-B52:01	3W39	7461	QPLQVAKIMKLEID	-6.90336	-7.01676
HLA-B52:01	3W39	7461	QPLQVAKIMKLEID	-4.80833	-5.84363
HLA-A11:01	4UQ2	7461	QPLQVAKIMKLEID	-9.82261	-9.93601
HLA-A24:02	5HGA	7461	QPLQVAKIMKLEID	-9.78612	-9.89952
HLA-A24:02	5HGA	7461	QPLQVAKIMKLEID	-4.98992	-6.02522
HLA-B27:05	6PYJ	7461	QPLQVAKIMKLEID	-5.31553	-6.35083
HLA-B44:05	3DX8	7461	QPLQVAKIMKLEID	-5.70582	-5.81922
HLA-B44:05	3DX8	7461	QPLQVAKIMKLEID	-4.32241	-5.35771

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Vaccine Design for the FusionNeoAntigens of SYNPO2-METTL14

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
SYNPO2-METTL14	chr4	119810296	chr4	119621705	10	19	VAKIMKLEI	GTTGCAAAGATTATGAAGTTAGAAATT
SYNPO2-METTL14	chr4	119810296	chr4	119621705	5	14	KQPLQVAKI	AAGCAGCCCTTACAAGTTGCAAAGATT
SYNPO2-METTL14	chr4	119810296	chr4	119621705	6	14	QPLQVAKI	CAGCCCTTACAAGTTGCAAAGATT
SYNPO2-METTL14	chr4	119810296	chr4	119621705	6	15	QPLQVAKIM	CAGCCCTTACAAGTTGCAAAGATTATG
SYNPO2-METTL14	chr4	119810296	chr4	119621705	6	17	QPLQVAKIMKL	CAGCCCTTACAAGTTGCAAAGATTATGAAGTTA
SYNPO2-METTL14	chr4	119810296	chr4	119621705	8	17	LQVAKIMKL	TTACAAGTTGCAAAGATTATGAAGTTA

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
SYNPO2-METTL14	chr4	119810296	chr4	119621705	10	25	VAKIMKLEIDEIAAP	GTTGCAAAGATTATGAAGTTAGAAATTGATGAGATTGCAGCACCT
SYNPO2-METTL14	chr4	119810296	chr4	119621705	11	26	AKIMKLEIDEIAAPR	GCAAAGATTATGAAGTTAGAAATTGATGAGATTGCAGCACCTCGA
SYNPO2-METTL14	chr4	119810296	chr4	119621705	5	20	KQPLQVAKIMKLEID	AAGCAGCCCTTACAAGTTGCAAAGATTATGAAGTTAGAAATTGAT
SYNPO2-METTL14	chr4	119810296	chr4	119621705	6	21	QPLQVAKIMKLEIDE	CAGCCCTTACAAGTTGCAAAGATTATGAAGTTAGAAATTGATGAG
SYNPO2-METTL14	chr4	119810296	chr4	119621705	7	22	PLQVAKIMKLEIDEI	CCCTTACAAGTTGCAAAGATTATGAAGTTAGAAATTGATGAGATT
SYNPO2-METTL14	chr4	119810296	chr4	119621705	9	24	QVAKIMKLEIDEIAA	CAAGTTGCAAAGATTATGAAGTTAGAAATTGATGAGATTGCAGCA

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Information of the samples that have these potential fusion neoantigens of SYNPO2-METTL14

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
PCPG	SYNPO2-METTL14	chr4	119810296	ENST00000307142	chr4	119621705	ENST00000388822	TCGA-QR-A707-01A

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Potential target of CAR-T therapy development for SYNPO2-METTL14

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 SYNPO2-METTL14

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 SYNPO2-METTL14

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)