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Fusion Protein:MARCH9-YEATS4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MARCH9-YEATS4
	FusionPDB ID: 51723
	FusionGDB2.0 ID: 51723
		Hgene	Tgene
	Gene symbol	MARCH9	YEATS4
	Gene ID	92979	8089
	Gene name	membrane associated ring-CH-type finger 9	YEATS domain containing 4
	Synonyms	MARCH-IX\|MARCH9\|RNF179	4930573H17Rik\|B230215M10Rik\|GAS41\|NUBI-1\|YAF9
	Cytomap	12q14.1	12q15
	Type of gene	protein-coding	protein-coding
	Description	E3 ubiquitin-protein ligase MARCH9RING finger protein 179RING-type E3 ubiquitin transferase MARCH9membrane associated ring finger 9membrane-associated RING finger protein 9membrane-associated RING-CH protein IXmembrane-associated ring finger (C3HC4)	YEATS domain-containing protein 4NuMA binding protein 1glioma-amplified sequence 41nuBI1
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000266643, ENST00000548358,	ENST00000247843, ENST00000548020,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 6 X 6=324	10 X 4 X 4=160
	# samples	10	10
	** MAII score	log2(10/324*10)=-1.6959938131099 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/160*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: MARCH9 [Title/Abstract] AND YEATS4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: MARCH9 [Title/Abstract] AND YEATS4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MARCH9(58150867)-YEATS4(69756568), # samples:2
Anticipated loss of major functional domain due to fusion event.	MARCH9-YEATS4 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. MARCH9-YEATS4 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. MARCH9-YEATS4 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. MARCH9-YEATS4 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	YEATS4	GO:0043967	histone H4 acetylation	14966270
Tgene	YEATS4	GO:0043968	histone H2A acetylation	14966270

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:58150867/chr12:69756568)
- 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 MARCH9 (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 YEATS4 (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)

ENST00000266643

MARCH9

chr12

58150867

ENST00000247843

YEATS4

chr12

69756568

2057

944

1576

520

ENST00000266643

MARCH9

chr12

58150867

ENST00000548020

YEATS4

chr12

69756568

1730

944

1414

466

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
ENST00000266643	ENST00000247843	MARCH9	chr12	58150867	+	YEATS4	chr12	69756568	+	0.006667204	0.9933328
ENST00000266643	ENST00000548020	MARCH9	chr12	58150867	+	YEATS4	chr12	69756568	+	0.030981071	0.96901894

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 MARCH9-YEATS4

+/-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
MARCH9	chr12	58150867	YEATS4	chr12	69756568	944	310	YQVLAISTKNPLQGVTIVKPIVYGNV

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Potential FusionNeoAntigen Information of MARCH9-YEATS4 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.

MARCH9-YEATS4_58150867_69756568.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)
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-A30:08	STKNPLQGV	0.9937	0.746	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B35:02	NPLQGVTIV	0.9512	0.9492	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B35:04	NPLQGVTIV	0.9512	0.9492	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B35:03	NPLQGVTIV	0.928	0.8464	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B08:09	NPLQGVTIV	0.6053	0.6736	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B39:10	NPLQGVTI	0.5801	0.7793	9	17
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-C15:06	STKNPLQGV	0.9991	0.8606	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-C06:03	STKNPLQGV	0.9888	0.9685	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-C12:04	STKNPLQGV	0.9886	0.9784	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B78:01	NPLQGVTIV	0.9754	0.5548	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B35:12	NPLQGVTIV	0.9512	0.9492	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-C02:06	STKNPLQGV	0.8003	0.9292	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B42:02	NPLQGVTIV	0.787	0.7451	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B42:01	NPLQGVTIV	0.7242	0.7402	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B39:10	NPLQGVTIV	0.4462	0.8589	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B78:02	NPLQGVTI	0.9912	0.5389	9	17
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-C15:02	STKNPLQGV	0.9993	0.8338	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-C15:05	STKNPLQGV	0.9992	0.8613	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-A30:01	STKNPLQGV	0.994	0.7975	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B78:02	NPLQGVTIV	0.9819	0.5952	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-A02:03	STKNPLQGV	0.9513	0.6256	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B35:09	NPLQGVTIV	0.9512	0.9492	9	18
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-A69:01	STKNPLQGV	0.9492	0.7631	6	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	HLA-B67:01	NPLQGVTIV	0.6434	0.6931	9	18

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Potential FusionNeoAntigen Information of MARCH9-YEATS4 in HLA II

MARCH9-YEATS4_58150867_69756568.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)
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-0303	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-0324	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1113	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1117	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1117	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1152	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1152	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1189	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1189	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1201	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1201	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1201	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1203	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1203	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1203	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1204	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1204	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1205	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1205	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1205	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1206	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1206	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1206	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1207	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1207	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1207	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1208	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1208	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1208	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1209	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1209	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1210	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1210	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1210	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1211	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1211	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1211	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1212	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1212	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1212	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1213	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1213	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1213	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1214	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1214	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1214	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1215	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1215	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1215	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1217	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1217	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1217	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1218	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1218	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1218	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1219	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1219	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1219	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1220	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1220	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1221	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1221	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1222	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1222	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1223	PLQGVTIVKPIVYGN	10	25
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1223	LQGVTIVKPIVYGNV	11	26
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1223	NPLQGVTIVKPIVYG	9	24
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1331	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1354	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1376	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1377	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1381	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1401	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1401	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1404	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1404	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1405	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1405	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1406	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1407	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1407	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1408	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1408	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1411	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1411	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1414	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1414	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1416	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1418	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1418	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1420	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1421	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1423	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1423	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1424	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1426	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1426	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1428	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1428	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1429	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1431	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1431	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1432	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1432	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1433	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1434	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1434	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1435	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1435	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1436	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1436	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1437	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1438	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1438	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1439	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1439	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1442	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1442	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1443	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1443	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1444	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1444	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1445	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1445	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1448	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1449	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1450	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1450	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1451	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1454	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1454	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1455	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1455	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1456	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1456	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1458	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1458	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1459	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1459	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1460	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1460	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1461	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1461	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1462	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1462	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1464	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1464	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1465	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1465	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1468	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1468	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1470	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1470	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1471	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1471	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1472	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1472	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1473	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1474	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1475	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1475	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1480	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1481	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1481	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1482	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1482	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1483	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1486	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1486	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1487	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1487	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1488	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1488	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1490	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1490	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1491	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1491	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1493	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1493	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1495	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1495	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1496	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1496	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1497	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1497	QVLAISTKNPLQGVT	1	16
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1499	YQVLAISTKNPLQGV	0	15
MARCH9-YEATS4	chr12	58150867	chr12	69756568	944	DRB1-1499	QVLAISTKNPLQGVT	1	16

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Fusion breakpoint peptide structures of MARCH9-YEATS4

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
9108	STKNPLQGVTIVKP	MARCH9	YEATS4	chr12	58150867	chr12	69756568	944

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MARCH9-YEATS4

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	9108	STKNPLQGVTIVKP	-6.12283	-6.12283
HLA-A24:02	5HGA	9108	STKNPLQGVTIVKP	-7.36995	-7.36995

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Vaccine Design for the FusionNeoAntigens of MARCH9-YEATS4

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
MARCH9-YEATS4	chr12	58150867	chr12	69756568	6	15	STKNPLQGV	AGCACCAAGAACCCACTGCAGGGTGTT
MARCH9-YEATS4	chr12	58150867	chr12	69756568	9	17	NPLQGVTI	AACCCACTGCAGGGTGTTACTATC
MARCH9-YEATS4	chr12	58150867	chr12	69756568	9	18	NPLQGVTIV	AACCCACTGCAGGGTGTTACTATCGTT

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
MARCH9-YEATS4	chr12	58150867	chr12	69756568	0	15	YQVLAISTKNPLQGV	TACCAGGTCCTGGCGATCAGCACCAAGAACCCACTGCAGGGTGTT
MARCH9-YEATS4	chr12	58150867	chr12	69756568	1	16	QVLAISTKNPLQGVT	CAGGTCCTGGCGATCAGCACCAAGAACCCACTGCAGGGTGTTACT
MARCH9-YEATS4	chr12	58150867	chr12	69756568	10	25	PLQGVTIVKPIVYGN	CCACTGCAGGGTGTTACTATCGTTAAACCAATAGTTTACGGTAAT
MARCH9-YEATS4	chr12	58150867	chr12	69756568	11	26	LQGVTIVKPIVYGNV	CTGCAGGGTGTTACTATCGTTAAACCAATAGTTTACGGTAATGTT
MARCH9-YEATS4	chr12	58150867	chr12	69756568	9	24	NPLQGVTIVKPIVYG	AACCCACTGCAGGGTGTTACTATCGTTAAACCAATAGTTTACGGT

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Information of the samples that have these potential fusion neoantigens of MARCH9-YEATS4

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
SARC	MARCH9-YEATS4	chr12	58150867	ENST00000266643	chr12	69756568	ENST00000247843	TCGA-DX-A3LT-01A

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Potential target of CAR-T therapy development for MARCH9-YEATS4

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 MARCH9-YEATS4

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 MARCH9-YEATS4

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)