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Fusion Protein:MMP28-ATP6V0A1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MMP28-ATP6V0A1
	FusionPDB ID: 54423
	FusionGDB2.0 ID: 54423
		Hgene	Tgene
	Gene symbol	MMP28	ATP6V0A1
	Gene ID	79148	535
	Gene name	matrix metallopeptidase 28	ATPase H+ transporting V0 subunit a1
	Synonyms	EPILYSIN\|MM28\|MMP-25\|MMP-28\|MMP25	ATP6N1\|ATP6N1A\|Stv1\|VPP1\|Vph1\|a1
	Cytomap	17q12	17q21.2
	Type of gene	protein-coding	protein-coding
	Description	matrix metalloproteinase-28matrix metalloprotease MMP25	V-type proton ATPase 116 kDa subunit a isoform 1V-type proton ATPase 116 kDa subunit aATPase, H+ transporting, lysosomal V0 subunit a1ATPase, H+ transporting, lysosomal non-catalytic accessory protein 1 (110/116kD)H(+)-transporting two-sector ATPase,
	Modification date	20200313	20200324
	UniProtAcc	Q9H239 Main function of 5'-partner protein: FUNCTION: Can degrade casein. Could play a role in tissues homeostasis and repair.	Q93050 Main function of 5'-partner protein: FUNCTION: Required for assembly and activity of the vacuolar ATPase. Potential role in differential targeting and regulation of the enzyme for a specific organelle (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000250144,	ENST00000587797, ENST00000546249, ENST00000264649, ENST00000343619, ENST00000393829, ENST00000537728, ENST00000544137, ENST00000585525,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 2 X 3=18	8 X 10 X 4=320
	# samples	3	9
	** MAII score	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(9/320*10)=-1.83007499855769 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: MMP28 [Title/Abstract] AND ATP6V0A1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: MMP28 [Title/Abstract] AND ATP6V0A1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MMP28(34122271)-ATP6V0A1(40665879), # samples:1
Anticipated loss of major functional domain due to fusion event.	MMP28-ATP6V0A1 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. MMP28-ATP6V0A1 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. MMP28-ATP6V0A1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. MMP28-ATP6V0A1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. MMP28-ATP6V0A1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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/chr17:34122271/chr17:40665879)
- 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 MMP28 (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 ATP6V0A1 (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)
ENST00000250144	MMP28	chr17	34122271	-	ENST00000393829	ATP6V0A1	chr17	40665879	+	1190	441	511	2	170
ENST00000250144	MMP28	chr17	34122271	-	ENST00000537728	ATP6V0A1	chr17	40665879	+	1099	441	330	824	164
ENST00000250144	MMP28	chr17	34122271	-	ENST00000264649	ATP6V0A1	chr17	40665879	+	2287	441	330	824	164
ENST00000250144	MMP28	chr17	34122271	-	ENST00000585525	ATP6V0A1	chr17	40665879	+	996	441	511	2	170
ENST00000250144	MMP28	chr17	34122271	-	ENST00000343619	ATP6V0A1	chr17	40665879	+	2316	441	511	2	170
ENST00000250144	MMP28	chr17	34122271	-	ENST00000544137	ATP6V0A1	chr17	40665879	+	2283	441	511	2	170

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
ENST00000250144	ENST00000393829	MMP28	chr17	34122271	-	ATP6V0A1	chr17	40665879	+	0.02346411	0.97653586
ENST00000250144	ENST00000537728	MMP28	chr17	34122271	-	ATP6V0A1	chr17	40665879	+	0.032475077	0.967525
ENST00000250144	ENST00000264649	MMP28	chr17	34122271	-	ATP6V0A1	chr17	40665879	+	0.026488258	0.9735118
ENST00000250144	ENST00000585525	MMP28	chr17	34122271	-	ATP6V0A1	chr17	40665879	+	0.034537584	0.9654624
ENST00000250144	ENST00000343619	MMP28	chr17	34122271	-	ATP6V0A1	chr17	40665879	+	0.027790004	0.97221
ENST00000250144	ENST00000544137	MMP28	chr17	34122271	-	ATP6V0A1	chr17	40665879	+	0.026312115	0.9736878

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 MMP28-ATP6V0A1

+/-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
MMP28	chr17	34122271	ATP6V0A1	chr17	40665879	441	37	AERGGQELRKEAEFDFGDTMVHQAIH

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Potential FusionNeoAntigen Information of MMP28-ATP6V0A1 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.

MMP28-ATP6V0A1_34122271_40665879.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)
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:03	QELRKEAEF	0.9987	0.9763	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B47:01	QELRKEAEF	0.9969	0.5232	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B13:01	AEFDFGDTM	0.9951	0.9796	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:03	AEFDFGDTM	0.9929	0.9823	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:01	QELRKEAEF	0.9872	0.939	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B27:02	LRKEAEFDF	0.9867	0.8984	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B27:07	LRKEAEFDF	0.9791	0.6545	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:02	AEFDFGDTM	0.9722	0.6143	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:01	AEFDFGDTM	0.9259	0.9519	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B47:01	AEFDFGDTM	0.9064	0.7772	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B45:01	AEFDFGDTM	0.8913	0.9557	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:13	AEFDFGDTM	0.5287	0.9795	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B38:02	AEFDFGDTM	0.4776	0.9813	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B41:01	AEFDFGDTM	0.368	0.9476	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:01	AEFDFGDTM	0.1969	0.8423	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B15:03	AEFDFGDTM	0.1963	0.9191	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:02	AEFDFGDTMV	0.9949	0.7707	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B45:01	AEFDFGDTMV	0.9901	0.9628	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:01	AEFDFGDTMV	0.9856	0.6065	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B41:01	AEFDFGDTMV	0.865	0.9861	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:01	AEFDFGDTMV	0.7912	0.9153	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B35:04	EAEFDFGDTM	0.7315	0.9688	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B35:02	EAEFDFGDTM	0.7315	0.9688	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:01	EAEFDFGDTM	0.2861	0.9313	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B47:01	KEAEFDFGDTM	0.9997	0.56	9	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B47:01	AEFDFGDTMVH	0.9995	0.7521	11	22
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:13	KEAEFDFGDTM	0.9975	0.8852	9	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:10	EFDFGDTM	0.9999	0.701	12	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:07	EFDFGDTM	0.9999	0.7286	12	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:14	EFDFGDTM	0.9516	0.6824	12	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:06	AEFDFGDTM	0.9981	0.8146	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:10	EFDFGDTMV	0.9959	0.9041	12	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:07	EFDFGDTMV	0.9937	0.9264	12	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:09	AEFDFGDTM	0.9919	0.6406	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:10	AEFDFGDTM	0.9893	0.6491	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:08	AEFDFGDTM	0.9831	0.5317	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:05	LRKEAEFDF	0.9478	0.9845	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:95	LRKEAEFDF	0.9477	0.8823	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:03	AEFDFGDTM	0.9232	0.531	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:27	LRKEAEFDF	0.9078	0.9833	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:19	LRKEAEFDF	0.7846	0.9101	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:80	LRKEAEFDF	0.7685	0.9831	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:67	LRKEAEFDF	0.7685	0.9831	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:10	LRKEAEFDF	0.7671	0.9893	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:46	LRKEAEFDF	0.7387	0.9627	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:08	AEFDFGDTM	0.5793	0.9214	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:05	AEFDFGDTM	0.4738	0.9608	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:06	AEFDFGDTMV	0.9982	0.9485	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:10	AEFDFGDTMV	0.986	0.8451	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B35:12	EAEFDFGDTM	0.7315	0.9688	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:03	AEFDFGDTMVH	0.9997	0.5742	11	22
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:10	KEAEFDFGDTM	0.9992	0.56	9	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:08	KEAEFDFGDTM	0.999	0.8447	9	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:01	EFDFGDTM	0.9999	0.7286	12	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C18:01	EFDFGDTM	0.9998	0.7288	12	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:07	QELRKEAEF	0.9987	0.9763	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:13	QELRKEAEF	0.9987	0.9763	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:26	QELRKEAEF	0.9987	0.9763	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:04	AEFDFGDTM	0.998	0.9231	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C18:01	EFDFGDTMV	0.9951	0.919	12	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C04:01	EFDFGDTMV	0.9937	0.9264	12	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:26	AEFDFGDTM	0.9929	0.9823	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:07	AEFDFGDTM	0.9929	0.9823	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B44:13	AEFDFGDTM	0.9929	0.9823	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B27:08	LRKEAEFDF	0.9873	0.9528	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:05	QELRKEAEF	0.9872	0.939	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:06	QELRKEAEF	0.9868	0.9405	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:08	QELRKEAEF	0.9854	0.8754	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:04	QELRKEAEF	0.9848	0.9453	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:04	QELRKEAEF	0.978	0.7297	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:01	LRKEAEFDF	0.9646	0.877	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:11	QELRKEAEF	0.9616	0.9321	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:03	QELRKEAEF	0.9587	0.934	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B27:09	LRKEAEFDF	0.947	0.9678	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:07	AEFDFGDTM	0.9444	0.9256	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:04	AEFDFGDTM	0.9397	0.9588	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:05	AEFDFGDTM	0.9259	0.9519	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:08	AEFDFGDTM	0.9171	0.9029	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:06	AEFDFGDTM	0.8957	0.9594	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:03	AEFDFGDTM	0.8597	0.947	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:11	AEFDFGDTM	0.8577	0.9394	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:02	LRKEAEFDF	0.7685	0.9831	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B41:03	QELRKEAEF	0.654	0.7837	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-C07:22	LRKEAEFDF	0.5761	0.8767	7	16
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:11	AEFDFGDTM	0.5695	0.8877	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B48:02	QELRKEAEF	0.5638	0.9538	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B15:53	QELRKEAEF	0.5627	0.8237	5	14
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:31	AEFDFGDTM	0.5365	0.967	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B39:02	AEFDFGDTM	0.53	0.9803	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B41:03	AEFDFGDTM	0.4634	0.8454	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B35:20	AEFDFGDTM	0.4308	0.9793	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B35:28	AEFDFGDTM	0.3967	0.9781	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B48:02	AEFDFGDTM	0.3718	0.9775	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B15:53	AEFDFGDTM	0.3136	0.9699	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:05	AEFDFGDTM	0.1969	0.8423	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:04	AEFDFGDTM	0.1969	0.8423	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B15:54	AEFDFGDTM	0.1297	0.9682	11	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:04	AEFDFGDTMV	0.9934	0.9612	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:36	AEFDFGDTMV	0.9852	0.6086	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:49	AEFDFGDTMV	0.9839	0.5994	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:04	AEFDFGDTMV	0.7912	0.9153	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B50:05	AEFDFGDTMV	0.7912	0.9153	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B41:03	AEFDFGDTMV	0.7789	0.9358	11	21
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B35:09	EAEFDFGDTM	0.7315	0.9688	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:11	EAEFDFGDTM	0.4811	0.8928	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:04	EAEFDFGDTM	0.373	0.8037	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:06	EAEFDFGDTM	0.304	0.9347	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:05	EAEFDFGDTM	0.2861	0.9313	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:08	EAEFDFGDTM	0.2716	0.8919	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B18:03	EAEFDFGDTM	0.258	0.9266	10	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B40:04	KEAEFDFGDTM	0.9998	0.7475	9	20
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	441	HLA-B41:03	KEAEFDFGDTM	0.9868	0.6714	9	20

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Potential FusionNeoAntigen Information of MMP28-ATP6V0A1 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 MMP28-ATP6V0A1

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
1919	ELRKEAEFDFGDTM	MMP28	ATP6V0A1	chr17	34122271	chr17	40665879	441

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MMP28-ATP6V0A1

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	1919	ELRKEAEFDFGDTM	-6.15238	-6.26578
HLA-B14:02	3BVN	1919	ELRKEAEFDFGDTM	-5.35203	-6.38733
HLA-B52:01	3W39	1919	ELRKEAEFDFGDTM	-5.804	-6.8393
HLA-B52:01	3W39	1919	ELRKEAEFDFGDTM	-5.45277	-5.56617
HLA-A11:01	4UQ2	1919	ELRKEAEFDFGDTM	-8.28119	-9.31649
HLA-A24:02	5HGA	1919	ELRKEAEFDFGDTM	-9.93626	-10.0497
HLA-A24:02	5HGA	1919	ELRKEAEFDFGDTM	-5.67154	-6.70684
HLA-B27:05	6PYJ	1919	ELRKEAEFDFGDTM	-4.30966	-5.34496
HLA-B44:05	3DX8	1919	ELRKEAEFDFGDTM	-7.17842	-7.29182
HLA-B44:05	3DX8	1919	ELRKEAEFDFGDTM	-4.14208	-5.17738
HLA-A02:01	6TDR	1919	ELRKEAEFDFGDTM	-5.17192	-5.28532

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Vaccine Design for the FusionNeoAntigens of MMP28-ATP6V0A1

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
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	10	20	EAEFDFGDTM	GAGGCGGAGTTTGACTTTGGGGACACCATG
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	11	20	AEFDFGDTM	GCGGAGTTTGACTTTGGGGACACCATG
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	11	21	AEFDFGDTMV	GCGGAGTTTGACTTTGGGGACACCATGGTC
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	11	22	AEFDFGDTMVH	GCGGAGTTTGACTTTGGGGACACCATGGTCCAC
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	12	20	EFDFGDTM	GAGTTTGACTTTGGGGACACCATG
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	12	21	EFDFGDTMV	GAGTTTGACTTTGGGGACACCATGGTC
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	5	14	QELRKEAEF	CAGGAGCTGCGCAAGGAGGCGGAGTTT
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	7	16	LRKEAEFDF	CTGCGCAAGGAGGCGGAGTTTGACTTT
MMP28-ATP6V0A1	chr17	34122271	chr17	40665879	9	20	KEAEFDFGDTM	AAGGAGGCGGAGTTTGACTTTGGGGACACCATG

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 MMP28-ATP6V0A1

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
STAD	MMP28-ATP6V0A1	chr17	34122271	ENST00000250144	chr17	40665879	ENST00000264649	TCGA-CG-5724-01A

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Potential target of CAR-T therapy development for MMP28-ATP6V0A1

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

ATP6V0A1

chr17:34122271

chr17:40665879

ENST00000264649

725_749

839.0

Transmembrane

Helical

Tgene

ATP6V0A1

chr17:34122271

chr17:40665879

ENST00000264649

771_809

839.0

Transmembrane

Helical

Tgene

ATP6V0A1

chr17:34122271

chr17:40665879

ENST00000343619

725_749

838.0

Transmembrane

Helical

Tgene

ATP6V0A1

chr17:34122271

chr17:40665879

ENST00000343619

771_809

838.0

Transmembrane

Helical

Tgene

ATP6V0A1

chr17:34122271

chr17:40665879

ENST00000393829

725_749

832.0

Transmembrane

Helical

Tgene

ATP6V0A1

chr17:34122271

chr17:40665879

ENST00000393829

771_809

832.0

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 MMP28-ATP6V0A1

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 MMP28-ATP6V0A1

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)