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Fusion Protein:ITGA9-SMOC2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ITGA9-SMOC2
	FusionPDB ID: 40473
	FusionGDB2.0 ID: 40473
		Hgene	Tgene
	Gene symbol	ITGA9	SMOC2
	Gene ID	3680	64094
	Gene name	integrin subunit alpha 9	SPARC related modular calcium binding 2
	Synonyms	ALPHA-RLC\|ITGA4L\|RLC	DTDP1\|MST117\|MSTP117\|MSTP140\|SMAP2\|bA270C4A.1\|bA37D8.1\|dJ421D16.1
	Cytomap	3p22.2	6q27
	Type of gene	protein-coding	protein-coding
	Description	integrin alpha-9integrin alpha-RLC	SPARC-related modular calcium-binding protein 2SMAP-2SMOC-2secreted modular calcium-binding protein 2smooth muscle associated protein 2thyroglobulin type-1 repeat containing protein
	Modification date	20200313	20200313
	UniProtAcc	Q13797 Main function of 5'-partner protein: FUNCTION: Integrin alpha-9/beta-1 (ITGA9:ITGB1) is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G-I-E-L in cytotactin. {ECO:0000250}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000264741, ENST00000422441,	ENST00000477998, ENST00000354536, ENST00000356284,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 8 X 10=960	10 X 8 X 7=560
	# samples	13	10
	** MAII score	log2(13/960*10)=-2.88452278258006 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/560*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ITGA9 [Title/Abstract] AND SMOC2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ITGA9 [Title/Abstract] AND SMOC2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ITGA9(37584076)-SMOC2(168910594), # samples:1
Anticipated loss of major functional domain due to fusion event.	ITGA9-SMOC2 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. ITGA9-SMOC2 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. ITGA9-SMOC2 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. ITGA9-SMOC2 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	SMOC2	GO:0010595	positive regulation of endothelial cell migration	16774925
Tgene	SMOC2	GO:0035470	positive regulation of vascular wound healing	16774925
Tgene	SMOC2	GO:0045743	positive regulation of fibroblast growth factor receptor signaling pathway	16774925
Tgene	SMOC2	GO:0045766	positive regulation of angiogenesis	16774925
Tgene	SMOC2	GO:0045931	positive regulation of mitotic cell cycle	16774925
Tgene	SMOC2	GO:1900748	positive regulation of vascular endothelial growth factor signaling pathway	16774925
Tgene	SMOC2	GO:2000573	positive regulation of DNA biosynthetic process	16774925

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:37584076/chr6:168910594)
- 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 ITGA9 (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 SMOC2 (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)

ENST00000264741

ITGA9

chr3

37584076

ENST00000356284

SMOC2

chr6

168910594

4758

1945

250

3201

983

ENST00000264741

ITGA9

chr3

37584076

ENST00000354536

SMOC2

chr6

168910594

4791

1945

250

3234

994

ENST00000422441

ITGA9

chr3

37584076

ENST00000356284

SMOC2

chr6

168910594

4762

1949

254

3205

983

ENST00000422441

ITGA9

chr3

37584076

ENST00000354536

SMOC2

chr6

168910594

4795

1949

254

3238

994

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
ENST00000264741	ENST00000356284	ITGA9	chr3	37584076	+	SMOC2	chr6	168910594	+	0.000447007	0.999553
ENST00000264741	ENST00000354536	ITGA9	chr3	37584076	+	SMOC2	chr6	168910594	+	0.000438983	0.999561
ENST00000422441	ENST00000356284	ITGA9	chr3	37584076	+	SMOC2	chr6	168910594	+	0.000449914	0.99955004
ENST00000422441	ENST00000354536	ITGA9	chr3	37584076	+	SMOC2	chr6	168910594	+	0.000441388	0.9995586

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 ITGA9-SMOC2

+/-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
ITGA9	chr3	37584076	SMOC2	chr6	168910594	1945	564	YMEETCRHYVAHVKFLRVDQDKDKDC
ITGA9	chr3	37584076	SMOC2	chr6	168910594	1949	564	YMEETCRHYVAHVKFLRVDQDKDKDC

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Potential FusionNeoAntigen Information of ITGA9-SMOC2 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.

ITGA9-SMOC2_37584076_168910594.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)
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B08:01	VAHVKFLRV	0.984	0.7418	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B08:09	VAHVKFLRV	0.9837	0.8442	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B52:01	VAHVKFLRV	0.9378	0.993	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:01	RHYVAHVKF	0.9033	0.8753	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B38:01	RHYVAHVKF	0.7891	0.9037	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B38:02	RHYVAHVKF	0.7879	0.9128	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:13	RHYVAHVKF	0.7437	0.877	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B14:01	RHYVAHVKF	0.558	0.6091	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B14:02	RHYVAHVKF	0.558	0.6091	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B15:18	RHYVAHVKF	0.5423	0.6364	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B15:03	RHYVAHVKF	0.4437	0.6439	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B15:10	RHYVAHVKF	0.4215	0.5088	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C03:07	YVAHVKFL	0.9994	0.9861	8	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:80	HYVAHVKF	0.9912	0.928	7	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:67	HYVAHVKF	0.9912	0.928	7	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:10	HYVAHVKF	0.9907	0.9559	7	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C15:06	VAHVKFLRV	0.9955	0.9624	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:95	RHYVAHVKF	0.9935	0.648	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C15:04	VAHVKFLRV	0.9935	0.9397	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:27	RHYVAHVKF	0.9785	0.9568	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C12:04	VAHVKFLRV	0.9734	0.9922	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C06:03	VAHVKFLRV	0.9721	0.9945	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B51:07	VAHVKFLRV	0.9549	0.8782	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:29	RHYVAHVKF	0.9488	0.9336	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:05	RHYVAHVKF	0.9452	0.8902	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:12	RHYVAHVKF	0.9415	0.8933	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:09	RHYVAHVKF	0.9279	0.6329	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C12:12	VAHVKFLRV	0.8839	0.9793	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:19	RHYVAHVKF	0.8717	0.6793	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:46	RHYVAHVKF	0.8679	0.8901	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:13	RHYVAHVKF	0.8669	0.9504	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:80	RHYVAHVKF	0.8611	0.953	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:67	RHYVAHVKF	0.8611	0.953	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:10	RHYVAHVKF	0.8443	0.9732	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:05	RHYVAHVKF	0.7414	0.8563	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C02:06	VAHVKFLRV	0.5433	0.9767	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:29	HYVAHVKFL	0.2818	0.965	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:13	HYVAHVKFL	0.2766	0.9516	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:80	HYVAHVKFL	0.2666	0.9519	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:67	HYVAHVKFL	0.2666	0.9519	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:10	HYVAHVKFL	0.2423	0.9738	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:05	HYVAHVKFL	0.2413	0.9727	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:27	HYVAHVKFL	0.2157	0.9702	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:19	HYVAHVKFL	0.205	0.7406	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:46	HYVAHVKFL	0.1563	0.8974	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:95	HYVAHVKFL	0.1472	0.7671	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B14:03	RHYVAHVKF	0.142	0.7232	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C12:16	RHYVAHVKF	0.0444	0.9645	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C12:16	HYVAHVKFL	0.0421	0.9783	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:02	HYVAHVKF	0.9912	0.928	7	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C14:02	HYVAHVKF	0.9445	0.9535	7	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C14:03	HYVAHVKF	0.9445	0.9535	7	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C15:02	VAHVKFLRV	0.9983	0.9535	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C15:05	VAHVKFLRV	0.9973	0.9716	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C15:09	VAHVKFLRV	0.9935	0.9397	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:01	RHYVAHVKF	0.9927	0.6048	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B08:18	VAHVKFLRV	0.984	0.7418	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:17	RHYVAHVKF	0.9527	0.9657	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:02	RHYVAHVKF	0.9315	0.8793	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C16:02	VAHVKFLRV	0.9121	0.9942	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C16:04	VAHVKFLRV	0.8979	0.985	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:31	RHYVAHVKF	0.8895	0.8926	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C12:03	VAHVKFLRV	0.8731	0.9856	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:02	RHYVAHVKF	0.8611	0.953	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B27:06	RHYVAHVKF	0.7927	0.7963	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B38:05	RHYVAHVKF	0.7891	0.9037	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:22	RHYVAHVKF	0.7527	0.7183	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C16:01	VAHVKFLRV	0.657	0.9876	9	18
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:22	HYVAHVKFL	0.3568	0.8464	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B48:02	RHYVAHVKF	0.3034	0.9257	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:17	HYVAHVKFL	0.2798	0.9768	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:02	HYVAHVKFL	0.2666	0.9519	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C03:67	HYVAHVKFL	0.2352	0.9687	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B39:11	RHYVAHVKF	0.188	0.7423	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:01	HYVAHVKFL	0.1719	0.7216	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C03:67	RHYVAHVKF	0.1468	0.9049	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C07:04	HYVAHVKFL	0.1417	0.9551	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C06:02	HYVAHVKFL	0.1281	0.9955	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C06:17	HYVAHVKFL	0.1281	0.9955	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B15:09	RHYVAHVKF	0.1075	0.7128	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B15:54	RHYVAHVKF	0.097	0.8682	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-B15:68	RHYVAHVKF	0.0922	0.5795	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C14:02	HYVAHVKFL	0.0779	0.9812	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C14:03	HYVAHVKFL	0.0779	0.9812	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C04:04	HYVAHVKFL	0.0525	0.7921	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C06:08	HYVAHVKFL	0.0431	0.9917	7	16
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C06:06	RHYVAHVKF	0.0226	0.9912	6	15
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	HLA-C06:06	HYVAHVKFL	0.0121	0.9935	7	16

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Potential FusionNeoAntigen Information of ITGA9-SMOC2 in HLA II

ITGA9-SMOC2_37584076_168910594.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)
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0411	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0411	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0411	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0451	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0459	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0467	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0467	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0467	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0480	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0487	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0487	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0491	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0491	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0491	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0805	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0818	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0832	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-0840	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1002	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1114	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1114	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1114	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1120	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1120	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1120	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1168	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1168	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1168	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1182	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1182	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1186	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1186	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1186	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1302	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1302	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1302	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1316	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1316	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1316	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1323	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1323	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1323	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1329	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1329	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1329	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1334	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1334	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1334	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1336	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1336	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1339	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1339	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1339	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1341	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1341	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1341	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1373	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1373	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1373	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1374	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1374	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1374	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1396	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1396	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1396	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1397	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1397	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1397	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1399	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1399	CRHYVAHVKFLRVDQ	5	20
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1399	TCRHYVAHVKFLRVD	4	19
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB1-1424	RHYVAHVKFLRVDQD	6	21
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0101	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0101	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0101	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0101	HYVAHVKFLRVDQDK	7	22
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0103	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0103	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0103	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0103	HYVAHVKFLRVDQDK	7	22
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0104	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0104	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0104	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0106	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0106	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0106	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0106	HYVAHVKFLRVDQDK	7	22
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0107	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0107	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0107	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0107	HYVAHVKFLRVDQDK	7	22
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0108	VAHVKFLRVDQDKDK	9	24
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0108	YVAHVKFLRVDQDKD	8	23
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0108	AHVKFLRVDQDKDKD	10	25
ITGA9-SMOC2	chr3	37584076	chr6	168910594	1945	DRB4-0108	HYVAHVKFLRVDQDK	7	22

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Fusion breakpoint peptide structures of ITGA9-SMOC2

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
7925	RHYVAHVKFLRVDQ	ITGA9	SMOC2	chr3	37584076	chr6	168910594	1945

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ITGA9-SMOC2

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	7925	RHYVAHVKFLRVDQ	-7.9962	-8.1096
HLA-B14:02	3BVN	7925	RHYVAHVKFLRVDQ	-5.70842	-6.74372
HLA-B52:01	3W39	7925	RHYVAHVKFLRVDQ	-6.83737	-6.95077
HLA-B52:01	3W39	7925	RHYVAHVKFLRVDQ	-4.4836	-5.5189
HLA-A11:01	4UQ2	7925	RHYVAHVKFLRVDQ	-10.0067	-10.1201
HLA-A11:01	4UQ2	7925	RHYVAHVKFLRVDQ	-9.03915	-10.0745
HLA-A24:02	5HGA	7925	RHYVAHVKFLRVDQ	-6.56204	-6.67544
HLA-A24:02	5HGA	7925	RHYVAHVKFLRVDQ	-5.42271	-6.45801
HLA-B44:05	3DX8	7925	RHYVAHVKFLRVDQ	-7.85648	-8.89178
HLA-B44:05	3DX8	7925	RHYVAHVKFLRVDQ	-5.3978	-5.5112
HLA-A02:01	6TDR	7925	RHYVAHVKFLRVDQ	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of ITGA9-SMOC2

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
ITGA9-SMOC2	chr3	37584076	chr6	168910594	6	15	RHYVAHVKF	CACTATGTGGCCCATGTGAAGTTTTTG
ITGA9-SMOC2	chr3	37584076	chr6	168910594	7	15	HYVAHVKF	TATGTGGCCCATGTGAAGTTTTTG
ITGA9-SMOC2	chr3	37584076	chr6	168910594	7	16	HYVAHVKFL	TATGTGGCCCATGTGAAGTTTTTGAGA
ITGA9-SMOC2	chr3	37584076	chr6	168910594	8	16	YVAHVKFL	GTGGCCCATGTGAAGTTTTTGAGA
ITGA9-SMOC2	chr3	37584076	chr6	168910594	9	18	VAHVKFLRV	GCCCATGTGAAGTTTTTGAGAGTGGAT

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
ITGA9-SMOC2	chr3	37584076	chr6	168910594	10	25	AHVKFLRVDQDKDKD	CATGTGAAGTTTTTGAGAGTGGATCAAGATAAAGACAAGGATTGT
ITGA9-SMOC2	chr3	37584076	chr6	168910594	4	19	TCRHYVAHVKFLRVD	TGTCGTCACTATGTGGCCCATGTGAAGTTTTTGAGAGTGGATCAA
ITGA9-SMOC2	chr3	37584076	chr6	168910594	5	20	CRHYVAHVKFLRVDQ	CGTCACTATGTGGCCCATGTGAAGTTTTTGAGAGTGGATCAAGAT
ITGA9-SMOC2	chr3	37584076	chr6	168910594	6	21	RHYVAHVKFLRVDQD	CACTATGTGGCCCATGTGAAGTTTTTGAGAGTGGATCAAGATAAA
ITGA9-SMOC2	chr3	37584076	chr6	168910594	7	22	HYVAHVKFLRVDQDK	TATGTGGCCCATGTGAAGTTTTTGAGAGTGGATCAAGATAAAGAC
ITGA9-SMOC2	chr3	37584076	chr6	168910594	8	23	YVAHVKFLRVDQDKD	GTGGCCCATGTGAAGTTTTTGAGAGTGGATCAAGATAAAGACAAG
ITGA9-SMOC2	chr3	37584076	chr6	168910594	9	24	VAHVKFLRVDQDKDK	GCCCATGTGAAGTTTTTGAGAGTGGATCAAGATAAAGACAAGGAT

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Information of the samples that have these potential fusion neoantigens of ITGA9-SMOC2

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
Non-Cancer	ITGA9-SMOC2	chr3	37584076	ENST00000264741	chr6	168910594	ENST00000354536	145N

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Potential target of CAR-T therapy development for ITGA9-SMOC2

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 ITGA9-SMOC2

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 ITGA9-SMOC2

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)