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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ITGA5-MMP9

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ITGA5-MMP9
FusionPDB ID: 40436
FusionGDB2.0 ID: 40436
HgeneTgene
Gene symbol

ITGA5

MMP9

Gene ID

3678

4318

Gene nameintegrin subunit alpha 5matrix metallopeptidase 9
SynonymsCD49e|FNRA|VLA-5|VLA5ACLG4B|GELB|MANDP2|MMP-9
Cytomap

12q13.13

20q13.12

Type of geneprotein-codingprotein-coding
Descriptionintegrin alpha-5CD49 antigen-like family member EITGA5/SLC9B1 fusionfibronectin receptor subunit alphafibronectin receptor, alpha polypeptidefibronectin receptor, alpha subunitintegrin alpha-Fintegrin, alpha 5 (fibronectin receptor, alpha polypeptimatrix metalloproteinase-9macrophage gelatinasematrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)type V collagenase
Modification date2020032920200329
UniProtAcc

P08648

Main function of 5'-partner protein: FUNCTION: Integrin alpha-5/beta-1 (ITGA5:ITGB1) is a receptor for fibronectin and fibrinogen. It recognizes the sequence R-G-D in its ligands. ITGA5:ITGB1 binds to PLA2G2A via a site (site 2) which is distinct from the classical ligand-binding site (site 1) and this induces integrin conformational changes and enhanced ligand binding to site 1 (PubMed:18635536, PubMed:25398877). ITGA5:ITGB1 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (PubMed:12807887, PubMed:17158881). ITGA5:ITGB1 is a receptor for IL1B and binding is essential for IL1B signaling (PubMed:29030430). ITGA5:ITGB3 is a receptor for soluble CD40LG and is required for CD40/CD40LG signaling (PubMed:31331973). {ECO:0000269|PubMed:12807887, ECO:0000269|PubMed:17158881, ECO:0000269|PubMed:18635536, ECO:0000269|PubMed:25398877, ECO:0000269|PubMed:29030430, ECO:0000269|PubMed:31331973}.; FUNCTION: (Microbial infection) Integrin ITGA5:ITGB1 acts as a receptor for Human metapneumovirus. {ECO:0000269|PubMed:12907437}.; FUNCTION: (Microbial infection) Integrin ITGA2:ITGB1 acts as a receptor for Human parvovirus B19. {ECO:0000269|PubMed:24478423}.; FUNCTION: (Microbial infection) In case of HIV-1 infection, the interaction with extracellular viral Tat protein seems to enhance angiogenesis in Kaposi's sarcoma lesions. {ECO:0000269|PubMed:10397733}.

P14780

Main function of 5'-partner protein: FUNCTION: May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide. {ECO:0000269|PubMed:1480034}.
Ensembl transtripts involved in fusion geneENST idsENST00000293379, ENST00000547744, 
ENST00000372330, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score3 X 4 X 4=485 X 4 X 4=80
# samples 45
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ITGA5 [Title/Abstract] AND MMP9 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ITGA5 [Title/Abstract] AND MMP9 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ITGA5(54805618)-MMP9(44642763), # samples:1
Anticipated loss of major functional domain due to fusion event.ITGA5-MMP9 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.
ITGA5-MMP9 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneITGA5

GO:0007155

cell adhesion

19703720

HgeneITGA5

GO:0007229

integrin-mediated signaling pathway

31331973

HgeneITGA5

GO:0023035

CD40 signaling pathway

31331973

HgeneITGA5

GO:0033627

cell adhesion mediated by integrin

12807887|17158881

TgeneMMP9

GO:0006508

proteolysis

2551898|15863497|19022250|24164424

TgeneMMP9

GO:0034614

cellular response to reactive oxygen species

26514923

TgeneMMP9

GO:0043388

positive regulation of DNA binding

22984561

TgeneMMP9

GO:0071276

cellular response to cadmium ion

26514923

TgeneMMP9

GO:1900122

positive regulation of receptor binding

24164424

TgeneMMP9

GO:2001258

negative regulation of cation channel activity

24164424



check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:54805618/chr20:44642763)
- 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.
FGviewer

check buttonRetention 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.

check buttonFusion gene breakpoints across ITGA5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across MMP9 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000293379ITGA5chr1254805618-ENST00000372330MMP9chr2044642763+1178611115984289

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000293379ENST00000372330ITGA5chr1254805618-MMP9chr2044642763+0.406323670.5936764

check button 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 ITGA5-MMP9

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ITGA5chr1254805618MMP9chr2044642763611165SPTQCTPIEFDSKGRQVWVYTGASVL

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Potential FusionNeoAntigen Information of ITGA5-MMP9 in HLA I

check button 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.
ITGA5-MMP9_54805618_44642763.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:02FDSKGRQVW0.8130.5055918
ITGA5-MMP9chr1254805618chr2044642763611HLA-B15:03SKGRQVWVY0.20960.53371120
ITGA5-MMP9chr1254805618chr2044642763611HLA-B50:01IEFDSKGRQV0.93770.6094717
ITGA5-MMP9chr1254805618chr2044642763611HLA-B41:01IEFDSKGRQV0.89130.7549717
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:02IEFDSKGRQVW0.99990.62718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:03IEFDSKGRQVW0.99990.9581718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:05IEFDSKGRQVW0.99970.7693718
ITGA5-MMP9chr1254805618chr2044642763611HLA-C04:10EFDSKGRQV0.99960.8324817
ITGA5-MMP9chr1254805618chr2044642763611HLA-C04:07EFDSKGRQV0.99950.8406817
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:08FDSKGRQVW0.84120.6533918
ITGA5-MMP9chr1254805618chr2044642763611HLA-C04:14EFDSKGRQV0.7760.8373817
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:06EFDSKGRQVW0.94950.5809818
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:04IEFDSKGRQVW0.99990.5288718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:08IEFDSKGRQVW0.99990.6846718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B40:03IEFDSKGRQVW0.99980.5734718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:09IEFDSKGRQVW0.99980.7153718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:10IEFDSKGRQVW0.99520.7636718
ITGA5-MMP9chr1254805618chr2044642763611HLA-C04:01EFDSKGRQV0.99950.8406817
ITGA5-MMP9chr1254805618chr2044642763611HLA-C18:01EFDSKGRQV0.99930.8343817
ITGA5-MMP9chr1254805618chr2044642763611HLA-C04:04EFDSKGRQV0.95620.8776817
ITGA5-MMP9chr1254805618chr2044642763611HLA-C06:06EFDSKGRQV0.94770.9555817
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:22FDSKGRQVW0.8130.5055918
ITGA5-MMP9chr1254805618chr2044642763611HLA-C07:04EFDSKGRQV0.57280.8298817
ITGA5-MMP9chr1254805618chr2044642763611HLA-B48:02SKGRQVWVY0.22870.61661120
ITGA5-MMP9chr1254805618chr2044642763611HLA-B15:54SKGRQVWVY0.00970.57281120
ITGA5-MMP9chr1254805618chr2044642763611HLA-C18:01IEFDSKGRQV0.99720.6777717
ITGA5-MMP9chr1254805618chr2044642763611HLA-B50:04IEFDSKGRQV0.93770.6094717
ITGA5-MMP9chr1254805618chr2044642763611HLA-B50:05IEFDSKGRQV0.93770.6094717
ITGA5-MMP9chr1254805618chr2044642763611HLA-B15:13EFDSKGRQVW0.91840.9258818
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:07IEFDSKGRQVW0.99990.9581718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:13IEFDSKGRQVW0.99990.9581718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:22IEFDSKGRQVW0.99990.62718
ITGA5-MMP9chr1254805618chr2044642763611HLA-B44:26IEFDSKGRQVW0.99990.9581718

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Potential FusionNeoAntigen Information of ITGA5-MMP9 in HLA II

check button 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.
ITGA5-MMP9_54805618_44642763.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0301TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0301CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0301QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0301TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0303TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0303CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0303QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0303TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0305TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0305CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0305QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0307TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0307CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0307QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0307TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0310CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0310TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0310QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0310TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0313TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0313CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0313QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0313TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0315TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0315CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0315QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0315TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0318TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0318CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0318QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0318TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0320TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0320CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0320QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0320TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0322TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0322CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0322QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0322TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0324CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0324TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0324QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0324TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0326TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0326CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0326QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0326TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0328TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0328CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0328QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0328TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0330TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0330CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0330QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0330TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0332TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0332CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0332QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0332TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0334TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0334CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0334QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0334TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0336TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0336CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0336QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0336TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0340TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0340CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0340QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0342TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0342CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0342QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0342TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0344TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0344CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0344QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0344TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0346TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0346CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0346QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0346TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0348CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0348TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0348QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0348TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0350TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0350CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0350QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0350TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0352TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0352CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0352QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0352TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0354TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0354CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0354QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-0354TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1107TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1107CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1107QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1107TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1179CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1179TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1179QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1394CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1394TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1394QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1394TQCTPIEFDSKGRQV217
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1421CTPIEFDSKGRQVWV419
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1421TPIEFDSKGRQVWVY520
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1421QCTPIEFDSKGRQVW318
ITGA5-MMP9chr1254805618chr2044642763611DRB1-1421TQCTPIEFDSKGRQV217

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Fusion breakpoint peptide structures of ITGA5-MMP9

check button3D 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 nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
6694PIEFDSKGRQVWVYITGA5MMP9chr1254805618chr2044642763611

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ITGA5-MMP9

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN6694PIEFDSKGRQVWVY-7.9962-8.1096
HLA-B14:023BVN6694PIEFDSKGRQVWVY-5.70842-6.74372
HLA-B52:013W396694PIEFDSKGRQVWVY-6.83737-6.95077
HLA-B52:013W396694PIEFDSKGRQVWVY-4.4836-5.5189
HLA-A11:014UQ26694PIEFDSKGRQVWVY-10.0067-10.1201
HLA-A11:014UQ26694PIEFDSKGRQVWVY-9.03915-10.0745
HLA-A24:025HGA6694PIEFDSKGRQVWVY-6.56204-6.67544
HLA-A24:025HGA6694PIEFDSKGRQVWVY-5.42271-6.45801
HLA-B44:053DX86694PIEFDSKGRQVWVY-7.85648-8.89178
HLA-B44:053DX86694PIEFDSKGRQVWVY-5.3978-5.5112
HLA-A02:016TDR6694PIEFDSKGRQVWVY-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ITGA5-MMP9

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
ITGA5-MMP9chr1254805618chr20446427631120SKGRQVWVYGCAAAGGGCGCCAGGTGTGGGTGTACA
ITGA5-MMP9chr1254805618chr2044642763717IEFDSKGRQVTTGAATTTGACAGCAAAGGGCGCCAGGTGT
ITGA5-MMP9chr1254805618chr2044642763718IEFDSKGRQVWTTGAATTTGACAGCAAAGGGCGCCAGGTGTGGG
ITGA5-MMP9chr1254805618chr2044642763817EFDSKGRQVAATTTGACAGCAAAGGGCGCCAGGTGT
ITGA5-MMP9chr1254805618chr2044642763818EFDSKGRQVWAATTTGACAGCAAAGGGCGCCAGGTGTGGG
ITGA5-MMP9chr1254805618chr2044642763918FDSKGRQVWTTGACAGCAAAGGGCGCCAGGTGTGGG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ITGA5-MMP9chr1254805618chr2044642763217TQCTPIEFDSKGRQVCACAGTGCACCCCCATTGAATTTGACAGCAAAGGGCGCCAGGTGT
ITGA5-MMP9chr1254805618chr2044642763318QCTPIEFDSKGRQVWAGTGCACCCCCATTGAATTTGACAGCAAAGGGCGCCAGGTGTGGG
ITGA5-MMP9chr1254805618chr2044642763419CTPIEFDSKGRQVWVGCACCCCCATTGAATTTGACAGCAAAGGGCGCCAGGTGTGGGTGT
ITGA5-MMP9chr1254805618chr2044642763520TPIEFDSKGRQVWVYCCCCCATTGAATTTGACAGCAAAGGGCGCCAGGTGTGGGTGTACA

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Information of the samples that have these potential fusion neoantigens of ITGA5-MMP9

check button 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 typeFusion geneHchrHbpHenstTchrTbpTenstSample
SARCITGA5-MMP9chr1254805618ENST00000293379chr2044642763ENST00000372330TCGA-HB-A2OT-01A

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Potential target of CAR-T therapy development for ITGA5-MMP9

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention 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'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button 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.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to ITGA5-MMP9

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to ITGA5-MMP9

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource