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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:ITGB4-LLGL2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ITGB4-LLGL2
FusionPDB ID: 40536
FusionGDB2.0 ID: 40536
HgeneTgene
Gene symbol

ITGB4

LLGL2

Gene ID

3691

3993

Gene nameintegrin subunit beta 4LLGL scribble cell polarity complex component 2
SynonymsCD104|GP150HGL|Hugl-2|LGL2
Cytomap

17q25.1

17q25.1

Type of geneprotein-codingprotein-coding
Descriptionintegrin beta-4CD104 antigenLLGL scribble cell polarity complex component 2LLGL2, scribble cell polarity complex componenthuman giant larvae homologlethal giant larvae homolog 2, scribble cell polarity complex componentlethal(2) giant larvae protein homolog 2
Modification date2020032920200320
UniProtAcc

P16144

Main function of 5'-partner protein: FUNCTION: Integrin alpha-6/beta-4 is a receptor for laminin. Plays a critical structural role in the hemidesmosome of epithelial cells. Is required for the regulation of keratinocyte polarity and motility. ITGA6:ITGB4 binds to NRG1 (via EGF domain) and this binding is essential for NRG1-ERBB signaling (PubMed:20682778). ITGA6:ITGB4 binds to IGF1 and this binding is essential for IGF1 signaling (PubMed:22351760). ITGA6:ITGB4 binds to IGF2 and this binding is essential for IGF2 signaling (PubMed:28873464). {ECO:0000269|PubMed:12482924, ECO:0000269|PubMed:19403692, ECO:0000269|PubMed:20682778, ECO:0000269|PubMed:22351760, ECO:0000269|PubMed:28873464}.

Q6P1M3

Main function of 5'-partner protein: FUNCTION: Part of a complex with GPSM2/LGN, PRKCI/aPKC and PARD6B/Par-6, which may ensure the correct organization and orientation of bipolar spindles for normal cell division. This complex plays roles in the initial phase of the establishment of epithelial cell polarity. {ECO:0000269|PubMed:15632202}.
Ensembl transtripts involved in fusion geneENST idsENST00000584558, ENST00000200181, 
ENST00000339591, ENST00000449880, 
ENST00000450894, ENST00000579662, 
ENST00000167462, ENST00000375227, 
ENST00000392550, ENST00000577200, 
ENST00000578363, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 19 X 10=437010 X 11 X 6=660
# samples 2914
** MAII scorelog2(29/4370*10)=-3.91350847437303
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/660*10)=-2.23703919730085
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ITGB4 [Title/Abstract] AND LLGL2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ITGB4 [Title/Abstract] AND LLGL2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LLGL2(73529786)-ITGB4(73748255), # samples:2
ITGB4(73723586)-LLGL2(73552127), # samples:1
ITGB4(73723586)-LLGL2(73552126), # samples:1
Anticipated loss of major functional domain due to fusion event.ITGB4-LLGL2 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.
ITGB4-LLGL2 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.
ITGB4-LLGL2 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.
ITGB4-LLGL2 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
HgeneITGB4

GO:0009611

response to wounding

19403692

HgeneITGB4

GO:0031581

hemidesmosome assembly

12482924

TgeneLLGL2

GO:0032878

regulation of establishment or maintenance of cell polarity

12725730



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/chr17:73529786/chr17:73748255)
- 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 ITGB4 (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 LLGL2 (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)
ENST00000579662ITGB4chr1773723586+ENST00000167462LLGL2chr1773552127+378551024634821078
ENST00000579662ITGB4chr1773723586+ENST00000375227LLGL2chr1773552127+16855102461505419
ENST00000579662ITGB4chr1773723586+ENST00000392550LLGL2chr1773552127+382751024634971083
ENST00000579662ITGB4chr1773723586+ENST00000578363LLGL2chr1773552127+16875102461505419
ENST00000579662ITGB4chr1773723586+ENST00000577200LLGL2chr1773552127+352351024634941082
ENST00000339591ITGB4chr1773723586+ENST00000167462LLGL2chr1773552127+372645116334231086
ENST00000339591ITGB4chr1773723586+ENST00000375227LLGL2chr1773552127+16264511631446427
ENST00000339591ITGB4chr1773723586+ENST00000392550LLGL2chr1773552127+376845116334381091
ENST00000339591ITGB4chr1773723586+ENST00000578363LLGL2chr1773552127+16284511631446427
ENST00000339591ITGB4chr1773723586+ENST00000577200LLGL2chr1773552127+346445116334351090
ENST00000200181ITGB4chr1773723586+ENST00000167462LLGL2chr1773552127+372645116334231086
ENST00000200181ITGB4chr1773723586+ENST00000375227LLGL2chr1773552127+16264511631446427
ENST00000200181ITGB4chr1773723586+ENST00000392550LLGL2chr1773552127+376845116334381091
ENST00000200181ITGB4chr1773723586+ENST00000578363LLGL2chr1773552127+16284511631446427
ENST00000200181ITGB4chr1773723586+ENST00000577200LLGL2chr1773552127+346445116334351090
ENST00000450894ITGB4chr1773723586+ENST00000167462LLGL2chr1773552127+366539010233621086
ENST00000450894ITGB4chr1773723586+ENST00000375227LLGL2chr1773552127+15653901021385427
ENST00000450894ITGB4chr1773723586+ENST00000392550LLGL2chr1773552127+370739010233771091
ENST00000450894ITGB4chr1773723586+ENST00000578363LLGL2chr1773552127+15673901021385427
ENST00000450894ITGB4chr1773723586+ENST00000577200LLGL2chr1773552127+340339010233741090
ENST00000449880ITGB4chr1773723586+ENST00000167462LLGL2chr1773552127+3547272832441078
ENST00000449880ITGB4chr1773723586+ENST00000375227LLGL2chr1773552127+144727281267419
ENST00000449880ITGB4chr1773723586+ENST00000392550LLGL2chr1773552127+3589272832591083
ENST00000449880ITGB4chr1773723586+ENST00000578363LLGL2chr1773552127+144927281267419
ENST00000449880ITGB4chr1773723586+ENST00000577200LLGL2chr1773552127+3285272832561082
ENST00000579662ITGB4chr1773723586+ENST00000167462LLGL2chr1773552126+378551024634821078
ENST00000579662ITGB4chr1773723586+ENST00000375227LLGL2chr1773552126+16855102461505419
ENST00000579662ITGB4chr1773723586+ENST00000392550LLGL2chr1773552126+382751024634971083
ENST00000579662ITGB4chr1773723586+ENST00000578363LLGL2chr1773552126+16875102461505419
ENST00000579662ITGB4chr1773723586+ENST00000577200LLGL2chr1773552126+352351024634941082
ENST00000339591ITGB4chr1773723586+ENST00000167462LLGL2chr1773552126+372645116334231086
ENST00000339591ITGB4chr1773723586+ENST00000375227LLGL2chr1773552126+16264511631446427
ENST00000339591ITGB4chr1773723586+ENST00000392550LLGL2chr1773552126+376845116334381091
ENST00000339591ITGB4chr1773723586+ENST00000578363LLGL2chr1773552126+16284511631446427
ENST00000339591ITGB4chr1773723586+ENST00000577200LLGL2chr1773552126+346445116334351090
ENST00000200181ITGB4chr1773723586+ENST00000167462LLGL2chr1773552126+372645116334231086
ENST00000200181ITGB4chr1773723586+ENST00000375227LLGL2chr1773552126+16264511631446427
ENST00000200181ITGB4chr1773723586+ENST00000392550LLGL2chr1773552126+376845116334381091
ENST00000200181ITGB4chr1773723586+ENST00000578363LLGL2chr1773552126+16284511631446427
ENST00000200181ITGB4chr1773723586+ENST00000577200LLGL2chr1773552126+346445116334351090
ENST00000450894ITGB4chr1773723586+ENST00000167462LLGL2chr1773552126+366539010233621086
ENST00000450894ITGB4chr1773723586+ENST00000375227LLGL2chr1773552126+15653901021385427
ENST00000450894ITGB4chr1773723586+ENST00000392550LLGL2chr1773552126+370739010233771091
ENST00000450894ITGB4chr1773723586+ENST00000578363LLGL2chr1773552126+15673901021385427
ENST00000450894ITGB4chr1773723586+ENST00000577200LLGL2chr1773552126+340339010233741090
ENST00000449880ITGB4chr1773723586+ENST00000167462LLGL2chr1773552126+3547272832441078
ENST00000449880ITGB4chr1773723586+ENST00000375227LLGL2chr1773552126+144727281267419
ENST00000449880ITGB4chr1773723586+ENST00000392550LLGL2chr1773552126+3589272832591083
ENST00000449880ITGB4chr1773723586+ENST00000578363LLGL2chr1773552126+144927281267419
ENST00000449880ITGB4chr1773723586+ENST00000577200LLGL2chr1773552126+3285272832561082

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
ENST00000579662ENST00000167462ITGB4chr1773723586+LLGL2chr1773552127+0.0079956930.99200433
ENST00000579662ENST00000375227ITGB4chr1773723586+LLGL2chr1773552127+0.141874210.8581258
ENST00000579662ENST00000392550ITGB4chr1773723586+LLGL2chr1773552127+0.0074726230.99252737
ENST00000579662ENST00000578363ITGB4chr1773723586+LLGL2chr1773552127+0.14174110.8582589
ENST00000579662ENST00000577200ITGB4chr1773723586+LLGL2chr1773552127+0.0118253290.9881747
ENST00000339591ENST00000167462ITGB4chr1773723586+LLGL2chr1773552127+0.0081914040.9918086
ENST00000339591ENST00000375227ITGB4chr1773723586+LLGL2chr1773552127+0.138512660.8614873
ENST00000339591ENST00000392550ITGB4chr1773723586+LLGL2chr1773552127+0.0076544470.99234563
ENST00000339591ENST00000578363ITGB4chr1773723586+LLGL2chr1773552127+0.138276890.86172307
ENST00000339591ENST00000577200ITGB4chr1773723586+LLGL2chr1773552127+0.0123495110.98765045
ENST00000200181ENST00000167462ITGB4chr1773723586+LLGL2chr1773552127+0.0081914040.9918086
ENST00000200181ENST00000375227ITGB4chr1773723586+LLGL2chr1773552127+0.138512660.8614873
ENST00000200181ENST00000392550ITGB4chr1773723586+LLGL2chr1773552127+0.0076544470.99234563
ENST00000200181ENST00000578363ITGB4chr1773723586+LLGL2chr1773552127+0.138276890.86172307
ENST00000200181ENST00000577200ITGB4chr1773723586+LLGL2chr1773552127+0.0123495110.98765045
ENST00000450894ENST00000167462ITGB4chr1773723586+LLGL2chr1773552127+0.0078911930.99210876
ENST00000450894ENST00000375227ITGB4chr1773723586+LLGL2chr1773552127+0.129966040.8700339
ENST00000450894ENST00000392550ITGB4chr1773723586+LLGL2chr1773552127+0.0073619840.992638
ENST00000450894ENST00000578363ITGB4chr1773723586+LLGL2chr1773552127+0.129666330.8703336
ENST00000450894ENST00000577200ITGB4chr1773723586+LLGL2chr1773552127+0.0119535610.9880464
ENST00000449880ENST00000167462ITGB4chr1773723586+LLGL2chr1773552127+0.006875050.99312496
ENST00000449880ENST00000375227ITGB4chr1773723586+LLGL2chr1773552127+0.14961780.8503822
ENST00000449880ENST00000392550ITGB4chr1773723586+LLGL2chr1773552127+0.0064126110.9935874
ENST00000449880ENST00000578363ITGB4chr1773723586+LLGL2chr1773552127+0.148922340.8510777
ENST00000449880ENST00000577200ITGB4chr1773723586+LLGL2chr1773552127+0.0105410450.9894589
ENST00000579662ENST00000167462ITGB4chr1773723586+LLGL2chr1773552126+0.0079956930.99200433
ENST00000579662ENST00000375227ITGB4chr1773723586+LLGL2chr1773552126+0.141874210.8581258
ENST00000579662ENST00000392550ITGB4chr1773723586+LLGL2chr1773552126+0.0074726230.99252737
ENST00000579662ENST00000578363ITGB4chr1773723586+LLGL2chr1773552126+0.14174110.8582589
ENST00000579662ENST00000577200ITGB4chr1773723586+LLGL2chr1773552126+0.0118253290.9881747
ENST00000339591ENST00000167462ITGB4chr1773723586+LLGL2chr1773552126+0.0081914040.9918086
ENST00000339591ENST00000375227ITGB4chr1773723586+LLGL2chr1773552126+0.138512660.8614873
ENST00000339591ENST00000392550ITGB4chr1773723586+LLGL2chr1773552126+0.0076544470.99234563
ENST00000339591ENST00000578363ITGB4chr1773723586+LLGL2chr1773552126+0.138276890.86172307
ENST00000339591ENST00000577200ITGB4chr1773723586+LLGL2chr1773552126+0.0123495110.98765045
ENST00000200181ENST00000167462ITGB4chr1773723586+LLGL2chr1773552126+0.0081914040.9918086
ENST00000200181ENST00000375227ITGB4chr1773723586+LLGL2chr1773552126+0.138512660.8614873
ENST00000200181ENST00000392550ITGB4chr1773723586+LLGL2chr1773552126+0.0076544470.99234563
ENST00000200181ENST00000578363ITGB4chr1773723586+LLGL2chr1773552126+0.138276890.86172307
ENST00000200181ENST00000577200ITGB4chr1773723586+LLGL2chr1773552126+0.0123495110.98765045
ENST00000450894ENST00000167462ITGB4chr1773723586+LLGL2chr1773552126+0.0078911930.99210876
ENST00000450894ENST00000375227ITGB4chr1773723586+LLGL2chr1773552126+0.129966040.8700339
ENST00000450894ENST00000392550ITGB4chr1773723586+LLGL2chr1773552126+0.0073619840.992638
ENST00000450894ENST00000578363ITGB4chr1773723586+LLGL2chr1773552126+0.129666330.8703336
ENST00000450894ENST00000577200ITGB4chr1773723586+LLGL2chr1773552126+0.0119535610.9880464
ENST00000449880ENST00000167462ITGB4chr1773723586+LLGL2chr1773552126+0.006875050.99312496
ENST00000449880ENST00000375227ITGB4chr1773723586+LLGL2chr1773552126+0.14961780.8503822
ENST00000449880ENST00000392550ITGB4chr1773723586+LLGL2chr1773552126+0.0064126110.9935874
ENST00000449880ENST00000578363ITGB4chr1773723586+LLGL2chr1773552126+0.148922340.8510777
ENST00000449880ENST00000577200ITGB4chr1773723586+LLGL2chr1773552126+0.0105410450.9894589

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 ITGB4-LLGL2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ITGB4chr1773723586LLGL2chr177355212627288SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212639096SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212645196SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212651088SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212727288SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212739096SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212745196SIVVMESSFQITETVEHGFPHQPSAL
ITGB4chr1773723586LLGL2chr177355212751088SIVVMESSFQITETVEHGFPHQPSAL

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Potential FusionNeoAntigen Information of ITGB4-LLGL2 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.
ITGB4-LLGL2_73723586_73552126.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)
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B18:01TETVEHGF0.99750.95911119
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B51:02SSFQITETV0.99160.5174615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A26:02ETVEHGFPH0.98730.59851221
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B51:01SSFQITETV0.98360.5261615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B52:01SSFQITETV0.98270.9778615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A26:15ETVEHGFPH0.98110.68211221
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A26:14ETVEHGFPH0.98110.68211221
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A66:01ETVEHGFPH0.97330.66551221
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A26:03ETVEHGFPH0.97190.68721221
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B13:02SSFQITETV0.95210.7731615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:16SSFQITETV0.94370.8876615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A02:21SSFQITETV0.89210.7892615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:03FQITETVEH0.80880.9034817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:18FQITETVEH0.80620.8857817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B57:03ITETVEHGF0.62290.8391019
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B45:01ETVEHGFPHQP0.99130.9771223
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C15:06SSFQITETV0.99980.8948615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C15:04SSFQITETV0.99960.8554615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C05:09ITETVEHGF0.99910.93671019
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C03:19SSFQITETV0.99520.994615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C03:08SSFQITETV0.99510.9306615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C12:04SSFQITETV0.99010.9954615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C06:03SSFQITETV0.98940.9961615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B51:07SSFQITETV0.98210.9644615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A26:01ETVEHGFPH0.98110.68211221
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C12:12SSFQITETV0.96660.9649615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:04FQITETVEH0.95770.9726817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C02:06SSFQITETV0.88640.9636615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:05FQITETVEH0.86730.9651817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:05FQITETVEHGF0.99610.9496819
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B18:05TETVEHGF0.99750.95911119
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B18:06TETVEHGF0.99740.94451119
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B18:08TETVEHGF0.99660.76971119
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B18:03TETVEHGF0.99570.95771119
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B18:11TETVEHGF0.99410.93211119
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C15:02SSFQITETV0.99980.8679615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C15:05SSFQITETV0.99980.9239615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C15:09SSFQITETV0.99960.8554615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C05:01ITETVEHGF0.99910.93671019
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C04:03ITETVEHGF0.99910.89971019
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:50FQITETVEH0.99890.9648817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:53FQITETVEH0.99730.9572817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C03:17SSFQITETV0.99470.9846615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A68:02SSFQITETV0.99360.7015615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C16:04SSFQITETV0.99090.991615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C03:06SSFQITETV0.98830.9942615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A69:01SSFQITETV0.98760.8651615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C16:02SSFQITETV0.98460.9944615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B51:14SSFQITETV0.980.5748615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C12:03SSFQITETV0.97420.9874615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:54FQITETVEH0.97080.9509817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C17:01SSFQITETV0.96470.9752615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:68FQITETVEH0.9320.8389817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A02:14SSFQITETV0.89580.7412615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A02:06SSFQITETV0.89210.7892615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-C06:08SSFQITETV0.88810.9913615
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:20FQITETVEH0.85530.9743817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B35:28FQITETVEH0.83790.974817
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B57:04ITETVEHGF0.78520.64811019
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B57:02ITETVEHGF0.65630.78271019
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A68:02ESSFQITETV0.99820.7015515
ITGB4-LLGL2chr1773723586chr1773552126451HLA-A69:01ESSFQITETV0.99430.765515
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:24FQITETVEHGF0.99990.9358819
ITGB4-LLGL2chr1773723586chr1773552126451HLA-B15:20FQITETVEHGF0.99570.9671819

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Potential FusionNeoAntigen Information of ITGB4-LLGL2 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.
ITGB4-LLGL2_73723586_73552126.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)
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0401ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0407ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0407MESSFQITETVEHGF419
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0419ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0424ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0431ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0433ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0435ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0438ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0443ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0461ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0462ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0463ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0464ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0469ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0469MESSFQITETVEHGF419
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0469VMESSFQITETVEHG318
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0474ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0474MESSFQITETVEHGF419
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0476ESSFQITETVEHGFP520
ITGB4-LLGL2chr1773723586chr1773552126451DRB1-0482ESSFQITETVEHGFP520

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Fusion breakpoint peptide structures of ITGB4-LLGL2

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
9004SSFQITETVEHGFPITGB4LLGL2chr1773723586chr1773552126451

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ITGB4-LLGL2

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-B14:023BVN9004SSFQITETVEHGFP-7.15543-7.26883
HLA-B14:023BVN9004SSFQITETVEHGFP-4.77435-5.80965
HLA-B52:013W399004SSFQITETVEHGFP-6.80875-6.92215
HLA-B52:013W399004SSFQITETVEHGFP-4.20386-5.23916
HLA-A11:014UQ29004SSFQITETVEHGFP-7.5194-8.5547
HLA-A11:014UQ29004SSFQITETVEHGFP-6.9601-7.0735
HLA-A24:025HGA9004SSFQITETVEHGFP-7.52403-7.63743
HLA-A24:025HGA9004SSFQITETVEHGFP-5.82433-6.85963
HLA-B27:056PYJ9004SSFQITETVEHGFP-3.28285-4.31815
HLA-B44:053DX89004SSFQITETVEHGFP-5.91172-6.94702
HLA-B44:053DX89004SSFQITETVEHGFP-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of ITGB4-LLGL2

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
ITGB4-LLGL2chr1773723586chr17735521261019ITETVEHGFATCACAGAGACGGTGGAGCATGGCTTC
ITGB4-LLGL2chr1773723586chr17735521261119TETVEHGFACAGAGACGGTGGAGCATGGCTTC
ITGB4-LLGL2chr1773723586chr17735521261221ETVEHGFPHGAGACGGTGGAGCATGGCTTCCCGCAC
ITGB4-LLGL2chr1773723586chr17735521261223ETVEHGFPHQPGAGACGGTGGAGCATGGCTTCCCGCACCAGCCC
ITGB4-LLGL2chr1773723586chr1773552126515ESSFQITETVGAGAGCAGCTTCCAAATCACAGAGACGGTG
ITGB4-LLGL2chr1773723586chr1773552126615SSFQITETVAGCAGCTTCCAAATCACAGAGACGGTG
ITGB4-LLGL2chr1773723586chr1773552126817FQITETVEHTTCCAAATCACAGAGACGGTGGAGCAT
ITGB4-LLGL2chr1773723586chr1773552126819FQITETVEHGFTTCCAAATCACAGAGACGGTGGAGCATGGCTTC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ITGB4-LLGL2chr1773723586chr1773552126318VMESSFQITETVEHGGTCATGGAGAGCAGCTTCCAAATCACAGAGACGGTGGAGCATGGC
ITGB4-LLGL2chr1773723586chr1773552126419MESSFQITETVEHGFATGGAGAGCAGCTTCCAAATCACAGAGACGGTGGAGCATGGCTTC
ITGB4-LLGL2chr1773723586chr1773552126520ESSFQITETVEHGFPGAGAGCAGCTTCCAAATCACAGAGACGGTGGAGCATGGCTTCCCG

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Information of the samples that have these potential fusion neoantigens of ITGB4-LLGL2

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
STADITGB4-LLGL2chr1773723586ENST00000200181chr1773552126ENST00000167462TCGA-VQ-A92D

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Potential target of CAR-T therapy development for ITGB4-LLGL2

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 ITGB4-LLGL2

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 ITGB4-LLGL2

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