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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:CUX1-BBS9

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CUX1-BBS9
FusionPDB ID: 20715
FusionGDB2.0 ID: 20715
HgeneTgene
Gene symbol

CUX1

BBS9

Gene ID

1523

27241

Gene namecut like homeobox 1Bardet-Biedl syndrome 9
SynonymsCASP|CDP|CDP/Cut|CDP1|COY1|CUTL1|CUX|Clox|Cux/CDP|GDDI|GOLIM6|Nbla10317|p100|p110|p200|p75B1|C18|D1|PTHB1
Cytomap

7q22.1

7p14.3

Type of geneprotein-codingprotein-coding
Descriptionprotein CASPHomeobox protein cut-like 1CCAAT displacement proteinCUX1 gene Alternatively Spliced Productcut homologgolgi integral membrane protein 6homeobox protein cux-1putative protein product of Nbla10317protein PTHB1PTH-responsive osteosarcoma B1 proteinbardet-Biedl syndrome 9 proteinparathyroid hormone-responsive B1 gene protein
Modification date2020032020200320
UniProtAcc

P39880

Main function of 5'-partner protein: FUNCTION: Transcription factor involved in the control of neuronal differentiation in the brain. Regulates dendrite development and branching, and dendritic spine formation in cortical layers II-III. Also involved in the control of synaptogenesis. In addition, it has probably a broad role in mammalian development as a repressor of developmentally regulated gene expression. May act by preventing binding of positively-activing CCAAT factors to promoters. Component of nf-munr repressor; binds to the matrix attachment regions (MARs) (5' and 3') of the immunoglobulin heavy chain enhancer. Represses T-cell receptor (TCR) beta enhancer function by binding to MARbeta, an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Binds to the TH enhancer; may require the basic helix-loop-helix protein TCF4 as a coactivator. {ECO:0000250|UniProtKB:P53564}.; FUNCTION: [CDP/Cux p110]: Plays a role in cell cycle progression, in particular at the G1/S transition. As cells progress into S phase, a fraction of CUX1 molecules is proteolytically processed into N-terminally truncated proteins of 110 kDa. While CUX1 only transiently binds to DNA and carries the CCAAT-displacement activity, CDP/Cux p110 makes a stable interaction with DNA and stimulates expression of genes such as POLA1. {ECO:0000269|PubMed:15099520}.

Q3SYG4

Main function of 5'-partner protein: FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. Required for proper BBSome complex assembly and its ciliary localization. {ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.
Ensembl transtripts involved in fusion geneENST idsENST00000560541, ENST00000292535, 
ENST00000292538, ENST00000360264, 
ENST00000393824, ENST00000425244, 
ENST00000437600, ENST00000546411, 
ENST00000547394, ENST00000549414, 
ENST00000550008, ENST00000556210, 
ENST00000242067, ENST00000350941, 
ENST00000354265, ENST00000355070, 
ENST00000396127, ENST00000425508, 
ENST00000482941, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score32 X 26 X 13=1081614 X 17 X 8=1904
# samples 3719
** MAII scorelog2(37/10816*10)=-4.86949797576587
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1904*10)=-3.324962154977
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CUX1 [Title/Abstract] AND BBS9 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CUX1 [Title/Abstract] AND BBS9 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CUX1(101755054)-BBS9(33296848), # samples:1
Anticipated loss of major functional domain due to fusion event.CUX1-BBS9 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.
CUX1-BBS9 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.
CUX1-BBS9 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.
CUX1-BBS9 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


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/chr7:101755054/chr7:33296848)
- 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 CUX1 (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 BBS9 (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)
ENST00000437600CUX1chr7101755054+ENST00000242067BBS9chr733296848+40569923523213953
ENST00000437600CUX1chr7101755054+ENST00000355070BBS9chr733296848+40419923523198948
ENST00000437600CUX1chr7101755054+ENST00000350941BBS9chr733296848+39369923523093913
ENST00000437600CUX1chr7101755054+ENST00000354265BBS9chr733296848+39519923523108918
ENST00000437600CUX1chr7101755054+ENST00000396127BBS9chr733296848+39519923523108918
ENST00000437600CUX1chr7101755054+ENST00000425508BBS9chr733296848+16189923521617422
ENST00000292538CUX1chr7101755054+ENST00000242067BBS9chr733296848+3730666262887953
ENST00000292538CUX1chr7101755054+ENST00000355070BBS9chr733296848+3715666262872948
ENST00000292538CUX1chr7101755054+ENST00000350941BBS9chr733296848+3610666262767913
ENST00000292538CUX1chr7101755054+ENST00000354265BBS9chr733296848+3625666262782918
ENST00000292538CUX1chr7101755054+ENST00000396127BBS9chr733296848+3625666262782918
ENST00000292538CUX1chr7101755054+ENST00000425508BBS9chr733296848+1292666261291422
ENST00000393824CUX1chr7101755054+ENST00000242067BBS9chr733296848+3616552232773916
ENST00000393824CUX1chr7101755054+ENST00000355070BBS9chr733296848+3601552232758911
ENST00000393824CUX1chr7101755054+ENST00000350941BBS9chr733296848+3496552232653876
ENST00000393824CUX1chr7101755054+ENST00000354265BBS9chr733296848+3511552232668881
ENST00000393824CUX1chr7101755054+ENST00000396127BBS9chr733296848+3511552232668881
ENST00000393824CUX1chr7101755054+ENST00000425508BBS9chr733296848+1178552231177385
ENST00000547394CUX1chr7101755054+ENST00000242067BBS9chr733296848+3678614222835937
ENST00000547394CUX1chr7101755054+ENST00000355070BBS9chr733296848+3663614222820932
ENST00000547394CUX1chr7101755054+ENST00000350941BBS9chr733296848+3558614222715897
ENST00000547394CUX1chr7101755054+ENST00000354265BBS9chr733296848+3573614222730902
ENST00000547394CUX1chr7101755054+ENST00000396127BBS9chr733296848+3573614222730902
ENST00000547394CUX1chr7101755054+ENST00000425508BBS9chr733296848+1240614221239406
ENST00000360264CUX1chr7101755054+ENST00000242067BBS9chr733296848+3724660202881953
ENST00000360264CUX1chr7101755054+ENST00000355070BBS9chr733296848+3709660202866948
ENST00000360264CUX1chr7101755054+ENST00000350941BBS9chr733296848+3604660202761913
ENST00000360264CUX1chr7101755054+ENST00000354265BBS9chr733296848+3619660202776918
ENST00000360264CUX1chr7101755054+ENST00000396127BBS9chr733296848+3619660202776918
ENST00000360264CUX1chr7101755054+ENST00000425508BBS9chr733296848+1286660201285422
ENST00000425244CUX1chr7101755054+ENST00000242067BBS9chr733296848+3576512102733907
ENST00000425244CUX1chr7101755054+ENST00000355070BBS9chr733296848+3561512102718902
ENST00000425244CUX1chr7101755054+ENST00000350941BBS9chr733296848+3456512102613867
ENST00000425244CUX1chr7101755054+ENST00000354265BBS9chr733296848+3471512102628872
ENST00000425244CUX1chr7101755054+ENST00000396127BBS9chr733296848+3471512102628872
ENST00000425244CUX1chr7101755054+ENST00000425508BBS9chr733296848+1138512101137376
ENST00000292535CUX1chr7101755054+ENST00000242067BBS9chr733296848+3709645382866942
ENST00000292535CUX1chr7101755054+ENST00000355070BBS9chr733296848+3694645382851937
ENST00000292535CUX1chr7101755054+ENST00000350941BBS9chr733296848+3589645382746902
ENST00000292535CUX1chr7101755054+ENST00000354265BBS9chr733296848+3604645382761907
ENST00000292535CUX1chr7101755054+ENST00000396127BBS9chr733296848+3604645382761907
ENST00000292535CUX1chr7101755054+ENST00000425508BBS9chr733296848+1271645381270411
ENST00000549414CUX1chr7101755054+ENST00000242067BBS9chr733296848+367160702828942
ENST00000549414CUX1chr7101755054+ENST00000355070BBS9chr733296848+365660702813937
ENST00000549414CUX1chr7101755054+ENST00000350941BBS9chr733296848+355160702708902
ENST00000549414CUX1chr7101755054+ENST00000354265BBS9chr733296848+356660702723907
ENST00000549414CUX1chr7101755054+ENST00000396127BBS9chr733296848+356660702723907
ENST00000549414CUX1chr7101755054+ENST00000425508BBS9chr733296848+123360701232410
ENST00000556210CUX1chr7101755054+ENST00000242067BBS9chr733296848+367160702828942
ENST00000556210CUX1chr7101755054+ENST00000355070BBS9chr733296848+365660702813937
ENST00000556210CUX1chr7101755054+ENST00000350941BBS9chr733296848+355160702708902
ENST00000556210CUX1chr7101755054+ENST00000354265BBS9chr733296848+356660702723907
ENST00000556210CUX1chr7101755054+ENST00000396127BBS9chr733296848+356660702723907
ENST00000556210CUX1chr7101755054+ENST00000425508BBS9chr733296848+123360701232410
ENST00000550008CUX1chr7101755054+ENST00000242067BBS9chr733296848+367160702828942
ENST00000550008CUX1chr7101755054+ENST00000355070BBS9chr733296848+365660702813937
ENST00000550008CUX1chr7101755054+ENST00000350941BBS9chr733296848+355160702708902
ENST00000550008CUX1chr7101755054+ENST00000354265BBS9chr733296848+356660702723907
ENST00000550008CUX1chr7101755054+ENST00000396127BBS9chr733296848+356660702723907
ENST00000550008CUX1chr7101755054+ENST00000425508BBS9chr733296848+123360701232410
ENST00000546411CUX1chr7101755054+ENST00000242067BBS9chr733296848+367160702828942
ENST00000546411CUX1chr7101755054+ENST00000355070BBS9chr733296848+365660702813937
ENST00000546411CUX1chr7101755054+ENST00000350941BBS9chr733296848+355160702708902
ENST00000546411CUX1chr7101755054+ENST00000354265BBS9chr733296848+356660702723907
ENST00000546411CUX1chr7101755054+ENST00000396127BBS9chr733296848+356660702723907
ENST00000546411CUX1chr7101755054+ENST00000425508BBS9chr733296848+123360701232410

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
ENST00000437600ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0006041690.99939585
ENST00000437600ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0006185860.9993814
ENST00000437600ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0009121370.9990878
ENST00000437600ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0008264940.99917346
ENST00000437600ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0008732750.99912673
ENST00000437600ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0021666180.99783343
ENST00000292538ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0005032010.9994968
ENST00000292538ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005160780.99948394
ENST00000292538ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007455290.9992544
ENST00000292538ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0006742220.99932575
ENST00000292538ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007113210.9992887
ENST00000292538ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0029671790.99703276
ENST00000393824ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0005319420.999468
ENST00000393824ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005263080.99947375
ENST00000393824ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007089960.99929094
ENST00000393824ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0006039130.9993961
ENST00000393824ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0006295270.9993705
ENST00000393824ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0023374420.99766254
ENST00000547394ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0002952610.99970466
ENST00000547394ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0002748270.99972516
ENST00000547394ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0003475160.9996525
ENST00000547394ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0003181220.99968195
ENST00000547394ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0003356420.9996643
ENST00000547394ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0019553540.9980446
ENST00000360264ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0004978630.9995022
ENST00000360264ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005117530.99948823
ENST00000360264ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007372740.99926275
ENST00000360264ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.000665490.9993345
ENST00000360264ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007025560.9992974
ENST00000360264ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.002892270.9971078
ENST00000425244ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0004677050.99953234
ENST00000425244ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0004473890.99955255
ENST00000425244ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0005657850.9994342
ENST00000425244ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0004798520.9995202
ENST00000425244ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.000502130.9994979
ENST00000425244ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0021444820.9978555
ENST00000292535ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0005904420.99940956
ENST00000292535ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005554860.99944454
ENST00000292535ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007112540.9992887
ENST00000292535ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0007057250.9992943
ENST00000292535ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007346930.99926525
ENST00000292535ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0045807490.99541926
ENST00000549414ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0006003110.99939966
ENST00000549414ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005659010.99943405
ENST00000549414ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007216410.99927837
ENST00000549414ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0007158680.9992842
ENST00000549414ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007448590.9992551
ENST00000549414ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0046521640.9953478
ENST00000556210ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0006003110.99939966
ENST00000556210ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005659010.99943405
ENST00000556210ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007216410.99927837
ENST00000556210ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0007158680.9992842
ENST00000556210ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007448590.9992551
ENST00000556210ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0046521640.9953478
ENST00000550008ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0006003110.99939966
ENST00000550008ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005659010.99943405
ENST00000550008ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007216410.99927837
ENST00000550008ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0007158680.9992842
ENST00000550008ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007448590.9992551
ENST00000550008ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0046521640.9953478
ENST00000546411ENST00000242067CUX1chr7101755054+BBS9chr733296848+0.0006003110.99939966
ENST00000546411ENST00000355070CUX1chr7101755054+BBS9chr733296848+0.0005659010.99943405
ENST00000546411ENST00000350941CUX1chr7101755054+BBS9chr733296848+0.0007216410.99927837
ENST00000546411ENST00000354265CUX1chr7101755054+BBS9chr733296848+0.0007158680.9992842
ENST00000546411ENST00000396127CUX1chr7101755054+BBS9chr733296848+0.0007448590.9992551
ENST00000546411ENST00000425508CUX1chr7101755054+BBS9chr733296848+0.0046521640.9953478

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 CUX1-BBS9

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CUX1chr7101755054BBS9chr733296848512167LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848552176LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848607202LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848614197LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848645202LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848660213LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848666213LEEAEHKVQSLQTGRDLICIQSMDGM
CUX1chr7101755054BBS9chr733296848992213LEEAEHKVQSLQTGRDLICIQSMDGM

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Potential FusionNeoAntigen Information of CUX1-BBS9 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.
CUX1-BBS9_101755054_33296848.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)
CUX1-BBS9chr7101755054chr733296848645HLA-A74:03KVQSLQTGR0.98760.5984615
CUX1-BBS9chr7101755054chr733296848645HLA-A74:09KVQSLQTGR0.98760.5984615
CUX1-BBS9chr7101755054chr733296848645HLA-A74:11KVQSLQTGR0.98760.5984615
CUX1-BBS9chr7101755054chr733296848645HLA-A31:02KVQSLQTGR0.93830.6595615
CUX1-BBS9chr7101755054chr733296848645HLA-A68:24EHKVQSLQTGR0.97410.7585415
CUX1-BBS9chr7101755054chr733296848645HLA-A31:01KVQSLQTGR0.98670.6075615
CUX1-BBS9chr7101755054chr733296848645HLA-A68:01EHKVQSLQTGR0.97410.7585415
CUX1-BBS9chr7101755054chr733296848645HLA-A74:01KVQSLQTGR0.98760.5984615

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Potential FusionNeoAntigen Information of CUX1-BBS9 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.
CUX1-BBS9_101755054_33296848.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)
CUX1-BBS9chr7101755054chr733296848645DRB1-0411AEHKVQSLQTGRDLI318
CUX1-BBS9chr7101755054chr733296848645DRB1-0467AEHKVQSLQTGRDLI318
CUX1-BBS9chr7101755054chr733296848645DRB1-0491AEHKVQSLQTGRDLI318

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Fusion breakpoint peptide structures of CUX1-BBS9

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
4693KVQSLQTGRDLICICUX1BBS9chr7101755054chr733296848645

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CUX1-BBS9

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-B14:023BVN4693KVQSLQTGRDLICI-7.15543-7.26883
HLA-B14:023BVN4693KVQSLQTGRDLICI-4.77435-5.80965
HLA-B52:013W394693KVQSLQTGRDLICI-6.80875-6.92215
HLA-B52:013W394693KVQSLQTGRDLICI-4.20386-5.23916
HLA-A11:014UQ24693KVQSLQTGRDLICI-7.5194-8.5547
HLA-A11:014UQ24693KVQSLQTGRDLICI-6.9601-7.0735
HLA-A24:025HGA4693KVQSLQTGRDLICI-7.52403-7.63743
HLA-A24:025HGA4693KVQSLQTGRDLICI-5.82433-6.85963
HLA-B27:056PYJ4693KVQSLQTGRDLICI-3.28285-4.31815
HLA-B44:053DX84693KVQSLQTGRDLICI-5.91172-6.94702
HLA-B44:053DX84693KVQSLQTGRDLICI-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of CUX1-BBS9

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
CUX1-BBS9chr7101755054chr733296848415EHKVQSLQTGRAGCATAAGGTTCAGAGCCTACAAACAGGTCGAG
CUX1-BBS9chr7101755054chr733296848615KVQSLQTGRAGGTTCAGAGCCTACAAACAGGTCGAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CUX1-BBS9chr7101755054chr733296848318AEHKVQSLQTGRDLICTGAGCATAAGGTTCAGAGCCTACAAACAGGTCGAGATTTAATTT

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Information of the samples that have these potential fusion neoantigens of CUX1-BBS9

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
STADCUX1-BBS9chr7101755054ENST00000292535chr733296848ENST00000242067TCGA-BR-A4PD-01A

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Potential target of CAR-T therapy development for CUX1-BBS9

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 CUX1-BBS9

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 CUX1-BBS9

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