FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

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

leaf

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

leaf

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

leaf

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

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

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

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:FUS-ALDH9A1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FUS-ALDH9A1
FusionPDB ID: 31789
FusionGDB2.0 ID: 31789
HgeneTgene
Gene symbol

FUS

ALDH9A1

Gene ID

2521

223

Gene nameFUS RNA binding proteinaldehyde dehydrogenase 9 family member A1
SynonymsALS6|ETM4|FUS1|HNRNPP2|POMP75|TLSALDH4|ALDH7|ALDH9|E3|TMABA-DH|TMABADH|TMABALDH
Cytomap

16p11.2

1q24.1

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein FUS75 kDa DNA-pairing proteinfus-like proteinfused in sarcomafusion gene in myxoid liposarcomaheterogeneous nuclear ribonucleoprotein P2oncogene FUSoncogene TLStranslocated in liposarcoma protein4-trimethylaminobutyraldehyde dehydrogenaseR-aminobutyraldehyde dehydrogenasealdehyde dehydrogenase (NAD+)aldehyde dehydrogenase E3 isozymealdehyde dehydrogenase family 9 member A1gamma-aminobutyraldehyde dehydrogenase
Modification date2020032920200313
UniProtAcc

P35637

Main function of 5'-partner protein: FUNCTION: DNA/RNA-binding protein that plays a role in various cellular processes such as transcription regulation, RNA splicing, RNA transport, DNA repair and damage response (PubMed:27731383). Binds to nascent pre-mRNAs and acts as a molecular mediator between RNA polymerase II and U1 small nuclear ribonucleoprotein thereby coupling transcription and splicing (PubMed:26124092). Binds also its own pre-mRNA and autoregulates its expression; this autoregulation mechanism is mediated by non-sense-mediated decay (PubMed:24204307). Plays a role in DNA repair mechanisms by promoting D-loop formation and homologous recombination during DNA double-strand break repair (PubMed:10567410). In neuronal cells, plays crucial roles in dendritic spine formation and stability, RNA transport, mRNA stability and synaptic homeostasis (By similarity). {ECO:0000250|UniProtKB:P56959, ECO:0000269|PubMed:10567410, ECO:0000269|PubMed:24204307, ECO:0000269|PubMed:26124092, ECO:0000269|PubMed:27731383}.

P49189

Main function of 5'-partner protein: FUNCTION: Converts gamma-trimethylaminobutyraldehyde into gamma-butyrobetaine with high efficiency (in vitro). Can catalyze the irreversible oxidation of a broad range of aldehydes to the corresponding acids in an NAD-dependent reaction, but with low efficiency. {ECO:0000269|PubMed:10702312, ECO:0000269|PubMed:30914451, ECO:0000269|PubMed:8645224}.
Ensembl transtripts involved in fusion geneENST idsENST00000254108, ENST00000380244, 
ENST00000568685, ENST00000474990, 
ENST00000461664, ENST00000354775, 
ENST00000538148, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score37 X 37 X 16=219044 X 3 X 3=36
# samples 444
** MAII scorelog2(44/21904*10)=-5.63754701773324
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: FUS [Title/Abstract] AND ALDH9A1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FUS [Title/Abstract] AND ALDH9A1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FUS(31196500)-ALDH9A1(165634367), # samples:1
Anticipated loss of major functional domain due to fusion event.FUS-ALDH9A1 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.
FUS-ALDH9A1 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.
FUS-ALDH9A1 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.
FUS-ALDH9A1 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
HgeneFUS

GO:0006355

regulation of transcription, DNA-templated

26124092

HgeneFUS

GO:0006357

regulation of transcription by RNA polymerase II

25453086

HgeneFUS

GO:0008380

RNA splicing

26124092

HgeneFUS

GO:0043484

regulation of RNA splicing

25453086|27731383

HgeneFUS

GO:0048255

mRNA stabilization

27378374

HgeneFUS

GO:0051260

protein homooligomerization

25453086

HgeneFUS

GO:1905168

positive regulation of double-strand break repair via homologous recombination

10567410

TgeneALDH9A1

GO:0006081

cellular aldehyde metabolic process

8645224|30914451

TgeneALDH9A1

GO:0042136

neurotransmitter biosynthetic process

2925663

TgeneALDH9A1

GO:0051289

protein homotetramerization

30914451

TgeneALDH9A1

GO:0055114

oxidation-reduction process

2925663



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/chr16:31196500/chr1:165634367)
- 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 FUS (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 ALDH9A1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000254108FUSchr1631196500+ENST00000354775ALDH9A1chr1165634367-1911869271076349
ENST00000254108FUSchr1631196500+ENST00000538148ALDH9A1chr1165634367-1316869271076349
ENST00000380244FUSchr1631196500+ENST00000354775ALDH9A1chr1165634367-1879837521044330
ENST00000380244FUSchr1631196500+ENST00000538148ALDH9A1chr1165634367-1284837521044330
ENST00000568685FUSchr1631196500+ENST00000354775ALDH9A1chr1165634367-1870828401035331
ENST00000568685FUSchr1631196500+ENST00000538148ALDH9A1chr1165634367-1275828401035331

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
ENST00000254108ENST00000354775FUSchr1631196500+ALDH9A1chr1165634367-0.0028573740.9971426
ENST00000254108ENST00000538148FUSchr1631196500+ALDH9A1chr1165634367-0.0055531020.9944469
ENST00000380244ENST00000354775FUSchr1631196500+ALDH9A1chr1165634367-0.0010498520.9989502
ENST00000380244ENST00000538148FUSchr1631196500+ALDH9A1chr1165634367-0.0026911240.99730885
ENST00000568685ENST00000354775FUSchr1631196500+ALDH9A1chr1165634367-0.0027976980.9972023
ENST00000568685ENST00000538148FUSchr1631196500+ALDH9A1chr1165634367-0.0057802210.9942198

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

Top

Fusion Protein Breakpoint Sequences for FUS-ALDH9A1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FUSchr1631196500ALDH9A1chr116563436782838PTQPGQGYSQQSSQPYGQQSYSGYSQ
FUSchr1631196500ALDH9A1chr116563436783738PTQPGQGYSQQSSQPYGQQSYSGYSQ
FUSchr1631196500ALDH9A1chr116563436786956PTQPGQGYSQQSSQPYGQQSYSGYSQ

Top

Potential FusionNeoAntigen Information of FUS-ALDH9A1 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.
FUS-ALDH9A1_31196500_165634367.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)
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:01SQQSSQPY0.99880.6814816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:25SQQSSQPY0.98180.7398816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:01SQPYGQQSY0.99930.56491221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:01YSQQSSQPY0.99790.6823716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:25YSQQSSQPY0.99640.6693716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:02YSQQSSQPY0.99420.6778716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:08YSQQSSQPY0.9680.6319716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:17YSQQSSQPY0.96450.6126716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:01YSQQSSQPY0.95770.6034716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:25SQPYGQQSY0.94210.68131221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:02SQPYGQQSY0.87160.71521221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:01SSQPYGQQSY0.99590.58891121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:25SSQPYGQQSY0.99580.66391121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:02SSQPYGQQSY0.9850.68741121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:17SSQPYGQQSY0.97740.67871121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B58:02SSQPYGQQSY0.88750.67861121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:01QSSQPYGQQSY0.99840.63951021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:05SQQSSQPY0.83610.6713816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:21YSQQSSQPY0.99340.6762716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:05YSQQSSQPY0.98050.5367716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:31YSQQSSQPY0.95850.5439716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:04SQPYGQQSY0.90690.60521221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:21SQPYGQQSY0.87590.62461221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:05SQPYGQQSY0.83140.53931221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:31SQPYGQQSY0.73040.55071221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C15:04YSQQSSQPY0.7160.7299716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C12:12YSQQSSQPY0.46870.8999716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C12:16SQPYGQQSY0.460.89991221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:19SQPYGQQSY0.45350.51141221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:67SQPYGQQSY0.38090.84971221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:80SQPYGQQSY0.38090.84971221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:46SQPYGQQSY0.37150.69771221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:10SQPYGQQSY0.3690.87121221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C03:14YSQQSSQPY0.310.8786716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C15:04SSQPYGQQSY0.98450.62021121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:05SSQPYGQQSY0.92550.521121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:31SSQPYGQQSY0.8770.51781121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:27SQQSSQPY0.99890.7182816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:34SQQSSQPY0.99880.6814816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:125SQQSSQPY0.99880.6814816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:33SQQSSQPY0.99880.6814816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:135SQQSSQPY0.99870.7225816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:50SQQSSQPY0.99860.7242816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:53SQQSSQPY0.99290.6202816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:12SQQSSQPY0.9920.6989816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:39SQQSSQPY0.98390.6047816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:54SQQSSQPY0.98140.5575816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:20SQQSSQPY0.8330.7653816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:28SQQSSQPY0.80510.8052816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B48:02SQQSSQPY0.4180.7547816
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:33SQPYGQQSY0.99930.56491221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:135SQPYGQQSY0.99930.63531221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:125SQPYGQQSY0.99930.56491221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:27SQPYGQQSY0.99930.6131221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:34SQPYGQQSY0.99930.56491221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:50SQPYGQQSY0.99840.63251221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:11SQPYGQQSY0.99820.52031221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:08SQPYGQQSY0.9980.5061221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:33YSQQSSQPY0.99790.6823716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:27YSQQSSQPY0.99790.743716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:125YSQQSSQPY0.99790.6823716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:34YSQQSSQPY0.99790.6823716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:135YSQQSSQPY0.99770.724716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:24SQPYGQQSY0.99680.74681221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:11YSQQSSQPY0.99670.6134716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:08YSQQSSQPY0.99640.6258716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:39YSQQSSQPY0.9960.5314716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:43YSQQSSQPY0.99530.6248716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:50YSQQSSQPY0.99470.7679716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:53SQPYGQQSY0.99380.5251221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:12YSQQSSQPY0.99350.6755716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:11YSQQSSQPY0.99190.6768716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:35YSQQSSQPY0.98960.6499716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:12SQPYGQQSY0.98780.59991221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:53YSQQSSQPY0.98720.6265716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:35SQPYGQQSY0.98660.56071221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:20YSQQSSQPY0.98140.6328716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:28YSQQSSQPY0.96990.6583716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:20YSQQSSQPY0.95870.6796716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:23YSQQSSQPY0.95780.6663716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:77YSQQSSQPY0.95770.6034716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C03:02YSQQSSQPY0.9410.8808716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:39SQPYGQQSY0.93980.54551221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:13YSQQSSQPY0.93660.5191716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:54YSQQSSQPY0.85210.5692716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:20SQPYGQQSY0.83710.60861221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C12:02YSQQSSQPY0.78880.9231716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:24YSQQSSQPY0.76330.6568716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:28SQPYGQQSY0.76020.63131221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:20SQPYGQQSY0.7170.64311221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C15:09YSQQSSQPY0.7160.7299716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C16:04YSQQSSQPY0.60270.9569716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B48:02YSQQSSQPY0.60010.6151716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C12:03YSQQSSQPY0.55950.9663716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B18:11SQPYGQQSY0.54760.53961221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:73SQPYGQQSY0.5340.75171221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B18:04SQPYGQQSY0.43780.64571221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:30SQPYGQQSY0.43480.61151221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B18:04YSQQSSQPY0.41430.6571716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:17SQPYGQQSY0.40540.88881221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C07:02SQPYGQQSY0.38090.84971221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C12:02SQPYGQQSY0.28880.9141221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B48:02SQPYGQQSY0.25270.59621221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C16:01YSQQSSQPY0.24860.9398716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B18:06SQPYGQQSY0.22180.63891221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B18:08SQPYGQQSY0.20450.63981221
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C16:02YSQQSSQPY0.16560.9764716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C02:02YSQQSSQPY0.05160.9327716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C02:10YSQQSSQPY0.05160.9327716
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:34SSQPYGQQSY0.99590.58891121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:33SSQPYGQQSY0.99590.58891121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:125SSQPYGQQSY0.99590.58891121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:39SSQPYGQQSY0.99540.53461121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:27SSQPYGQQSY0.99530.62181121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:53SSQPYGQQSY0.99530.5451121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:135SSQPYGQQSY0.99420.65161121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:50SSQPYGQQSY0.99050.57431121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:35SSQPYGQQSY0.98470.57131121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C15:09SSQPYGQQSY0.98450.62021121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:11SSQPYGQQSY0.98380.54561121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:24SSQPYGQQSY0.98360.71571121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:12SSQPYGQQSY0.98240.58221121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C03:02SSQPYGQQSY0.980.89481121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B58:06SSQPYGQQSY0.94420.67261121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:54SSQPYGQQSY0.9340.50581121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:20SSQPYGQQSY0.93270.56791121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:28SSQPYGQQSY0.90330.58771121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B35:20SSQPYGQQSY0.86710.58811121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C16:02SSQPYGQQSY0.78750.95761121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-C16:01SSQPYGQQSY0.55810.90681121
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:34QSSQPYGQQSY0.99840.63951021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:33QSSQPYGQQSY0.99840.63951021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:125QSSQPYGQQSY0.99840.63951021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:27QSSQPYGQQSY0.99810.69511021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:135QSSQPYGQQSY0.99780.67371021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:53QSSQPYGQQSY0.99690.63021021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B57:04QSSQPYGQQSY0.99130.62841021
FUS-ALDH9A1chr1631196500chr1165634367869HLA-B15:12QSSQPYGQQSY0.98750.71441021

Top

Potential FusionNeoAntigen Information of FUS-ALDH9A1 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.
FUS-ALDH9A1_31196500_165634367.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)
FUS-ALDH9A1chr1631196500chr1165634367869DRB1-1216GQGYSQQSSQPYGQQ419
FUS-ALDH9A1chr1631196500chr1165634367869DRB1-1222GQGYSQQSSQPYGQQ419
FUS-ALDH9A1chr1631196500chr1165634367869DRB1-1222PGQGYSQQSSQPYGQ318
FUS-ALDH9A1chr1631196500chr1165634367869DRB1-1446GQGYSQQSSQPYGQQ419

Top

Fusion breakpoint peptide structures of FUS-ALDH9A1

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
3258GYSQQSSQPYGQQSFUSALDH9A1chr1631196500chr1165634367869

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FUS-ALDH9A1

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-B14:023BVN3258GYSQQSSQPYGQQS-7.9962-8.1096
HLA-B14:023BVN3258GYSQQSSQPYGQQS-5.70842-6.74372
HLA-B52:013W393258GYSQQSSQPYGQQS-6.83737-6.95077
HLA-B52:013W393258GYSQQSSQPYGQQS-4.4836-5.5189
HLA-A11:014UQ23258GYSQQSSQPYGQQS-10.0067-10.1201
HLA-A11:014UQ23258GYSQQSSQPYGQQS-9.03915-10.0745
HLA-A24:025HGA3258GYSQQSSQPYGQQS-6.56204-6.67544
HLA-A24:025HGA3258GYSQQSSQPYGQQS-5.42271-6.45801
HLA-B44:053DX83258GYSQQSSQPYGQQS-7.85648-8.89178
HLA-B44:053DX83258GYSQQSSQPYGQQS-5.3978-5.5112
HLA-A02:016TDR3258GYSQQSSQPYGQQS-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of FUS-ALDH9A1

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
FUS-ALDH9A1chr1631196500chr11656343671021QSSQPYGQQSYTGGCATGGGGGACATCCAACGGGCTCATAGAGT
FUS-ALDH9A1chr1631196500chr11656343671121SSQPYGQQSYCATGGGGGACATCCAACGGGCTCATAGAGT
FUS-ALDH9A1chr1631196500chr11656343671221SQPYGQQSYGGGGGACATCCAACGGGCTCATAGAGT
FUS-ALDH9A1chr1631196500chr1165634367716YSQQSSQPYAGGCAGAGGTGGCATGGGGGACATCCA
FUS-ALDH9A1chr1631196500chr1165634367816SQQSSQPYCAGAGGTGGCATGGGGGACATCCA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
FUS-ALDH9A1chr1631196500chr1165634367318PGQGYSQQSSQPYGQAGGTGGCCGTGGAGGCAGAGGTGGCATGGGGGACATCCAACGGGC
FUS-ALDH9A1chr1631196500chr1165634367419GQGYSQQSSQPYGQQTGGCCGTGGAGGCAGAGGTGGCATGGGGGACATCCAACGGGCTCA

Top

Information of the samples that have these potential fusion neoantigens of FUS-ALDH9A1

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
BRCAFUS-ALDH9A1chr1631196500ENST00000254108chr1165634367ENST00000354775TCGA-AO-A12F

Top

Potential target of CAR-T therapy development for FUS-ALDH9A1

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

Top

Related Drugs to FUS-ALDH9A1

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

Top

Related Diseases to FUS-ALDH9A1

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
HgeneFUSC1842675AMYOTROPHIC LATERAL SCLEROSIS 6 (disorder)5UNIPROT
HgeneFUSC3468114Juvenile amyotrophic lateral sclerosis5ORPHANET
HgeneFUSC0002736Amyotrophic Lateral Sclerosis2CTD_human;ORPHANET
HgeneFUSC0206634Liposarcoma, Myxoid2CTD_human;ORPHANET
HgeneFUSC0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
HgeneFUSC0497327Dementia1GENOMICS_ENGLAND
HgeneFUSC0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
HgeneFUSC3539195TREMOR, HEREDITARY ESSENTIAL, 41CTD_human;UNIPROT
HgeneFUSC3888102Frontotemporal Dementia With Motor Neuron Disease1ORPHANET