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:NOVA1-FUS

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NOVA1-FUS
FusionPDB ID: 59799
FusionGDB2.0 ID: 59799
HgeneTgene
Gene symbol

NOVA1

FUS

Gene ID

4857

2521

Gene nameNOVA alternative splicing regulator 1FUS RNA binding protein
SynonymsNova-1ALS6|ETM4|FUS1|HNRNPP2|POMP75|TLS
Cytomap

14q12

16p11.2

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein Nova-1neuro-oncological ventral antigen 1onconeural ventral antigen 1paraneoplastic Ri antigenventral neuron-specific protein 1RNA-binding protein FUS75 kDa DNA-pairing proteinfus-like proteinfused in sarcomafusion gene in myxoid liposarcomaheterogeneous nuclear ribonucleoprotein P2oncogene FUSoncogene TLStranslocated in liposarcoma protein
Modification date2020032720200329
UniProtAcc

P51513

Main function of 5'-partner protein: FUNCTION: May regulate RNA splicing or metabolism in a specific subset of developing neurons.

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}.
Ensembl transtripts involved in fusion geneENST idsENST00000344429, ENST00000465357, 
ENST00000539517, ENST00000547619, 
ENST00000574031, ENST00000267422, 
ENST00000551754, 
ENST00000474990, 
ENST00000254108, ENST00000380244, 
ENST00000568685, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 5 X 5=17520 X 13 X 10=2600
# samples 822
** MAII scorelog2(8/175*10)=-1.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(22/2600*10)=-3.56293619439116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NOVA1 [Title/Abstract] AND FUS [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NOVA1 [Title/Abstract] AND FUS [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NOVA1(27064616)-FUS(31199646), # samples:1
Anticipated loss of major functional domain due to fusion event.NOVA1-FUS 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.
NOVA1-FUS 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.
NOVA1-FUS 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.
NOVA1-FUS 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
TgeneFUS

GO:0006355

regulation of transcription, DNA-templated

26124092

TgeneFUS

GO:0006357

regulation of transcription by RNA polymerase II

25453086

TgeneFUS

GO:0008380

RNA splicing

26124092

TgeneFUS

GO:0043484

regulation of RNA splicing

25453086|27731383

TgeneFUS

GO:0048255

mRNA stabilization

27378374

TgeneFUS

GO:0051260

protein homooligomerization

25453086

TgeneFUS

GO:1905168

positive regulation of double-strand break repair via homologous recombination

10567410



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/chr14:27064616/chr16:31199646)
- 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 NOVA1 (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 FUS (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)
ENST00000465357NOVA1chr1427064616-ENST00000254108FUSchr1631199646+1480330501111353
ENST00000465357NOVA1chr1427064616-ENST00000380244FUSchr1631199646+1276330501111353
ENST00000465357NOVA1chr1427064616-ENST00000568685FUSchr1631199646+1252330501114354
ENST00000539517NOVA1chr1427064616-ENST00000254108FUSchr1631199646+17485983181379353
ENST00000539517NOVA1chr1427064616-ENST00000380244FUSchr1631199646+15445983181379353
ENST00000539517NOVA1chr1427064616-ENST00000568685FUSchr1631199646+15205983181382354
ENST00000344429NOVA1chr1427064616-ENST00000254108FUSchr1631199646+143428441065353
ENST00000344429NOVA1chr1427064616-ENST00000380244FUSchr1631199646+123028441065353
ENST00000344429NOVA1chr1427064616-ENST00000568685FUSchr1631199646+120628441068354
ENST00000547619NOVA1chr1427064616-ENST00000254108FUSchr1631199646+1489339591120353
ENST00000547619NOVA1chr1427064616-ENST00000380244FUSchr1631199646+1285339591120353
ENST00000547619NOVA1chr1427064616-ENST00000568685FUSchr1631199646+1261339591123354
ENST00000574031NOVA1chr1427064616-ENST00000254108FUSchr1631199646+1454304241085353
ENST00000574031NOVA1chr1427064616-ENST00000380244FUSchr1631199646+1250304241085353
ENST00000574031NOVA1chr1427064616-ENST00000568685FUSchr1631199646+1226304241088354

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
ENST00000465357ENST00000254108NOVA1chr1427064616-FUSchr1631199646+0.0016050910.9983949
ENST00000465357ENST00000380244NOVA1chr1427064616-FUSchr1631199646+0.0017955540.99820447
ENST00000465357ENST00000568685NOVA1chr1427064616-FUSchr1631199646+0.0011094150.9988906
ENST00000539517ENST00000254108NOVA1chr1427064616-FUSchr1631199646+0.00176640.99823356
ENST00000539517ENST00000380244NOVA1chr1427064616-FUSchr1631199646+0.0019928890.9980071
ENST00000539517ENST00000568685NOVA1chr1427064616-FUSchr1631199646+0.0011688230.9988312
ENST00000344429ENST00000254108NOVA1chr1427064616-FUSchr1631199646+0.001583370.99841666
ENST00000344429ENST00000380244NOVA1chr1427064616-FUSchr1631199646+0.001841890.99815816
ENST00000344429ENST00000568685NOVA1chr1427064616-FUSchr1631199646+0.0011067770.9988932
ENST00000547619ENST00000254108NOVA1chr1427064616-FUSchr1631199646+0.0015565010.99844354
ENST00000547619ENST00000380244NOVA1chr1427064616-FUSchr1631199646+0.0017622310.9982377
ENST00000547619ENST00000568685NOVA1chr1427064616-FUSchr1631199646+0.0010973720.99890256
ENST00000574031ENST00000254108NOVA1chr1427064616-FUSchr1631199646+0.0016490060.998351
ENST00000574031ENST00000380244NOVA1chr1427064616-FUSchr1631199646+0.0018472990.9981527
ENST00000574031ENST00000568685NOVA1chr1427064616-FUSchr1631199646+0.0011801580.99881977

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 NOVA1-FUS

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NOVA1chr1427064616FUSchr1631199646284208ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646284209ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646284209TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr1631199646284210TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr163119964628493ATIKLSKSKDFYPGPRDQGSRHDSAE
NOVA1chr1427064616FUSchr163119964628493ATIKLSKSKDFYPGPRDQGSRHDSEQ
NOVA1chr1427064616FUSchr1631199646304208ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646304209ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646304209TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr1631199646304210TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr163119964630493ATIKLSKSKDFYPGPRDQGSRHDSAE
NOVA1chr1427064616FUSchr163119964630493ATIKLSKSKDFYPGPRDQGSRHDSEQ
NOVA1chr1427064616FUSchr1631199646330208ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646330209ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646330209TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr1631199646330210TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr163119964633093ATIKLSKSKDFYPGPRDQGSRHDSAE
NOVA1chr1427064616FUSchr163119964633093ATIKLSKSKDFYPGPRDQGSRHDSEQ
NOVA1chr1427064616FUSchr1631199646339208ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646339209ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646339209TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr1631199646339210TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr163119964633993ATIKLSKSKDFYPGPRDQGSRHDSAE
NOVA1chr1427064616FUSchr163119964633993ATIKLSKSKDFYPGPRDQGSRHDSEQ
NOVA1chr1427064616FUSchr1631199646598208ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646598209ATRRADFNRGGGNGRGGRGRGGPMGR
NOVA1chr1427064616FUSchr1631199646598209TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr1631199646598210TRRADFNRGGGNGRGGRGRGGPMGRG
NOVA1chr1427064616FUSchr163119964659893ATIKLSKSKDFYPGPRDQGSRHDSAE
NOVA1chr1427064616FUSchr163119964659893ATIKLSKSKDFYPGPRDQGSRHDSEQ

Top

Potential FusionNeoAntigen Information of NOVA1-FUS 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.

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)

Top

Potential FusionNeoAntigen Information of NOVA1-FUS 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.

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)

Top

Fusion breakpoint peptide structures of NOVA1-FUS

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.

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NOVA1-FUS

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

Top

Vaccine Design for the FusionNeoAntigens of NOVA1-FUS

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

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

Top

Information of the samples that have these potential fusion neoantigens of NOVA1-FUS

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

Top

Potential target of CAR-T therapy development for NOVA1-FUS

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 NOVA1-FUS

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

Top

Related Diseases to NOVA1-FUS

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
TgeneFUSC1842675AMYOTROPHIC LATERAL SCLEROSIS 6 (disorder)5UNIPROT
TgeneFUSC3468114Juvenile amyotrophic lateral sclerosis5ORPHANET
TgeneFUSC0002736Amyotrophic Lateral Sclerosis2CTD_human;ORPHANET
TgeneFUSC0206634Liposarcoma, Myxoid2CTD_human;ORPHANET
TgeneFUSC0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
TgeneFUSC0497327Dementia1GENOMICS_ENGLAND
TgeneFUSC0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
TgeneFUSC3539195TREMOR, HEREDITARY ESSENTIAL, 41CTD_human;UNIPROT
TgeneFUSC3888102Frontotemporal Dementia With Motor Neuron Disease1ORPHANET