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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:TP73-CEP104

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TP73-CEP104
FusionPDB ID: 93255
FusionGDB2.0 ID: 93255
HgeneTgene
Gene symbol

TP73

CEP104

Gene ID

7161

9731

Gene nametumor protein p73centrosomal protein 104
SynonymsP73CFAP256|GlyBP|JBTS25|KIAA0562|ROC22
Cytomap

1p36.32

1p36.32

Type of geneprotein-codingprotein-coding
Descriptiontumor protein p73p53-like transcription factorp53-related proteincentrosomal protein of 104 kDacentrosomal protein 104kDa
Modification date2020032720200313
UniProtAcc.

O60308

Main function of 5'-partner protein: FUNCTION: Required for ciliogenesis and for structural integrity at the ciliary tip. {ECO:0000269|PubMed:23970417}.
Ensembl transtripts involved in fusion geneENST idsENST00000346387, ENST00000354437, 
ENST00000357733, ENST00000378295, 
ENST00000603362, ENST00000604074, 
ENST00000604479, ENST00000378280, 
ENST00000378285, ENST00000378288, 
ENST00000378290, 
ENST00000378223, 
ENST00000378230, ENST00000460038, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score2 X 2 X 3=124 X 5 X 5=100
# samples 35
** MAII scorelog2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: TP73 [Title/Abstract] AND CEP104 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TP73 [Title/Abstract] AND CEP104 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TP73(3599744)-CEP104(3740126), # samples:1
TP73(3599744)-CEP104(3768985), # samples:1
Anticipated loss of major functional domain due to fusion event.TP73-CEP104 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.
TP73-CEP104 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.
TP73-CEP104 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.
TP73-CEP104 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
HgeneTP73

GO:0006974

cellular response to DNA damage stimulus

18174154

HgeneTP73

GO:0042771

intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

18174154|19490146

HgeneTP73

GO:0045893

positive regulation of transcription, DNA-templated

15678106|16343436

HgeneTP73

GO:0045944

positive regulation of transcription by RNA polymerase II

16343436|18174154|18421303|19490146|24652652

HgeneTP73

GO:0071158

positive regulation of cell cycle arrest

18421303



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/chr1:3599744/chr1:3740126)
- 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 TP73 (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 CEP104 (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)
ENST00000378295TP73chr13599744+ENST00000378230CEP104chr13740126-4076341107754215
ENST00000604074TP73chr13599744+ENST00000378230CEP104chr13740126-4076341107754215
ENST00000354437TP73chr13599744+ENST00000378230CEP104chr13740126-403129662709215
ENST00000346387TP73chr13599744+ENST00000378230CEP104chr13740126-403129662709215
ENST00000357733TP73chr13599744+ENST00000378230CEP104chr13740126-403129662709215
ENST00000603362TP73chr13599744+ENST00000378230CEP104chr13740126-39211860599199
ENST00000604479TP73chr13599744+ENST00000378230CEP104chr13740126-39211860599199

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
ENST00000378295ENST00000378230TP73chr13599744+CEP104chr13740126-0.0281866940.9718133
ENST00000604074ENST00000378230TP73chr13599744+CEP104chr13740126-0.0281866940.9718133
ENST00000354437ENST00000378230TP73chr13599744+CEP104chr13740126-0.0258698220.97413015
ENST00000346387ENST00000378230TP73chr13599744+CEP104chr13740126-0.0258698220.97413015
ENST00000357733ENST00000378230TP73chr13599744+CEP104chr13740126-0.0258698220.97413015
ENST00000603362ENST00000378230TP73chr13599744+CEP104chr13740126-0.0246631170.97533685
ENST00000604479ENST00000378230TP73chr13599744+CEP104chr13740126-0.0246631170.97533685

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 TP73-CEP104

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TP73chr13599744CEP104chr1374012618662DVFHLEGMTTSVMVVEISSLTEHLLT
TP73chr13599744CEP104chr1374012629678DVFHLEGMTTSVMVVEISSLTEHLLT
TP73chr13599744CEP104chr1374012634178DVFHLEGMTTSVMVVEISSLTEHLLT

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Potential FusionNeoAntigen Information of TP73-CEP104 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.
TP73-CEP104_3599744_3740126.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)
TP73-CEP104chr13599744chr13740126296HLA-A02:13GMTTSVMVV0.99360.5416615
TP73-CEP104chr13599744chr13740126296HLA-A02:38GMTTSVMVV0.98550.5597615
TP73-CEP104chr13599744chr13740126296HLA-B13:02GMTTSVMVV0.12710.8649615
TP73-CEP104chr13599744chr13740126296HLA-A02:03GMTTSVMVV0.99720.5065615
TP73-CEP104chr13599744chr13740126296HLA-A68:02MVVEISSLT0.98280.551221
TP73-CEP104chr13599744chr13740126296HLA-B15:73VMVVEISSL0.96850.79641120
TP73-CEP104chr13599744chr13740126296HLA-B15:30VMVVEISSL0.93820.72151120

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Potential FusionNeoAntigen Information of TP73-CEP104 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.
TP73-CEP104_3599744_3740126.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)
TP73-CEP104chr13599744chr13740126296DRB1-1503VMVVEISSLTEHLLT1126
TP73-CEP104chr13599744chr13740126296DRB1-1523VMVVEISSLTEHLLT1126

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Fusion breakpoint peptide structures of TP73-CEP104

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
2990GMTTSVMVVEISSLTP73CEP104chr13599744chr13740126296

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TP73-CEP104

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-B14:023BVN2990GMTTSVMVVEISSL-7.15543-7.26883
HLA-B14:023BVN2990GMTTSVMVVEISSL-4.77435-5.80965
HLA-B52:013W392990GMTTSVMVVEISSL-6.80875-6.92215
HLA-B52:013W392990GMTTSVMVVEISSL-4.20386-5.23916
HLA-A11:014UQ22990GMTTSVMVVEISSL-7.5194-8.5547
HLA-A11:014UQ22990GMTTSVMVVEISSL-6.9601-7.0735
HLA-A24:025HGA2990GMTTSVMVVEISSL-7.52403-7.63743
HLA-A24:025HGA2990GMTTSVMVVEISSL-5.82433-6.85963
HLA-B27:056PYJ2990GMTTSVMVVEISSL-3.28285-4.31815
HLA-B44:053DX82990GMTTSVMVVEISSL-5.91172-6.94702
HLA-B44:053DX82990GMTTSVMVVEISSL-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of TP73-CEP104

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
TP73-CEP104chr13599744chr137401261120VMVVEISSLGTCATGGTGGTCGAGATATCCAGTCTG
TP73-CEP104chr13599744chr137401261221MVVEISSLTATGGTGGTCGAGATATCCAGTCTGACG
TP73-CEP104chr13599744chr13740126615GMTTSVMVVGGCATGACTACATCTGTCATGGTGGTC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
TP73-CEP104chr13599744chr137401261126VMVVEISSLTEHLLTGTCATGGTGGTCGAGATATCCAGTCTGACGGAGCACTTGCTGACG

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Information of the samples that have these potential fusion neoantigens of TP73-CEP104

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
OVTP73-CEP104chr13599744ENST00000346387chr13740126ENST00000378230TCGA-13-0899

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Potential target of CAR-T therapy development for TP73-CEP104

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 TP73-CEP104

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 TP73-CEP104

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