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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:CTNNBL1-TSHZ2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CTNNBL1-TSHZ2
FusionPDB ID: 20353
FusionGDB2.0 ID: 20353
HgeneTgene
Gene symbol

CTNNBL1

TSHZ2

Gene ID

56259

128553

Gene namecatenin beta like 1teashirt zinc finger homeobox 2
SynonymsC20orf33|NAP|P14L|PP8304|dJ633O20.1C20orf17|OVC10-2|TSH2|ZABC2|ZNF218
Cytomap

20q11.23

20q13.2

Type of geneprotein-codingprotein-coding
Descriptionbeta-catenin-like protein 1nuclear associated proteintestis development protein NYD-SP19teashirt homolog 2cell growth-inhibiting protein 7ovarian cancer-related protein 10-2serologically defined colon cancer antigen 33 liketeashirt family zinc finger 2zinc finger protein 218
Modification date2020032720200313
UniProtAcc

Q8WYA6

Main function of 5'-partner protein: FUNCTION: Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. Participates in AID/AICDA-mediated Ig class switching recombination (CSR). May induce apoptosis.
.
Ensembl transtripts involved in fusion geneENST idsENST00000473857, ENST00000361383, 
ENST00000373469, ENST00000373473, 
ENST00000405275, 
ENST00000329613, 
ENST00000371497, ENST00000603338, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 5 X 5=17540 X 23 X 9=8280
# samples 750
** MAII scorelog2(7/175*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(50/8280*10)=-4.0496307677246
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CTNNBL1 [Title/Abstract] AND TSHZ2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CTNNBL1 [Title/Abstract] AND TSHZ2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CTNNBL1(36431450)-TSHZ2(51870038), # samples:1
Anticipated loss of major functional domain due to fusion event.CTNNBL1-TSHZ2 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.
CTNNBL1-TSHZ2 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.
CTNNBL1-TSHZ2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CTNNBL1-TSHZ2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
CTNNBL1-TSHZ2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted 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
HgeneCTNNBL1

GO:0043065

positive regulation of apoptotic process

12659813



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/chr20:36431450/chr20:51870038)
- 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 CTNNBL1 (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 TSHZ2 (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)
ENST00000361383CTNNBL1chr2036431450+ENST00000371497TSHZ2chr2051870038+12590133011743941425
ENST00000361383CTNNBL1chr2036431450+ENST00000603338TSHZ2chr2051870038+4739133011743941425
ENST00000405275CTNNBL1chr2036431450+ENST00000371497TSHZ2chr2051870038+12635137524344391398
ENST00000405275CTNNBL1chr2036431450+ENST00000603338TSHZ2chr2051870038+4784137524344391398
ENST00000373473CTNNBL1chr2036431450+ENST00000371497TSHZ2chr2051870038+1215889824639621238
ENST00000373473CTNNBL1chr2036431450+ENST00000603338TSHZ2chr2051870038+430789824639621238
ENST00000373469CTNNBL1chr2036431450+ENST00000371497TSHZ2chr2051870038+117955357835991173
ENST00000373469CTNNBL1chr2036431450+ENST00000603338TSHZ2chr2051870038+39445357835991173

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
ENST00000361383ENST00000371497CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0001773490.9998227
ENST00000361383ENST00000603338CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0012654580.99873453
ENST00000405275ENST00000371497CTNNBL1chr2036431450+TSHZ2chr2051870038+0.000201660.99979836
ENST00000405275ENST00000603338CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0013420580.99865794
ENST00000373473ENST00000371497CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0001858120.9998142
ENST00000373473ENST00000603338CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0014278530.9985721
ENST00000373469ENST00000371497CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0001436710.99985635
ENST00000373469ENST00000603338CTNNBL1chr2036431450+TSHZ2chr2051870038+0.0012971970.99870276

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 CTNNBL1-TSHZ2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CTNNBL1chr2036431450TSHZ2chr20518700381330404KIKKVGTTEKEHEGYAQEEQLKEEEE
CTNNBL1chr2036431450TSHZ2chr20518700381375377KIKKVGTTEKEHEGYAQEEQLKEEEE
CTNNBL1chr2036431450TSHZ2chr2051870038535152KIKKVGTTEKEHEGYAQEEQLKEEEE
CTNNBL1chr2036431450TSHZ2chr2051870038898217KIKKVGTTEKEHEGYAQEEQLKEEEE

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Potential FusionNeoAntigen Information of CTNNBL1-TSHZ2 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.
CTNNBL1-TSHZ2_36431450_51870038.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)
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:01TEKEHEGY0.99580.9491715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B45:01TEKEHEGYA0.93350.8312716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B50:02TEKEHEGYA0.88420.57716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B41:01TEKEHEGYA0.25640.8522716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B50:01TEKEHEGYA0.04250.6353716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B40:01HEGYAQEEQL0.95640.6111121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B41:02HEGYAQEEQL0.84590.52151121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:13HEGYAQEEQL0.64530.98611121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:01EHEGYAQEEQL0.99770.91491021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B38:01EHEGYAQEEQL0.99650.94611021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:24EHEGYAQEEQL0.99620.7091021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B38:02EHEGYAQEEQL0.99520.94661021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B40:06TEKEHEGYA0.95240.6297716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B48:03HEGYAQEEQL0.88040.68971121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:09EHEGYAQEEQL0.99720.84281021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:05EHEGYAQEEQL0.99610.90651021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:08TEKEHEGY0.99640.7893715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:04TEKEHEGY0.9960.9517715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:05TEKEHEGY0.99580.9491715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:06TEKEHEGY0.99480.9513715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:03TEKEHEGY0.99420.9442715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B18:11TEKEHEGY0.99090.9157715
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B50:04TEKEHEGYA0.04250.6353716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B50:05TEKEHEGYA0.04250.6353716
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B40:04HEGYAQEEQL0.97390.88081121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B40:36HEGYAQEEQL0.95970.61271121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B40:49HEGYAQEEQL0.94860.63071121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B40:12HEGYAQEEQL0.88040.68971121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B41:03HEGYAQEEQL0.64130.92871121
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:31EHEGYAQEEQL0.99820.91381021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B38:05EHEGYAQEEQL0.99650.94611021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B39:11EHEGYAQEEQL0.99450.78961021
CTNNBL1-TSHZ2chr2036431450chr20518700381330HLA-B15:09EHEGYAQEEQL0.9740.78961021

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Potential FusionNeoAntigen Information of CTNNBL1-TSHZ2 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.
CTNNBL1-TSHZ2_36431450_51870038.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)
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-0840HEGYAQEEQLKEEEE1126
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-0840EHEGYAQEEQLKEEE1025
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-13101HEGYAQEEQLKEEEE1126
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-13101EHEGYAQEEQLKEEE1025
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-1310HEGYAQEEQLKEEEE1126
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-1310EHEGYAQEEQLKEEE1025
CTNNBL1-TSHZ2chr2036431450chr20518700381330DRB1-1388HEGYAQEEQLKEEEE1126

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Fusion breakpoint peptide structures of CTNNBL1-TSHZ2

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
9685TTEKEHEGYAQEEQCTNNBL1TSHZ2chr2036431450chr20518700381330

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CTNNBL1-TSHZ2

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-B14:023BVN9685TTEKEHEGYAQEEQ-7.9962-8.1096
HLA-B14:023BVN9685TTEKEHEGYAQEEQ-5.70842-6.74372
HLA-B52:013W399685TTEKEHEGYAQEEQ-6.83737-6.95077
HLA-B52:013W399685TTEKEHEGYAQEEQ-4.4836-5.5189
HLA-A11:014UQ29685TTEKEHEGYAQEEQ-10.0067-10.1201
HLA-A11:014UQ29685TTEKEHEGYAQEEQ-9.03915-10.0745
HLA-A24:025HGA9685TTEKEHEGYAQEEQ-6.56204-6.67544
HLA-A24:025HGA9685TTEKEHEGYAQEEQ-5.42271-6.45801
HLA-B44:053DX89685TTEKEHEGYAQEEQ-7.85648-8.89178
HLA-B44:053DX89685TTEKEHEGYAQEEQ-5.3978-5.5112
HLA-A02:016TDR9685TTEKEHEGYAQEEQ-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of CTNNBL1-TSHZ2

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
CTNNBL1-TSHZ2chr2036431450chr20518700381021EHEGYAQEEQLAACATGAAGGCTACGCCCAGGAGGAACAGCTGA
CTNNBL1-TSHZ2chr2036431450chr20518700381121HEGYAQEEQLATGAAGGCTACGCCCAGGAGGAACAGCTGA
CTNNBL1-TSHZ2chr2036431450chr2051870038715TEKEHEGYCTGAGAAGGAACATGAAGGCTACG
CTNNBL1-TSHZ2chr2036431450chr2051870038716TEKEHEGYACTGAGAAGGAACATGAAGGCTACGCCC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
CTNNBL1-TSHZ2chr2036431450chr20518700381025EHEGYAQEEQLKEEEAACATGAAGGCTACGCCCAGGAGGAACAGCTGAAAGAAGAGGAGG
CTNNBL1-TSHZ2chr2036431450chr20518700381126HEGYAQEEQLKEEEEATGAAGGCTACGCCCAGGAGGAACAGCTGAAAGAAGAGGAGGAAA

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Information of the samples that have these potential fusion neoantigens of CTNNBL1-TSHZ2

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
BRCACTNNBL1-TSHZ2chr2036431450ENST00000361383chr2051870038ENST00000371497TCGA-AO-A03M-01B

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Potential target of CAR-T therapy development for CTNNBL1-TSHZ2

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 CTNNBL1-TSHZ2

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 CTNNBL1-TSHZ2

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