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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:TTLL5-JDP2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TTLL5-JDP2
FusionPDB ID: 95182
FusionGDB2.0 ID: 95182
HgeneTgene
Gene symbol

TTLL5

JDP2

Gene ID

254173

122953

Gene nametubulin tyrosine ligase like 10Jun dimerization protein 2
SynonymsTTLL5JUNDM2
Cytomap

1p36.33

14q24.3

Type of geneprotein-codingprotein-coding
Descriptioninactive polyglycylase TTLL10tubulin tyrosine ligase-like family, member 10tubulin tyrosine ligase-like family, member 5tubulin--tyrosine ligase-like protein 10jun dimerization protein 2progesterone receptor co-activator
Modification date2020031320200313
UniProtAcc.

Q8WYK2

Main function of 5'-partner protein: FUNCTION: Component of the AP-1 transcription factor that represses transactivation mediated by the Jun family of proteins. Involved in a variety of transcriptional responses associated with AP-1 such as UV-induced apoptosis, cell differentiation, tumorigenesis and antitumogeneris. Can also function as a repressor by recruiting histone deacetylase 3/HDAC3 to the promoter region of JUN. May control transcription via direct regulation of the modification of histones and the assembly of chromatin. {ECO:0000269|PubMed:12707301, ECO:0000269|PubMed:12903123, ECO:0000269|PubMed:16026868, ECO:0000269|PubMed:16518400}.
Ensembl transtripts involved in fusion geneENST idsENST00000286650, ENST00000298832, 
ENST00000556977, ENST00000557636, 
ENST00000554510, ENST00000556893, 
ENST00000555422, 
ENST00000559773, 
ENST00000267569, ENST00000419727, 
ENST00000435893, ENST00000437176, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score22 X 22 X 16=77444 X 5 X 4=80
# samples 316
** MAII scorelog2(31/7744*10)=-4.64273883200036
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: TTLL5 [Title/Abstract] AND JDP2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TTLL5 [Title/Abstract] AND JDP2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TTLL5(76259443)-JDP2(75928128), # samples:2
TTLL5(76129566)-JDP2(75904601), # samples:2
Anticipated loss of major functional domain due to fusion event.TTLL5-JDP2 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.
TTLL5-JDP2 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.
TTLL5-JDP2 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.
TTLL5-JDP2 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
HgeneTTLL5

GO:0018094

protein polyglycylation

19524510

TgeneJDP2

GO:0000122

negative regulation of transcription by RNA polymerase II

18671972



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/chr14:76259443/chr14:75928128)
- 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 TTLL5 (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 JDP2 (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)
ENST00000557636TTLL5chr1476259443+ENST00000419727JDP2chr1475928128+4045343121537211168
ENST00000298832TTLL5chr1476259443+ENST00000419727JDP2chr1475928128+3990337620536661153
ENST00000556893TTLL5chr1476259443+ENST00000419727JDP2chr1475928128+25081894432184713
ENST00000554510TTLL5chr1476259443+ENST00000419727JDP2chr1475928128+243118171192107662
ENST00000557636TTLL5chr1476259443-ENST00000419727JDP2chr1475928129+4045343121537211168
ENST00000298832TTLL5chr1476259443-ENST00000419727JDP2chr1475928129+3990337620536661153
ENST00000556893TTLL5chr1476259443-ENST00000419727JDP2chr1475928129+25081894432184713
ENST00000554510TTLL5chr1476259443-ENST00000419727JDP2chr1475928129+243118171192107662

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
ENST00000557636ENST00000419727TTLL5chr1476259443+JDP2chr1475928128+0.0028176780.99718237
ENST00000298832ENST00000419727TTLL5chr1476259443+JDP2chr1475928128+0.0023079990.997692
ENST00000556893ENST00000419727TTLL5chr1476259443+JDP2chr1475928128+0.0118348650.98816514
ENST00000554510ENST00000419727TTLL5chr1476259443+JDP2chr1475928128+0.0309174210.96908253
ENST00000557636ENST00000419727TTLL5chr1476259443-JDP2chr1475928129+0.0028176780.99718237
ENST00000298832ENST00000419727TTLL5chr1476259443-JDP2chr1475928129+0.0023079990.997692
ENST00000556893ENST00000419727TTLL5chr1476259443-JDP2chr1475928129+0.0118348650.98816514
ENST00000554510ENST00000419727TTLL5chr1476259443-JDP2chr1475928129+0.0309174210.96908253

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 TTLL5-JDP2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TTLL5chr1476259443JDP2chr14759281281817565QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr14759281281894616QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr147592812833761056QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr147592812834311071QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr14759281291817565QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr14759281291894616QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr147592812933761056QYSPSSHINLLTQQLDEEEERRKRRR
TTLL5chr1476259443JDP2chr147592812934311071QYSPSSHINLLTQQLDEEEERRKRRR

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Potential FusionNeoAntigen Information of TTLL5-JDP2 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.
TTLL5-JDP2_76259443_75928128.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)
TTLL5-JDP2chr1476259443chr14759281283376HLA-B08:01HINLLTQQL0.38060.8008615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B13:01HINLLTQQL0.17470.9345615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:01SHINLLTQQL0.99920.9639515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:24SHINLLTQQL0.99920.5768515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:06SHINLLTQQL0.99860.7977515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B38:02SHINLLTQQL0.99860.9817515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B38:01SHINLLTQQL0.99850.9767515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B15:10SHINLLTQQL0.9950.6484515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B15:37SHINLLTQQL0.960.7191515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B15:18SHINLLTQQL0.94340.7513515
TTLL5-JDP2chr1476259443chr14759281283376HLA-C03:19HINLLTQQL0.99830.979615
TTLL5-JDP2chr1476259443chr14759281283376HLA-A02:05HINLLTQQL0.90520.5958615
TTLL5-JDP2chr1476259443chr14759281283376HLA-C02:06HINLLTQQL0.74950.9414615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:09SHINLLTQQL0.99920.7661515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:12SHINLLTQQL0.99910.9666515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:05SHINLLTQQL0.99870.9574515
TTLL5-JDP2chr1476259443chr14759281283376HLA-C03:05HINLLTQQL0.99330.9332615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B15:73HINLLTQQL0.71950.885615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B08:12HINLLTQQL0.6830.9197615
TTLL5-JDP2chr1476259443chr14759281283376HLA-C17:01HINLLTQQL0.64350.9191615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B15:30HINLLTQQL0.59310.8103615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B07:13HINLLTQQL0.51880.8132615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B08:18HINLLTQQL0.38060.8008615
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:31SHINLLTQQL0.99930.9639515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B38:05SHINLLTQQL0.99850.9767515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B15:09SHINLLTQQL0.98920.5827515
TTLL5-JDP2chr1476259443chr14759281283376HLA-B39:11SHINLLTQQL0.92310.8566515

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Potential FusionNeoAntigen Information of TTLL5-JDP2 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.
TTLL5-JDP2_76259443_75928128.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)
TTLL5-JDP2chr1476259443chr14759281283376DRB1-0810SSHINLLTQQLDEEE419
TTLL5-JDP2chr1476259443chr14759281283376DRB1-0812SSHINLLTQQLDEEE419
TTLL5-JDP2chr1476259443chr14759281283376DRB1-0832SSHINLLTQQLDEEE419
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0101HINLLTQQLDEEEER621
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0101SHINLLTQQLDEEEE520
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0101INLLTQQLDEEEERR722
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0103HINLLTQQLDEEEER621
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0103SHINLLTQQLDEEEE520
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0103INLLTQQLDEEEERR722
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0104HINLLTQQLDEEEER621
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0104SHINLLTQQLDEEEE520
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0106HINLLTQQLDEEEER621
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0106SHINLLTQQLDEEEE520
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0106INLLTQQLDEEEERR722
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0107HINLLTQQLDEEEER621
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0107SHINLLTQQLDEEEE520
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0107INLLTQQLDEEEERR722
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0108HINLLTQQLDEEEER621
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0108SHINLLTQQLDEEEE520
TTLL5-JDP2chr1476259443chr14759281283376DRB4-0108INLLTQQLDEEEERR722

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Fusion breakpoint peptide structures of TTLL5-JDP2

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
3370HINLLTQQLDEEEETTLL5JDP2chr1476259443chr14759281283376

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TTLL5-JDP2

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-B14:023BVN3370HINLLTQQLDEEEE-7.9962-8.1096
HLA-B14:023BVN3370HINLLTQQLDEEEE-5.70842-6.74372
HLA-B52:013W393370HINLLTQQLDEEEE-6.83737-6.95077
HLA-B52:013W393370HINLLTQQLDEEEE-4.4836-5.5189
HLA-A11:014UQ23370HINLLTQQLDEEEE-10.0067-10.1201
HLA-A11:014UQ23370HINLLTQQLDEEEE-9.03915-10.0745
HLA-A24:025HGA3370HINLLTQQLDEEEE-6.56204-6.67544
HLA-A24:025HGA3370HINLLTQQLDEEEE-5.42271-6.45801
HLA-B44:053DX83370HINLLTQQLDEEEE-7.85648-8.89178
HLA-B44:053DX83370HINLLTQQLDEEEE-5.3978-5.5112
HLA-A02:016TDR3370HINLLTQQLDEEEE-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of TTLL5-JDP2

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
TTLL5-JDP2chr1476259443chr1475928128515SHINLLTQQLCACATCAACCTCCTCACCCAACAGCTAGAT
TTLL5-JDP2chr1476259443chr1475928128615HINLLTQQLATCAACCTCCTCACCCAACAGCTAGAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
TTLL5-JDP2chr1476259443chr1475928128419SSHINLLTQQLDEEEAGCCACATCAACCTCCTCACCCAACAGCTAGATGAGGAAGAGGAG
TTLL5-JDP2chr1476259443chr1475928128520SHINLLTQQLDEEEECACATCAACCTCCTCACCCAACAGCTAGATGAGGAAGAGGAGCGA
TTLL5-JDP2chr1476259443chr1475928128621HINLLTQQLDEEEERATCAACCTCCTCACCCAACAGCTAGATGAGGAAGAGGAGCGAAGG
TTLL5-JDP2chr1476259443chr1475928128722INLLTQQLDEEEERRAACCTCCTCACCCAACAGCTAGATGAGGAAGAGGAGCGAAGGAAA

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Information of the samples that have these potential fusion neoantigens of TTLL5-JDP2

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
ESCATTLL5-JDP2chr1476259443ENST00000298832chr1475928128ENST00000419727TCGA-L5-A4OQ

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Potential target of CAR-T therapy development for TTLL5-JDP2

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 TTLL5-JDP2

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 TTLL5-JDP2

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