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:ITPR3-PPIL1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ITPR3-PPIL1
FusionPDB ID: 40724
FusionGDB2.0 ID: 40724
HgeneTgene
Gene symbol

ITPR3

PPIL1

Gene ID

3710

51645

Gene nameinositol 1,4,5-trisphosphate receptor type 3peptidylprolyl isomerase like 1
SynonymsIP3R|IP3R3CGI-124|CYPL1|PPIase|hCyPX
Cytomap

6p21.31

6p21.2

Type of geneprotein-codingprotein-coding
Descriptioninositol 1,4,5-trisphosphate receptor type 3IP3 receptorinositol 1,4,5-triphosphate receptor, type 3insP3R3type 3 InsP3 receptorpeptidyl-prolyl cis-trans isomerase-like 1cyclophilin like 1cyclophilin-related gene 1peptidyl-prolyl cis-trans isomerasepeptidylprolyl isomerase (cyclophilin)-like 1rotamase PPIL1
Modification date2020031320200313
UniProtAcc

Q14573

Main function of 5'-partner protein: FUNCTION: Receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium.
.
Ensembl transtripts involved in fusion geneENST idsENST00000374316, ENST00000605930, 
ENST00000483552, ENST00000373699, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 13 X 8=14562 X 1 X 2=4
# samples 152
** MAII scorelog2(15/1456*10)=-3.27897594970282
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/4*10)=2.32192809488736
Fusion gene context

PubMed: ITPR3 [Title/Abstract] AND PPIL1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ITPR3 [Title/Abstract] AND PPIL1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ITPR3(33589468)-PPIL1(36839648), # samples:1
Anticipated loss of major functional domain due to fusion event.ITPR3-PPIL1 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.
ITPR3-PPIL1 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.
ITPR3-PPIL1 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.
ITPR3-PPIL1 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
HgeneITPR3

GO:0051592

response to calcium ion

19052258

TgenePPIL1

GO:0000398

mRNA splicing, via spliceosome

28076346

TgenePPIL1

GO:0000413

protein peptidyl-prolyl isomerization

16595688|20676357



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/chr6:33589468/chr6:36839648)
- 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 ITPR3 (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 PPIL1 (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)
ENST00000374316ITPR3chr633589468+ENST00000373699PPIL1chr636839648-258011491695865276
ENST00000605930ITPR3chr633589468+ENST00000373699PPIL1chr636839648-1739308219752177

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
ENST00000374316ENST00000373699ITPR3chr633589468+PPIL1chr636839648-0.0084906130.99150944
ENST00000605930ENST00000373699ITPR3chr633589468+PPIL1chr636839648-0.0026107880.99738926

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 ITPR3-PPIL1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ITPR3chr633589468PPIL1chr63683964830830AEGSVNGFISTLGMGIIVLELYWKHA

Top

Potential FusionNeoAntigen Information of ITPR3-PPIL1 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.
ITPR3-PPIL1_33589468_36839648.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)
ITPR3-PPIL1chr633589468chr636839648308HLA-A02:04GMGIIVLEL0.93860.63551221
ITPR3-PPIL1chr633589468chr636839648308HLA-A69:01STLGMGIIV0.95250.6481918

Top

Potential FusionNeoAntigen Information of ITPR3-PPIL1 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 ITPR3-PPIL1

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
2774GFISTLGMGIIVLEITPR3PPIL1chr633589468chr636839648308

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ITPR3-PPIL1

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-B14:023BVN2774GFISTLGMGIIVLE-7.75776-7.86956
HLA-B14:023BVN2774GFISTLGMGIIVLE-4.52646-5.56956
HLA-B52:013W392774GFISTLGMGIIVLE-7.1873-7.2991
HLA-B52:013W392774GFISTLGMGIIVLE-2.81174-3.85484
HLA-A11:014UQ22774GFISTLGMGIIVLE-5.13576-5.24756
HLA-A24:025HGA2774GFISTLGMGIIVLE-8.42076-8.53256
HLA-A24:025HGA2774GFISTLGMGIIVLE-7.10496-8.14806
HLA-B27:056PYJ2774GFISTLGMGIIVLE-9.28296-9.39476
HLA-B44:053DX82774GFISTLGMGIIVLE-6.88262-6.99442
HLA-B44:053DX82774GFISTLGMGIIVLE-5.46822-6.51132

Top

Vaccine Design for the FusionNeoAntigens of ITPR3-PPIL1

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
ITPR3-PPIL1chr633589468chr6368396481221GMGIIVLELGGGCATGGGAATCATTGTGCTGGAGCT
ITPR3-PPIL1chr633589468chr636839648918STLGMGIIVCAGCACTTTGGGCATGGGAATCATTGT

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 ITPR3-PPIL1

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
READITPR3-PPIL1chr633589468ENST00000605930chr636839648ENST00000373699TCGA-AG-3587

Top

Potential target of CAR-T therapy development for ITPR3-PPIL1

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 ITPR3-PPIL1

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

Top

Related Diseases to ITPR3-PPIL1

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