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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:PTPRZ1-RCHY1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTPRZ1-RCHY1
FusionPDB ID: 70589
FusionGDB2.0 ID: 70589
HgeneTgene
Gene symbol

PTPRZ1

RCHY1

Gene ID

5803

25898

Gene nameprotein tyrosine phosphatase receptor type Z1ring finger and CHY zinc finger domain containing 1
SynonymsHPTPZ|HPTPzeta|PTP-ZETA|PTP18|PTPRZ|PTPZ|R-PTP-zeta-2|RPTPB|RPTPbeta|phosphacanARNIP|CHIMP|PIRH2|PRO1996|RNF199|ZCHY|ZNF363
Cytomap

7q31.32

4q21.1

Type of geneprotein-codingprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase zetaprotein tyrosine phosphatase, receptor-type, Z polypeptide 1protein tyrosine phosphatase, receptor-type, zeta polypeptide 1protein-tyrosine phosphatase receptor type Z polypeptide 2receptor-type tyrosine RING finger and CHY zinc finger domain-containing protein 1CH-rich interacting match with PLAG1E3 ubiquitin-protein ligase Pirh2RING finger protein 199RING-type E3 ubiquitin transferase RCHY1androgen-receptor N-terminal-interacting proteinp53-induce
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000393386, ENST00000449182, 
ENST00000483028, 
ENST00000380840, 
ENST00000451788, ENST00000512706, 
ENST00000513257, ENST00000514021, 
ENST00000324439, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 14 X 7=14704 X 4 X 3=48
# samples 194
** MAII scorelog2(19/1470*10)=-2.95174483139278
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PTPRZ1 [Title/Abstract] AND RCHY1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PTPRZ1 [Title/Abstract] AND RCHY1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PTPRZ1(121671613)-RCHY1(76407876), # samples:1
Anticipated loss of major functional domain due to fusion event.PTPRZ1-RCHY1 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.
PTPRZ1-RCHY1 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.
PTPRZ1-RCHY1 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.
PTPRZ1-RCHY1 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
TgeneRCHY1

GO:0006511

ubiquitin-dependent protein catabolic process

19483087

TgeneRCHY1

GO:0016567

protein ubiquitination

19043414|19483087

TgeneRCHY1

GO:0031398

positive regulation of protein ubiquitination

19483087

TgeneRCHY1

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

19483087



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/chr7:121671613/chr4:76407876)
- 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 PTPRZ1 (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 RCHY1 (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)
ENST00000393386PTPRZ1chr7121671613+ENST00000324439RCHY1chr476407876-9207557719257051837
ENST00000449182PTPRZ1chr7121671613+ENST00000324439RCHY1chr476407876-63552725912853920

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
ENST00000393386ENST00000324439PTPRZ1chr7121671613+RCHY1chr476407876-0.0002108920.9997892
ENST00000449182ENST00000324439PTPRZ1chr7121671613+RCHY1chr476407876-6.41E-050.999936

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 PTPRZ1-RCHY1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PTPRZ1chr7121671613RCHY1chr4764078762725876VADLHASSGFTEEFEILCNDCNGRST

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Potential FusionNeoAntigen Information of PTPRZ1-RCHY1 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.
PTPRZ1-RCHY1_121671613_76407876.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)
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B15:17ASSGFTEEF0.9950.9712514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B15:16ASSGFTEEF0.99290.7976514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B46:01ASSGFTEEF0.98670.6466514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B58:01ASSGFTEEF0.98270.9803514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B58:02ASSGFTEEF0.97750.9794514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B57:03ASSGFTEEF0.96510.994514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-A32:13ASSGFTEEF0.65830.9833514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B46:01HASSGFTEEF0.99840.6633414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B35:08HASSGFTEEF0.99190.8938414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B35:01HASSGFTEEF0.9720.9032414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B15:18LHASSGFTEEF0.99910.9091314
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B38:01LHASSGFTEEF0.99870.9958314
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B38:02LHASSGFTEEF0.99860.9961314
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C08:15FTEEFEIL10.9811917
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C15:04ASSGFTEEF0.98380.9812514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B15:05ASSGFTEEF0.96590.9385514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C12:12ASSGFTEEF0.85510.9764514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C06:03ASSGFTEEF0.83690.9984514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C12:04ASSGFTEEF0.83370.9985514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C03:14ASSGFTEEF0.78910.9956514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C02:06ASSGFTEEF0.24730.9842514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C08:02FTEEFEIL10.9811917
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C03:02ASSGFTEEF0.99740.9794514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B57:04ASSGFTEEF0.9960.8958514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B57:02ASSGFTEEF0.99090.9802514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B58:06ASSGFTEEF0.9880.9713514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C15:09ASSGFTEEF0.98380.9812514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B35:28ASSGFTEEF0.96650.9506514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-A32:01ASSGFTEEF0.9360.9905514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C12:02ASSGFTEEF0.9110.9901514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C16:04ASSGFTEEF0.90780.9948514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C16:01ASSGFTEEF0.83750.9932514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C16:02ASSGFTEEF0.74530.9979514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C02:10ASSGFTEEF0.25220.9909514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C02:02ASSGFTEEF0.25220.9909514
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C03:02HASSGFTEEF0.99960.9851414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B15:08HASSGFTEEF0.99770.9267414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B35:43HASSGFTEEF0.99710.9244414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B57:02HASSGFTEEF0.99650.9802414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C02:10HASSGFTEEF0.98810.9887414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-C02:02HASSGFTEEF0.98810.9887414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B35:77HASSGFTEEF0.9720.9032414
PTPRZ1-RCHY1chr7121671613chr4764078762725HLA-B38:05LHASSGFTEEF0.99870.9958314

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Potential FusionNeoAntigen Information of PTPRZ1-RCHY1 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)

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Fusion breakpoint peptide structures of PTPRZ1-RCHY1

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
9007SSGFTEEFEILCNDPTPRZ1RCHY1chr7121671613chr4764078762725

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRZ1-RCHY1

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-B14:023BVN9007SSGFTEEFEILCND-6.28876-6.31676
HLA-B14:023BVN9007SSGFTEEFEILCND-4.7105-6.5322
HLA-B52:013W399007SSGFTEEFEILCND-6.28475-8.10645
HLA-B52:013W399007SSGFTEEFEILCND-4.78578-4.81378
HLA-A24:025HGA9007SSGFTEEFEILCND-5.63112-5.65912
HLA-A24:025HGA9007SSGFTEEFEILCND-4.07067-5.89237
HLA-B44:053DX89007SSGFTEEFEILCND-3.29636-3.32436
HLA-B44:053DX89007SSGFTEEFEILCND-3.25499-5.07669

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Vaccine Design for the FusionNeoAntigens of PTPRZ1-RCHY1

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
PTPRZ1-RCHY1chr7121671613chr476407876314LHASSGFTEEFGCAAGTAGTGGGTTTACTGAAGAATTTGAGATT
PTPRZ1-RCHY1chr7121671613chr476407876414HASSGFTEEFAGTAGTGGGTTTACTGAAGAATTTGAGATT
PTPRZ1-RCHY1chr7121671613chr476407876514ASSGFTEEFAGTGGGTTTACTGAAGAATTTGAGATT
PTPRZ1-RCHY1chr7121671613chr476407876917FTEEFEILGAAGAATTTGAGATTCTCTGCAAT

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

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Information of the samples that have these potential fusion neoantigens of PTPRZ1-RCHY1

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
GBMPTPRZ1-RCHY1chr7121671613ENST00000449182chr476407876ENST00000324439TCGA-76-4928-01B

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Potential target of CAR-T therapy development for PTPRZ1-RCHY1

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
HgenePTPRZ1chr7:121671613chr4:76407876ENST00000393386+15301637_166217222316.0TransmembraneHelical

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 PTPRZ1-RCHY1

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 PTPRZ1-RCHY1

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