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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:ACTR3B-PTPRN2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ACTR3B-PTPRN2
FusionPDB ID: 1847
FusionGDB2.0 ID: 1847
HgeneTgene
Gene symbol

ACTR3B

PTPRN2

Gene ID

57180

5799

Gene nameactin related protein 3Bprotein tyrosine phosphatase receptor type N2
SynonymsARP11|ARP3BETAIA-2beta|IAR|ICAAR|PTPRP|R-PTP-N2
Cytomap

7q36.1-q36.2

7q36.3

Type of geneprotein-codingprotein-coding
Descriptionactin-related protein 3BARP3 actin related protein 3 homolog BARP3-betaactin-like protein 3Bactin-related protein 3-betaactin-related protein ARP4actin-related protein Arp11receptor-type tyrosine-protein phosphatase N2IAR/receptor-like protein-tyrosine phosphataseislet cell autoantigen-related proteinphogrinprotein tyrosine phosphatase receptor piprotein tyrosine phosphatase, receptor type, N polypeptide 2tyrosine phos
Modification date2020031320200313
UniProtAcc

Q9P1U1

Main function of 5'-partner protein: FUNCTION: Plays a role in the organization of the actin cytoskeleton. May function as ATP-binding component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks. May decrease the metastatic potential of tumors. {ECO:0000269|PubMed:14651955}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000256001, ENST00000377776, 
ENST00000397282, ENST00000537264, 
ENST00000488782, 		ENST00000389413, 
ENST00000389416, ENST00000389418, 
ENST00000404321, ENST00000409483, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 4 X 4=9616 X 17 X 9=2448
# samples 624
** MAII scorelog2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(24/2448*10)=-3.35049724708413
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ACTR3B [Title/Abstract] AND PTPRN2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ACTR3B [Title/Abstract] AND PTPRN2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ACTR3B(152522207)-PTPRN2(157388007), # samples:2
Anticipated loss of major functional domain due to fusion event.ACTR3B-PTPRN2 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.
ACTR3B-PTPRN2 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.
ACTR3B-PTPRN2 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.
ACTR3B-PTPRN2 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


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/chr7:152522207/chr7:157388007)
- 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 ACTR3B (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 PTPRN2 (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)
ENST00000377776ACTR3Bchr7152522207+ENST00000389413PTPRN2chr7157388007-33731085471714555
ENST00000377776ACTR3Bchr7152522207+ENST00000409483PTPRN2chr7157388007-33731085471714555
ENST00000377776ACTR3Bchr7152522207+ENST00000389416PTPRN2chr7157388007-33681085471714555
ENST00000377776ACTR3Bchr7152522207+ENST00000389418PTPRN2chr7157388007-33631085471714555
ENST00000377776ACTR3Bchr7152522207+ENST00000404321PTPRN2chr7157388007-17151085471714556
ENST00000256001ACTR3Bchr7152522207+ENST00000389413PTPRN2chr7157388007-33731085471714555
ENST00000256001ACTR3Bchr7152522207+ENST00000409483PTPRN2chr7157388007-33731085471714555
ENST00000256001ACTR3Bchr7152522207+ENST00000389416PTPRN2chr7157388007-33681085471714555
ENST00000256001ACTR3Bchr7152522207+ENST00000389418PTPRN2chr7157388007-33631085471714555
ENST00000256001ACTR3Bchr7152522207+ENST00000404321PTPRN2chr7157388007-17151085471714556
ENST00000397282ACTR3Bchr7152522207+ENST00000389413PTPRN2chr7157388007-32789901921619475
ENST00000397282ACTR3Bchr7152522207+ENST00000409483PTPRN2chr7157388007-32789901921619475
ENST00000397282ACTR3Bchr7152522207+ENST00000389416PTPRN2chr7157388007-32739901921619475
ENST00000397282ACTR3Bchr7152522207+ENST00000389418PTPRN2chr7157388007-32689901921619475
ENST00000397282ACTR3Bchr7152522207+ENST00000404321PTPRN2chr7157388007-16209901921619475
ENST00000537264ACTR3Bchr7152522207+ENST00000389413PTPRN2chr7157388007-31688801091509466
ENST00000537264ACTR3Bchr7152522207+ENST00000409483PTPRN2chr7157388007-31688801091509466
ENST00000537264ACTR3Bchr7152522207+ENST00000389416PTPRN2chr7157388007-31638801091509466
ENST00000537264ACTR3Bchr7152522207+ENST00000389418PTPRN2chr7157388007-31588801091509466
ENST00000537264ACTR3Bchr7152522207+ENST00000404321PTPRN2chr7157388007-15108801091509467

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
ENST00000377776ENST00000389413ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023800680.9976199
ENST00000377776ENST00000409483ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023800680.9976199
ENST00000377776ENST00000389416ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023924840.99760747
ENST00000377776ENST00000389418ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023834220.99761665
ENST00000377776ENST00000404321ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0039194340.9960806
ENST00000256001ENST00000389413ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023800680.9976199
ENST00000256001ENST00000409483ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023800680.9976199
ENST00000256001ENST00000389416ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023924840.99760747
ENST00000256001ENST00000389418ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0023834220.99761665
ENST00000256001ENST00000404321ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0039194340.9960806
ENST00000397282ENST00000389413ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0012854480.99871457
ENST00000397282ENST00000409483ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0012854480.99871457
ENST00000397282ENST00000389416ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0012844950.9987155
ENST00000397282ENST00000389418ACTR3Bchr7152522207+PTPRN2chr7157388007-0.001289850.99871016
ENST00000397282ENST00000404321ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0017387660.9982613
ENST00000537264ENST00000389413ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0013751410.9986249
ENST00000537264ENST00000409483ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0013751410.9986249
ENST00000537264ENST00000389416ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0013715760.9986285
ENST00000537264ENST00000389418ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0013783850.9986216
ENST00000537264ENST00000404321ACTR3Bchr7152522207+PTPRN2chr7157388007-0.0019475950.9980525

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 ACTR3B-PTPRN2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ACTR3Bchr7152522207PTPRN2chr7157388007108514RAGLAGGGADGDGALSGCRRGRAPRV
ACTR3Bchr7152522207PTPRN2chr7157388007880257QNCPIDVRRPLYKMDHDPRNPAYIAT
ACTR3Bchr7152522207PTPRN2chr7157388007990266QNCPIDVRRPLYKMDHDPRNPAYIAT

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Potential FusionNeoAntigen Information of ACTR3B-PTPRN2 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.
ACTR3B-PTPRN2_152522207_157388007.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)
ACTR3B-PTPRN2chr7152522207chr71573880071085HLA-C08:15GADGDGAL0.99990.9895715
ACTR3B-PTPRN2chr7152522207chr71573880071085HLA-C08:02GADGDGAL0.99990.9895715
ACTR3B-PTPRN2chr7152522207chr7157388007990HLA-A25:01DVRRPLYKM0.97550.5243514

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Potential FusionNeoAntigen Information of ACTR3B-PTPRN2 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.
ACTR3B-PTPRN2_152522207_157388007.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)
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0401RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0401RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0401VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0401PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0407RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0407RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0409RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0409RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0409VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0409PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0419RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0419RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0422RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0422RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0431RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0433RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0433RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0433VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0433PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0434RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0434RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0434VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0434PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0435RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0435RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0435VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0435PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0438RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0438RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0438VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0438PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0461RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0461RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0462RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0462RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0462VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0462PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0463RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0463RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0463VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0463PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0464RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0464RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0464VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0464PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0466RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0466RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0466VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0472RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0472RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0472VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0472PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0474RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0474RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0474VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0474PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0475RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0475RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0476RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0476RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0476VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0476PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0487RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB1-0487RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0202RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0202RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0205RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0205RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0210RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0210RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0211RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0212RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0212RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0213RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0213RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0213VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0213PLYKMDHDPRNPAYI924
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0215RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0215RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0216RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0217RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0217RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0217VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0218RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0218RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0219RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0219RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0219VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0220RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0220RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0222RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0222RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0222VRRPLYKMDHDPRNP621
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0223RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0223RRPLYKMDHDPRNPA722
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0225RPLYKMDHDPRNPAY823
ACTR3B-PTPRN2chr7152522207chr7157388007990DRB3-0225RRPLYKMDHDPRNPA722

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Fusion breakpoint peptide structures of ACTR3B-PTPRN2

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
2792GGADGDGALSGCRRACTR3BPTPRN2chr7152522207chr71573880071085
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
10246VRRPLYKMDHDPRNACTR3BPTPRN2chr7152522207chr7157388007990

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ACTR3B-PTPRN2

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-B14:023BVN2792GGADGDGALSGCRR-5.16857-5.28197
HLA-B14:023BVN2792GGADGDGALSGCRR-4.21097-5.24627
HLA-B52:013W392792GGADGDGALSGCRR-4.32839-4.44179
HLA-B52:013W392792GGADGDGALSGCRR-4.10962-5.14492
HLA-A24:025HGA2792GGADGDGALSGCRR-6.03661-6.15001
HLA-A24:025HGA2792GGADGDGALSGCRR-5.99594-7.03124
HLA-B44:053DX82792GGADGDGALSGCRR-6.27779-6.39119
HLA-B44:053DX82792GGADGDGALSGCRR-4.76488-5.80018
HLA-B14:023BVN10246VRRPLYKMDHDPRN-7.9962-8.1096
HLA-B14:023BVN10246VRRPLYKMDHDPRN-5.70842-6.74372
HLA-B52:013W3910246VRRPLYKMDHDPRN-6.83737-6.95077
HLA-B52:013W3910246VRRPLYKMDHDPRN-4.4836-5.5189
HLA-A11:014UQ210246VRRPLYKMDHDPRN-10.0067-10.1201
HLA-A11:014UQ210246VRRPLYKMDHDPRN-9.03915-10.0745
HLA-A24:025HGA10246VRRPLYKMDHDPRN-6.56204-6.67544
HLA-A24:025HGA10246VRRPLYKMDHDPRN-5.42271-6.45801
HLA-B44:053DX810246VRRPLYKMDHDPRN-7.85648-8.89178
HLA-B44:053DX810246VRRPLYKMDHDPRN-5.3978-5.5112
HLA-B35:011A1N10246VRRPLYKMDHDPRN-6.27422-6.38762
HLA-B35:011A1N10246VRRPLYKMDHDPRN-5.27424-6.30954
HLA-A02:016TDR10246VRRPLYKMDHDPRN-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ACTR3B-PTPRN2

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
ACTR3B-PTPRN2chr7152522207chr7157388007514DVRRPLYKMGATGTGCGGCGCCCGCTGTATAAGATG
ACTR3B-PTPRN2chr7152522207chr7157388007715GADGDGALCGGCGCCCGCTGTATAAGATGGAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ACTR3B-PTPRN2chr7152522207chr7157388007621VRRPLYKMDHDPRNPGTGCGGCGCCCGCTGTATAAGATGGATCACGACCCGAGGAACCCC
ACTR3B-PTPRN2chr7152522207chr7157388007722RRPLYKMDHDPRNPACGGCGCCCGCTGTATAAGATGGATCACGACCCGAGGAACCCCGCG
ACTR3B-PTPRN2chr7152522207chr7157388007823RPLYKMDHDPRNPAYCGCCCGCTGTATAAGATGGATCACGACCCGAGGAACCCCGCGTAC
ACTR3B-PTPRN2chr7152522207chr7157388007924PLYKMDHDPRNPAYICCGCTGTATAAGATGGATCACGACCCGAGGAACCCCGCGTACATC

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Information of the samples that have these potential fusion neoantigens of ACTR3B-PTPRN2

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
BRCAACTR3B-PTPRN2chr7152522207ENST00000256001chr7157388007ENST00000389413TCGA-C8-A12Q-01A
BRCAACTR3B-PTPRN2chr7152522207ENST00000397282chr7157388007ENST00000389413TCGA-C8-A12Q-01A

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Potential target of CAR-T therapy development for ACTR3B-PTPRN2

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 ACTR3B-PTPRN2

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 ACTR3B-PTPRN2

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