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:NRP1-ABI1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NRP1-ABI1
FusionPDB ID: 60338
FusionGDB2.0 ID: 60338
HgeneTgene
Gene symbol

NRP1

ABI1

Gene ID

8829

10006

Gene nameneuropilin 1abl interactor 1
SynonymsBDCA4|CD304|NP1|NRP|VEGF165RABI-1|ABLBP4|E3B1|NAP1BP|SSH3BP|SSH3BP1
Cytomap

10p11.22

10p12.1

Type of geneprotein-codingprotein-coding
Descriptionneuropilin-1transmembrane receptorvascular endothelial cell growth factor 165 receptorabl interactor 1Abelson interactor 1Abl-interactor protein 1 longabl-binding protein 4eps8 SH3 domain-binding proteininteractor protein AblBP4nap1 binding proteinspectrin SH3 domain-binding protein 1
Modification date2020032220200327
UniProtAcc

O14786

Main function of 5'-partner protein: FUNCTION: Cell-surface receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. Mediates the chemorepulsant activity of semaphorins (PubMed:9288753, PubMed:9529250, PubMed:10688880). Recognizes a C-end rule (CendR) motif R/KXXR/K on its ligands which causes cellular internalization and vascular leakage (PubMed:19805273). It binds to semaphorin 3A, the PLGF-2 isoform of PGF, the VEGF165 isoform of VEGFA and VEGFB (PubMed:9288753, PubMed:9529250, PubMed:10688880, PubMed:19805273). Coexpression with KDR results in increased VEGF165 binding to KDR as well as increased chemotaxis. Regulates VEGF-induced angiogenesis. Binding to VEGFA initiates a signaling pathway needed for motor neuron axon guidance and cell body migration, including for the caudal migration of facial motor neurons from rhombomere 4 to rhombomere 6 during embryonic development (By similarity). Regulates mitochondrial iron transport via interaction with ABCB8/MITOSUR (PubMed:30623799). {ECO:0000250|UniProtKB:P97333, ECO:0000269|PubMed:10688880, ECO:0000269|PubMed:19805273, ECO:0000269|PubMed:30623799, ECO:0000269|PubMed:9288753, ECO:0000269|PubMed:9529250}.; FUNCTION: [Isoform 2]: Binds VEGF-165 and may inhibit its binding to cells (PubMed:10748121, PubMed:26503042). May induce apoptosis by sequestering VEGF-165 (PubMed:10748121). May bind as well various members of the semaphorin family. Its expression has an averse effect on blood vessel number and integrity. {ECO:0000269|PubMed:10748121, ECO:0000269|PubMed:26503042}.; FUNCTION: (Microbial infection) Acts as a host factor for human coronavirus SARS-CoV-2 infection. Recognizes and binds to CendR motif RRAR on SARS-CoV-2 spike protein S1 which enhances SARS-CoV-2 infection. {ECO:0000269|PubMed:33082293, ECO:0000269|PubMed:33082294}.

Q8IZP0

Main function of 5'-partner protein: FUNCTION: May act in negative regulation of cell growth and transformation by interacting with nonreceptor tyrosine kinases ABL1 and/or ABL2. May play a role in regulation of EGF-induced Erk pathway activation. Involved in cytoskeletal reorganization and EGFR signaling. Together with EPS8 participates in transduction of signals from Ras to Rac. In vitro, a trimeric complex of ABI1, EPS8 and SOS1 exhibits Rac specific guanine nucleotide exchange factor (GEF) activity and ABI1 seems to act as an adapter in the complex. Regulates ABL1/c-Abl-mediated phosphorylation of ENAH. Recruits WASF1 to lamellipodia and there seems to regulate WASF1 protein level. In brain, seems to regulate the dendritic outgrowth and branching as well as to determine the shape and number of synaptic contacts of developing neurons. {ECO:0000269|PubMed:11003655, ECO:0000269|PubMed:18328268}.
Ensembl transtripts involved in fusion geneENST idsENST00000265371, ENST00000374816, 
ENST00000374821, ENST00000374822, 
ENST00000374823, ENST00000374867, 
ENST00000374875, ENST00000395995, 
ENST00000432372, 		ENST00000473481, 
ENST00000346832, ENST00000376134, 
ENST00000376137, ENST00000376140, 
ENST00000490841, ENST00000536334, 
ENST00000355394, ENST00000359188, 
ENST00000376138, ENST00000376139, 
ENST00000376142, ENST00000376160, 
ENST00000376166, ENST00000376170, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 6=70214 X 8 X 5=560
# samples 1413
** MAII scorelog2(14/702*10)=-2.32604420335959
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/560*10)=-2.10691520391651
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NRP1 [Title/Abstract] AND ABI1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NRP1 [Title/Abstract] AND ABI1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NRP1(33542956)-ABI1(27066170), # samples:1
Anticipated loss of major functional domain due to fusion event.NRP1-ABI1 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.
NRP1-ABI1 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.
NRP1-ABI1 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.
NRP1-ABI1 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.
NRP1-ABI1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
NRP1-ABI1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
NRP1-ABI1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneNRP1

GO:0051894

positive regulation of focal adhesion assembly

24863063

TgeneABI1

GO:0018108

peptidyl-tyrosine phosphorylation

17101133



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/chr10:33542956/chr10:27066170)
- 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 NRP1 (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 ABI1 (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)
ENST00000374867NRP1chr1033542956-ENST00000376170ABI1chr1027066170-455215044272574715
ENST00000374867NRP1chr1033542956-ENST00000359188ABI1chr1027066170-463915044272661744
ENST00000374867NRP1chr1033542956-ENST00000376142ABI1chr1027066170-472315044272745772
ENST00000374867NRP1chr1033542956-ENST00000376139ABI1chr1027066170-462715044272649740
ENST00000374867NRP1chr1033542956-ENST00000376160ABI1chr1027066170-462415044272646739
ENST00000374867NRP1chr1033542956-ENST00000376166ABI1chr1027066170-453715044272559710
ENST00000374867NRP1chr1033542956-ENST00000376138ABI1chr1027066170-455515044272577716
ENST00000374867NRP1chr1033542956-ENST00000355394ABI1chr1027066170-472315044272748773
ENST00000395995NRP1chr1033542956-ENST00000376170ABI1chr1027066170-402998102051683
ENST00000395995NRP1chr1033542956-ENST00000359188ABI1chr1027066170-411698102138712
ENST00000395995NRP1chr1033542956-ENST00000376142ABI1chr1027066170-420098102222740
ENST00000395995NRP1chr1033542956-ENST00000376139ABI1chr1027066170-410498102126708
ENST00000395995NRP1chr1033542956-ENST00000376160ABI1chr1027066170-410198102123707
ENST00000395995NRP1chr1033542956-ENST00000376166ABI1chr1027066170-401498102036678
ENST00000395995NRP1chr1033542956-ENST00000376138ABI1chr1027066170-403298102054684
ENST00000395995NRP1chr1033542956-ENST00000355394ABI1chr1027066170-420098102225741
ENST00000374821NRP1chr1033542956-ENST00000376170ABI1chr1027066170-41691121442191715
ENST00000374821NRP1chr1033542956-ENST00000359188ABI1chr1027066170-42561121442278744
ENST00000374821NRP1chr1033542956-ENST00000376142ABI1chr1027066170-43401121442362772
ENST00000374821NRP1chr1033542956-ENST00000376139ABI1chr1027066170-42441121442266740
ENST00000374821NRP1chr1033542956-ENST00000376160ABI1chr1027066170-42411121442263739
ENST00000374821NRP1chr1033542956-ENST00000376166ABI1chr1027066170-41541121442176710
ENST00000374821NRP1chr1033542956-ENST00000376138ABI1chr1027066170-41721121442194716
ENST00000374821NRP1chr1033542956-ENST00000355394ABI1chr1027066170-43401121442365773
ENST00000374822NRP1chr1033542956-ENST00000376170ABI1chr1027066170-428912411642311715
ENST00000374822NRP1chr1033542956-ENST00000359188ABI1chr1027066170-437612411642398744
ENST00000374822NRP1chr1033542956-ENST00000376142ABI1chr1027066170-446012411642482772
ENST00000374822NRP1chr1033542956-ENST00000376139ABI1chr1027066170-436412411642386740
ENST00000374822NRP1chr1033542956-ENST00000376160ABI1chr1027066170-436112411642383739
ENST00000374822NRP1chr1033542956-ENST00000376166ABI1chr1027066170-427412411642296710
ENST00000374822NRP1chr1033542956-ENST00000376138ABI1chr1027066170-429212411642314716
ENST00000374822NRP1chr1033542956-ENST00000355394ABI1chr1027066170-446012411642485773
ENST00000374823NRP1chr1033542956-ENST00000376170ABI1chr1027066170-402998102051683
ENST00000374823NRP1chr1033542956-ENST00000359188ABI1chr1027066170-411698102138712
ENST00000374823NRP1chr1033542956-ENST00000376142ABI1chr1027066170-420098102222740
ENST00000374823NRP1chr1033542956-ENST00000376139ABI1chr1027066170-410498102126708
ENST00000374823NRP1chr1033542956-ENST00000376160ABI1chr1027066170-410198102123707
ENST00000374823NRP1chr1033542956-ENST00000376166ABI1chr1027066170-401498102036678
ENST00000374823NRP1chr1033542956-ENST00000376138ABI1chr1027066170-403298102054684
ENST00000374823NRP1chr1033542956-ENST00000355394ABI1chr1027066170-420098102225741
ENST00000374816NRP1chr1033542956-ENST00000376170ABI1chr1027066170-41691121442191715
ENST00000374816NRP1chr1033542956-ENST00000359188ABI1chr1027066170-42561121442278744
ENST00000374816NRP1chr1033542956-ENST00000376142ABI1chr1027066170-43401121442362772
ENST00000374816NRP1chr1033542956-ENST00000376139ABI1chr1027066170-42441121442266740
ENST00000374816NRP1chr1033542956-ENST00000376160ABI1chr1027066170-42411121442263739
ENST00000374816NRP1chr1033542956-ENST00000376166ABI1chr1027066170-41541121442176710
ENST00000374816NRP1chr1033542956-ENST00000376138ABI1chr1027066170-41721121442194716
ENST00000374816NRP1chr1033542956-ENST00000355394ABI1chr1027066170-43401121442365773

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
ENST00000374867ENST00000376170NRP1chr1033542956-ABI1chr1027066170-0.0001648480.99983513
ENST00000374867ENST00000359188NRP1chr1033542956-ABI1chr1027066170-0.0001959640.9998041
ENST00000374867ENST00000376142NRP1chr1033542956-ABI1chr1027066170-0.0001820580.999818
ENST00000374867ENST00000376139NRP1chr1033542956-ABI1chr1027066170-0.0001427060.9998573
ENST00000374867ENST00000376160NRP1chr1033542956-ABI1chr1027066170-0.0001610010.99983895
ENST00000374867ENST00000376166NRP1chr1033542956-ABI1chr1027066170-0.0002057260.9997943
ENST00000374867ENST00000376138NRP1chr1033542956-ABI1chr1027066170-0.0001679350.99983203
ENST00000374867ENST00000355394NRP1chr1033542956-ABI1chr1027066170-0.0001969780.999803
ENST00000395995ENST00000376170NRP1chr1033542956-ABI1chr1027066170-0.000133340.9998666
ENST00000395995ENST00000359188NRP1chr1033542956-ABI1chr1027066170-0.0001602970.99983966
ENST00000395995ENST00000376142NRP1chr1033542956-ABI1chr1027066170-0.0001459850.99985397
ENST00000395995ENST00000376139NRP1chr1033542956-ABI1chr1027066170-0.0001176320.99988234
ENST00000395995ENST00000376160NRP1chr1033542956-ABI1chr1027066170-0.0001317230.9998683
ENST00000395995ENST00000376166NRP1chr1033542956-ABI1chr1027066170-0.0001649860.999835
ENST00000395995ENST00000376138NRP1chr1033542956-ABI1chr1027066170-0.0001364170.9998635
ENST00000395995ENST00000355394NRP1chr1033542956-ABI1chr1027066170-0.0001595890.9998404
ENST00000374821ENST00000376170NRP1chr1033542956-ABI1chr1027066170-0.0001423410.99985766
ENST00000374821ENST00000359188NRP1chr1033542956-ABI1chr1027066170-0.0001707030.9998293
ENST00000374821ENST00000376142NRP1chr1033542956-ABI1chr1027066170-0.0001568990.9998431
ENST00000374821ENST00000376139NRP1chr1033542956-ABI1chr1027066170-0.0001264690.9998735
ENST00000374821ENST00000376160NRP1chr1033542956-ABI1chr1027066170-0.0001414430.9998585
ENST00000374821ENST00000376166NRP1chr1033542956-ABI1chr1027066170-0.000175620.99982446
ENST00000374821ENST00000376138NRP1chr1033542956-ABI1chr1027066170-0.0001457330.9998542
ENST00000374821ENST00000355394NRP1chr1033542956-ABI1chr1027066170-0.0001713880.9998286
ENST00000374822ENST00000376170NRP1chr1033542956-ABI1chr1027066170-0.0001585330.99984145
ENST00000374822ENST00000359188NRP1chr1033542956-ABI1chr1027066170-0.0001867360.99981326
ENST00000374822ENST00000376142NRP1chr1033542956-ABI1chr1027066170-0.000173090.99982697
ENST00000374822ENST00000376139NRP1chr1033542956-ABI1chr1027066170-0.0001383530.9998616
ENST00000374822ENST00000376160NRP1chr1033542956-ABI1chr1027066170-0.000155530.99984443
ENST00000374822ENST00000376166NRP1chr1033542956-ABI1chr1027066170-0.000195830.9998042
ENST00000374822ENST00000376138NRP1chr1033542956-ABI1chr1027066170-0.0001620440.9998379
ENST00000374822ENST00000355394NRP1chr1033542956-ABI1chr1027066170-0.0001894330.99981064
ENST00000374823ENST00000376170NRP1chr1033542956-ABI1chr1027066170-0.000133340.9998666
ENST00000374823ENST00000359188NRP1chr1033542956-ABI1chr1027066170-0.0001602970.99983966
ENST00000374823ENST00000376142NRP1chr1033542956-ABI1chr1027066170-0.0001459850.99985397
ENST00000374823ENST00000376139NRP1chr1033542956-ABI1chr1027066170-0.0001176320.99988234
ENST00000374823ENST00000376160NRP1chr1033542956-ABI1chr1027066170-0.0001317230.9998683
ENST00000374823ENST00000376166NRP1chr1033542956-ABI1chr1027066170-0.0001649860.999835
ENST00000374823ENST00000376138NRP1chr1033542956-ABI1chr1027066170-0.0001364170.9998635
ENST00000374823ENST00000355394NRP1chr1033542956-ABI1chr1027066170-0.0001595890.9998404
ENST00000374816ENST00000376170NRP1chr1033542956-ABI1chr1027066170-0.0001423410.99985766
ENST00000374816ENST00000359188NRP1chr1033542956-ABI1chr1027066170-0.0001707030.9998293
ENST00000374816ENST00000376142NRP1chr1033542956-ABI1chr1027066170-0.0001568990.9998431
ENST00000374816ENST00000376139NRP1chr1033542956-ABI1chr1027066170-0.0001264690.9998735
ENST00000374816ENST00000376160NRP1chr1033542956-ABI1chr1027066170-0.0001414430.9998585
ENST00000374816ENST00000376166NRP1chr1033542956-ABI1chr1027066170-0.000175620.99982446
ENST00000374816ENST00000376138NRP1chr1033542956-ABI1chr1027066170-0.0001457330.9998542
ENST00000374816ENST00000355394NRP1chr1033542956-ABI1chr1027066170-0.0001713880.9998286

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 NRP1-ABI1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NRP1chr1033542956ABI1chr10270661701121357NGWTPGEDSYREWIQTVDIHKEKVAR
NRP1chr1033542956ABI1chr10270661701241357NGWTPGEDSYREWIQTVDIHKEKVAR
NRP1chr1033542956ABI1chr10270661701504357NGWTPGEDSYREWIQTVDIHKEKVAR
NRP1chr1033542956ABI1chr1027066170981325NGWTPGEDSYREWIQTVDIHKEKVAR

Top

Potential FusionNeoAntigen Information of NRP1-ABI1 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.
NRP1-ABI1_33542956_27066170.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)
NRP1-ABI1chr1033542956chr10270661701121HLA-B39:06YREWIQTV0.99960.9674917
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:15SYREWIQTV0.9810.6454817
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:20SYREWIQTV0.9810.6311817
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:31SYREWIQTV0.98020.6247817
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:25SYREWIQTV0.980.6328817
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:14SYREWIQTV0.93880.6238817
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:10SYREWIQTV0.90110.5286817
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:17SYREWIQTV0.8860.7037817
NRP1-ABI1chr1033542956chr10270661701121HLA-A31:08SYREWIQTV0.84970.6912817
NRP1-ABI1chr1033542956chr10270661701121HLA-B52:01SYREWIQTV0.61350.9949817
NRP1-ABI1chr1033542956chr10270661701121HLA-B08:09SYREWIQTV0.59050.6295817
NRP1-ABI1chr1033542956chr10270661701121HLA-B39:13REWIQTVDI0.24620.94571019
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:05YREWIQTV0.99890.9692917
NRP1-ABI1chr1033542956chr10270661701121HLA-C12:16YREWIQTV0.83080.9755917
NRP1-ABI1chr1033542956chr10270661701121HLA-B40:06REWIQTVDI0.99850.68511019
NRP1-ABI1chr1033542956chr10270661701121HLA-A24:02SYREWIQTV0.9810.6311817
NRP1-ABI1chr1033542956chr10270661701121HLA-C04:14SYREWIQTV0.73690.9604817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:05SYREWIQTV0.5420.9273817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:19SYREWIQTV0.34220.7897817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:29SYREWIQTV0.34060.9156817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:13SYREWIQTV0.33390.8944817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:80SYREWIQTV0.32690.9332817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:67SYREWIQTV0.32690.9332817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:10SYREWIQTV0.32540.9399817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:46SYREWIQTV0.31320.8792817
NRP1-ABI1chr1033542956chr10270661701121HLA-C12:16SYREWIQTV0.24120.9304817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:95SYREWIQTV0.21960.6711817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:27SYREWIQTV0.20820.9252817
NRP1-ABI1chr1033542956chr10270661701121HLA-B39:08GEDSYREWI0.19670.8546514
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:08YREWIQTV0.9860.9946917
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:17YREWIQTV0.93910.9964917
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:02YREWIQTV0.93910.9964917
NRP1-ABI1chr1033542956chr10270661701121HLA-B40:04REWIQTVDI0.99210.67651019
NRP1-ABI1chr1033542956chr10270661701121HLA-A30:01SYREWIQTV0.88670.8645817
NRP1-ABI1chr1033542956chr10270661701121HLA-C04:04SYREWIQTV0.77440.9637817
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:17SYREWIQTV0.67040.9872817
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:02SYREWIQTV0.67040.9872817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:04SYREWIQTV0.45480.9575817
NRP1-ABI1chr1033542956chr10270661701121HLA-B41:03REWIQTVDI0.45450.60871019
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:06SYREWIQTV0.40290.986817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:22SYREWIQTV0.39240.6064817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:17SYREWIQTV0.36330.9366817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:02SYREWIQTV0.32690.9332817
NRP1-ABI1chr1033542956chr10270661701121HLA-C06:08SYREWIQTV0.30640.9848817
NRP1-ABI1chr1033542956chr10270661701121HLA-C14:03SYREWIQTV0.25830.9441817
NRP1-ABI1chr1033542956chr10270661701121HLA-C14:02SYREWIQTV0.25830.9441817
NRP1-ABI1chr1033542956chr10270661701121HLA-C03:67SYREWIQTV0.250.9886817
NRP1-ABI1chr1033542956chr10270661701121HLA-C07:01SYREWIQTV0.21060.6488817
NRP1-ABI1chr1033542956chr10270661701121HLA-A68:02DSYREWIQTV0.99450.6862717
NRP1-ABI1chr1033542956chr10270661701121HLA-A69:01DSYREWIQTV0.96950.8261717

Top

Potential FusionNeoAntigen Information of NRP1-ABI1 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 NRP1-ABI1

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
1619EDSYREWIQTVDIHNRP1ABI1chr1033542956chr10270661701121

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NRP1-ABI1

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-B14:023BVN1619EDSYREWIQTVDIH-7.9962-8.1096
HLA-B14:023BVN1619EDSYREWIQTVDIH-5.70842-6.74372
HLA-B52:013W391619EDSYREWIQTVDIH-6.83737-6.95077
HLA-B52:013W391619EDSYREWIQTVDIH-4.4836-5.5189
HLA-A11:014UQ21619EDSYREWIQTVDIH-10.0067-10.1201
HLA-A11:014UQ21619EDSYREWIQTVDIH-9.03915-10.0745
HLA-A24:025HGA1619EDSYREWIQTVDIH-6.56204-6.67544
HLA-A24:025HGA1619EDSYREWIQTVDIH-5.42271-6.45801
HLA-B44:053DX81619EDSYREWIQTVDIH-7.85648-8.89178
HLA-B44:053DX81619EDSYREWIQTVDIH-5.3978-5.5112
HLA-A02:016TDR1619EDSYREWIQTVDIH-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of NRP1-ABI1

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
NRP1-ABI1chr1033542956chr10270661701019REWIQTVDITGGATACAGACTGTGGATATTCATAAG
NRP1-ABI1chr1033542956chr1027066170514GEDSYREWIGATTCCTACCGAGAGTGGATACAGACT
NRP1-ABI1chr1033542956chr1027066170717DSYREWIQTVTACCGAGAGTGGATACAGACTGTGGATATT
NRP1-ABI1chr1033542956chr1027066170817SYREWIQTVCGAGAGTGGATACAGACTGTGGATATT
NRP1-ABI1chr1033542956chr1027066170917YREWIQTVGAGTGGATACAGACTGTGGATATT

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 NRP1-ABI1

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
STADNRP1-ABI1chr1033542956ENST00000374816chr1027066170ENST00000355394TCGA-D7-A4Z0-01A

Top

Potential target of CAR-T therapy development for NRP1-ABI1

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 NRP1-ABI1

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

Top

Related Diseases to NRP1-ABI1

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
TgeneABI1C0019193Hepatitis, Toxic1CTD_human
TgeneABI1C0860207Drug-Induced Liver Disease1CTD_human
TgeneABI1C1262760Hepatitis, Drug-Induced1CTD_human
TgeneABI1C3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneABI1C4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneABI1C4279912Chemically-Induced Liver Toxicity1CTD_human