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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:ABI1-PTP4A3 (FusionGDB2 ID:HG10006TG11156)

Fusion Gene Summary for ABI1-PTP4A3

check button Fusion gene summary
Fusion gene informationFusion gene name: ABI1-PTP4A3
Fusion gene ID: hg10006tg11156
HgeneTgene
Gene symbol

ABI1

PTP4A3

Gene ID

10006

11156

Gene nameabl interactor 1protein tyrosine phosphatase 4A3
SynonymsABI-1|ABLBP4|E3B1|NAP1BP|SSH3BP|SSH3BP1PRL-3|PRL-R|PRL3
Cytomap('ABI1')('PTP4A3')

10p12.1

8q24.3

Type of geneprotein-codingprotein-coding
Descriptionabl interactor 1Abelson interactor 1Abl-interactor protein 1 longabl-binding protein 4eps8 SH3 domain-binding proteininteractor protein AblBP4nap1 binding proteinspectrin SH3 domain-binding protein 1protein tyrosine phosphatase type IVA 3phosphatase of regenerating liver 3potentially prenylated protein tyrosine phosphataseprotein tyrosine phosphatase type IVA, member 3protein-tyrosine phosphatase of regenerating liver 3
Modification date2020032720200313
UniProtAcc

Q8IZP0

.
Ensembl transtripts involved in fusion geneENST00000346832, ENST00000355394, 
ENST00000359188, ENST00000376134, 
ENST00000376137, ENST00000376138, 
ENST00000376139, ENST00000376140, 
ENST00000376142, ENST00000376160, 
ENST00000376166, ENST00000376170, 
ENST00000490841, ENST00000536334, 
ENST00000473481, 
Fusion gene scores* DoF score15 X 10 X 8=12005 X 4 X 4=80
# samples 155
** MAII scorelog2(15/1200*10)=-3
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ABI1 [Title/Abstract] AND PTP4A3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointABI1(27112067)-PTP4A3(142431488), # samples:4
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneABI1

GO:0018108

peptidyl-tyrosine phosphorylation

17101133

TgenePTP4A3

GO:0006355

regulation of transcription, DNA-templated

23178297

TgenePTP4A3

GO:1901224

positive regulation of NIK/NF-kappaB signaling

23178297



check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LGGTCGA-TQ-A7RV-01AABI1chr10

27112067

-PTP4A3chr8

142431488

+
ChimerDB4LGGTCGA-TQ-A7RV-02AABI1chr10

27112067

-PTP4A3chr8

142431488

+
ChimerDB4LGGTCGA-TQ-A7RVABI1chr10

27112067

-PTP4A3chr8

142431488

+


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Fusion Gene ORF analysis for ABI1-PTP4A3

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000346832ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000346832ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000355394ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000355394ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000359188ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000359188ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376134ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376134ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376137ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376137ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376138ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376138ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376139ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376139ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376140ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376140ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376142ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376142ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376160ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376160ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376166ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376166ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376170ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000376170ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000490841ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000490841ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000536334ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-5UTRENST00000536334ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000346832ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000346832ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000346832ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000355394ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000355394ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000355394ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000359188ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000359188ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000359188ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376134ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376134ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376134ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376137ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376137ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376137ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376138ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376138ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376138ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376139ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376139ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376139ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376140ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376140ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376140ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376142ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376142ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376142ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376160ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376160ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376160ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376166ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376166ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376166ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376170ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376170ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000376170ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000490841ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000490841ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000490841ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000536334ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000536334ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5CDS-intronENST00000536334ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5UTR-5UTRENST00000473481ENST00000520105ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5UTR-5UTRENST00000473481ENST00000521578ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5UTR-intronENST00000473481ENST00000329397ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5UTR-intronENST00000473481ENST00000349124ABI1chr10

27112067

-PTP4A3chr8

142431488

+
5UTR-intronENST00000473481ENST00000524028ABI1chr10

27112067

-PTP4A3chr8

142431488

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

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

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Fusion Genomic Features for ABI1-PTP4A3


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
ABI1chr1027112066-PTP4A3chr8142431487+2.65E-081
ABI1chr1027112066-PTP4A3chr8142431487+2.65E-081
ABI1chr1027112066-PTP4A3chr8142431487+2.65E-081
ABI1chr1027112066-PTP4A3chr8142431487+2.65E-081
ABI1chr1027112066-PTP4A3chr8142431487+2.65E-081
ABI1chr1027112066-PTP4A3chr8142431487+2.65E-081


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for ABI1-PTP4A3


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/:27112067/:142431488)
- 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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ABI1

Q8IZP0

.
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}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for ABI1-PTP4A3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for ABI1-PTP4A3


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for ABI1-PTP4A3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for ABI1-PTP4A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneABI1C0019193Hepatitis, Toxic1CTD_human
HgeneABI1C0860207Drug-Induced Liver Disease1CTD_human
HgeneABI1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneABI1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneABI1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneABI1C4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC0007102Malignant tumor of colon1CTD_human
TgeneC0009375Colonic Neoplasms1CTD_human