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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:ARFGEF2-NCOA3 (FusionGDB2 ID:HG10564TG8202)

Fusion Gene Summary for ARFGEF2-NCOA3

check button Fusion gene summary
Fusion gene informationFusion gene name: ARFGEF2-NCOA3
Fusion gene ID: hg10564tg8202
HgeneTgene
Gene symbol

ARFGEF2

NCOA3

Gene ID

10564

8202

Gene nameADP ribosylation factor guanine nucleotide exchange factor 2nuclear receptor coactivator 3
SynonymsBIG2|PVNH2|dJ1164I10.1ACTR|AIB-1|AIB1|CAGH16|CTG26|KAT13B|RAC3|SRC-3|SRC3|TNRC14|TNRC16|TRAM-1|bHLHe42|pCIP
Cytomap('ARFGEF2')('NCOA3')

20q13.13

20q13.12

Type of geneprotein-codingprotein-coding
Descriptionbrefeldin A-inhibited guanine nucleotide-exchange protein 2ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)brefeldin A-inhibited GEP 2nuclear receptor coactivator 3CBP-interacting proteinamplified in breast cancer 1 proteinclass E basic helix-loop-helix protein 42receptor-associated coactivator 3steroid receptor coactivator protein 3thyroid hormone receptor activator molecule 1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000371917, ENST00000493140, 
Fusion gene scores* DoF score15 X 13 X 9=175514 X 13 X 5=910
# samples 1515
** MAII scorelog2(15/1755*10)=-3.54843662469604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(15/910*10)=-2.60090404459018
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARFGEF2 [Title/Abstract] AND NCOA3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARFGEF2(47580435)-NCOA3(46211927), # samples:2
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
HgeneARFGEF2

GO:0001881

receptor recycling

16477018

HgeneARFGEF2

GO:0035556

intracellular signal transduction

12571360

TgeneNCOA3

GO:0045944

positive regulation of transcription by RNA polymerase II

9267036

TgeneNCOA3

GO:0071392

cellular response to estradiol stimulus

15831516



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
ChimerDB4BRCATCGA-A8-A09D-01AARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
ChimerDB4BRCATCGA-A8-A09D-01AARFGEF2chr20

47582560

+NCOA3chr20

46211927

+


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Fusion Gene ORF analysis for ARFGEF2-NCOA3

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-5UTRENST00000371917ENST00000341724ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000341724ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000371997ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000371997ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000371998ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000371998ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000372004ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
5CDS-5UTRENST00000371917ENST00000372004ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
5CDS-intronENST00000371917ENST00000497292ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
5CDS-intronENST00000371917ENST00000497292ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000341724ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000341724ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000371997ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000371997ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000371998ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000371998ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000372004ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
intron-5UTRENST00000493140ENST00000372004ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+
intron-intronENST00000493140ENST00000497292ARFGEF2chr20

47580435

+NCOA3chr20

46211927

+
intron-intronENST00000493140ENST00000497292ARFGEF2chr20

47582560

+NCOA3chr20

46211927

+

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 ARFGEF2-NCOA3


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)
ARFGEF2chr2047582560+NCOA3chr2046211926+1.28E-050.99998724
ARFGEF2chr2047580435+NCOA3chr2046211926+3.61E-081
ARFGEF2chr2047582560+NCOA3chr2046211926+1.28E-050.99998724
ARFGEF2chr2047580435+NCOA3chr2046211926+3.61E-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 ARFGEF2-NCOA3


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/:47580435/:46211927)
- 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
..
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}.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 ARFGEF2-NCOA3


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 ARFGEF2-NCOA3


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 ARFGEF2-NCOA3


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 ARFGEF2-NCOA3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARFGEF2C1842563Heterotopia, Periventricular, Autosomal Recessive3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneARFGEF2C1868720Periventricular Nodular Heterotopia2GENOMICS_ENGLAND;ORPHANET
TgeneC0023418leukemia2CTD_human
TgeneC0033578Prostatic Neoplasms2CTD_human
TgeneC0376358Malignant neoplasm of prostate2CTD_human
TgeneC0001418Adenocarcinoma1CTD_human
TgeneC0004114Astrocytoma1CTD_human
TgeneC0005967Bone neoplasms1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneC0205643Carcinoma, Cribriform1CTD_human
TgeneC0205644Carcinoma, Granular Cell1CTD_human
TgeneC0205645Adenocarcinoma, Tubular1CTD_human
TgeneC0205768Subependymal Giant Cell Astrocytoma1CTD_human
TgeneC0279530Malignant Bone Neoplasm1CTD_human
TgeneC0280783Juvenile Pilocytic Astrocytoma1CTD_human
TgeneC0280785Diffuse Astrocytoma1CTD_human
TgeneC0334579Anaplastic astrocytoma1CTD_human
TgeneC0334580Protoplasmic astrocytoma1CTD_human
TgeneC0334581Gemistocytic astrocytoma1CTD_human
TgeneC0334582Fibrillary Astrocytoma1CTD_human
TgeneC0334583Pilocytic Astrocytoma1CTD_human
TgeneC0338070Childhood Cerebral Astrocytoma1CTD_human
TgeneC0547065Mixed oligoastrocytoma1CTD_human
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0750935Cerebral Astrocytoma1CTD_human
TgeneC0750936Intracranial Astrocytoma1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1704230Grade I Astrocytoma1CTD_human
TgeneC4704874Mammary Carcinoma, Human1CTD_human