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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:ARHGEF3-FDFT1 (FusionGDB2 ID:HG50650TG2222)

Fusion Gene Summary for ARHGEF3-FDFT1

check button Fusion gene summary
Fusion gene informationFusion gene name: ARHGEF3-FDFT1
Fusion gene ID: hg50650tg2222
HgeneTgene
Gene symbol

ARHGEF3

FDFT1

Gene ID

50650

2222

Gene nameRho guanine nucleotide exchange factor 3farnesyl-diphosphate farnesyltransferase 1
SynonymsGEF3|STA3|XPLNDGPT|ERG9|SQS|SQSD|SS
Cytomap('ARHGEF3')('FDFT1')

3p14.3

8p23.1

Type of geneprotein-codingprotein-coding
Descriptionrho guanine nucleotide exchange factor 359.8 kDA proteinRho guanine nucleotide exchange factor (GEF) 3RhoGEF proteinexchange factor found in platelets and leukemic and neuronal tissues, XPLNsqualene synthaseFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthetase
Modification date2020032720200320
UniProtAcc

Q9NR81

P37268

Ensembl transtripts involved in fusion geneENST00000296315, ENST00000338458, 
ENST00000413728, ENST00000495373, 
ENST00000496106, ENST00000497267, 
ENST00000498517, 
Fusion gene scores* DoF score19 X 17 X 8=258412 X 9 X 5=540
# samples 2311
** MAII scorelog2(23/2584*10)=-3.48990030374955
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/540*10)=-2.29545588352617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARHGEF3 [Title/Abstract] AND FDFT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARHGEF3(56761449)-FDFT1(11653082), # samples:1
Anticipated loss of major functional domain due to fusion event.ARHGEF3-FDFT1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ARHGEF3-FDFT1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ARHGEF3-FDFT1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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


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
ChimerDB4PRADTCGA-CH-5761-01AARHGEF3chr3

56761449

-FDFT1chr8

11653082

+


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Fusion Gene ORF analysis for ARHGEF3-FDFT1

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-intronENST00000296315ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000296315ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000338458ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
5CDS-intronENST00000413728ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
Frame-shiftENST00000296315ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
Frame-shiftENST00000338458ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
Frame-shiftENST00000413728ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-3CDSENST00000495373ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-3CDSENST00000496106ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-3CDSENST00000497267ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-3CDSENST00000498517ENST00000538689ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000495373ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000496106ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000497267ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000220584ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000443614ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000446331ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000525777ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000525900ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000528643ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000528812ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+
intron-intronENST00000498517ENST00000530664ARHGEF3chr3

56761449

-FDFT1chr8

11653082

+

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 ARHGEF3-FDFT1


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)
ARHGEF3chr356761448-FDFT1chr811653081+0.258819250.7411807
ARHGEF3chr356761448-FDFT1chr811653081+0.258819250.7411807


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 ARHGEF3-FDFT1


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/:56761449/:11653082)
- 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
ARHGEF3

Q9NR81

FDFT1

P37268

FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA and RhoB GTPases. {ECO:0000269|PubMed:12221096}.FUNCTION: Catalyzes the condensation of 2 farnesyl pyrophosphate (FPP) moieties to form squalene. Proceeds in two distinct steps. In the first half-reaction, two molecules of FPP react to form the stable presqualene diphosphate intermediate (PSQPP), with concomitant release of a proton and a molecule of inorganic diphosphate. In the second half-reaction, PSQPP undergoes heterolysis, isomerization, and reduction with NADPH or NADH to form squalene. It is the first committed enzyme of the sterol biosynthesis pathway. {ECO:0000269|PubMed:10896663, ECO:0000269|PubMed:24531458}.

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 ARHGEF3-FDFT1


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 ARHGEF3-FDFT1


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 ARHGEF3-FDFT1


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 ARHGEF3-FDFT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0006868Cannabis Abuse1CTD_human
TgeneC0006870Cannabis Dependence1CTD_human
TgeneC0009171Cocaine Abuse1CTD_human
TgeneC0018614Hashish Abuse1CTD_human
TgeneC0024809Marijuana Abuse1CTD_human
TgeneC0031391Phencyclidine Abuse1CTD_human
TgeneC0036572Seizures1GENOMICS_ENGLAND
TgeneC0037268Skin Abnormalities1GENOMICS_ENGLAND
TgeneC0234398Visual Cortex Disorder1GENOMICS_ENGLAND
TgeneC0236735Cannabis-Related Disorder1CTD_human
TgeneC0236736Cocaine-Related Disorders1CTD_human
TgeneC0236742Phencyclidine-Related Disorders1CTD_human
TgeneC0600427Cocaine Dependence1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC3553450Profound global developmental delay1GENOMICS_ENGLAND
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4022810Abnormality of nervous system morphology1GENOMICS_ENGLAND
TgeneC4025871Abnormality of the face1GENOMICS_ENGLAND
TgeneC4048268Cortical visual impairment1GENOMICS_ENGLAND