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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-LINGO3 (FusionGDB2 ID:HG50650TG645191)

Fusion Gene Summary for ARHGEF3-LINGO3

check button Fusion gene summary
Fusion gene informationFusion gene name: ARHGEF3-LINGO3
Fusion gene ID: hg50650tg645191
HgeneTgene
Gene symbol

ARHGEF3

LINGO3

Gene ID

50650

645191

Gene nameRho guanine nucleotide exchange factor 3leucine rich repeat and Ig domain containing 3
SynonymsGEF3|STA3|XPLNLERN2|LRRN6B
Cytomap('ARHGEF3')('LINGO3')

3p14.3

19p13.3

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, XPLNleucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 3leucine rich repeat neuronal 6Bleucine-rich repeat neuronal protein 2leucine-rich repeat neuronal protein 6B
Modification date2020032720200313
UniProtAcc

Q9NR81

.
Ensembl transtripts involved in fusion geneENST00000338458, ENST00000296315, 
ENST00000413728, ENST00000495373, 
ENST00000496106, ENST00000497267, 
ENST00000498517, 
Fusion gene scores* DoF score19 X 17 X 8=25843 X 2 X 3=18
# samples 233
** MAII scorelog2(23/2584*10)=-3.48990030374955
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ARHGEF3 [Title/Abstract] AND LINGO3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARHGEF3(57069116)-LINGO3(2291821), # 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


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
ChimerDB4OVTCGA-24-2271-01AARHGEF3chr3

57069116

-LINGO3chr19

2291821

-


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Fusion Gene ORF analysis for ARHGEF3-LINGO3

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-5UTRENST00000338458ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
5CDS-5UTRENST00000338458ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000296315ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000296315ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000413728ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000413728ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000495373ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000495373ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000496106ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000496106ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000497267ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000497267ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000498517ENST00000404279ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-
intron-5UTRENST00000498517ENST00000585527ARHGEF3chr3

57069116

-LINGO3chr19

2291821

-

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-LINGO3


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)


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Fusion Protein Features for ARHGEF3-LINGO3


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/:57069116/:2291821)
- 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

.
FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA and RhoB GTPases. {ECO:0000269|PubMed:12221096}.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 ARHGEF3-LINGO3


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-LINGO3


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-LINGO3


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-LINGO3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource