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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:ARF3-CHFR (FusionGDB2 ID:HG377TG55743)

Fusion Gene Summary for ARF3-CHFR

check button Fusion gene summary
Fusion gene informationFusion gene name: ARF3-CHFR
Fusion gene ID: hg377tg55743
HgeneTgene
Gene symbol

ARF3

CHFR

Gene ID

377

55743

Gene nameADP ribosylation factor 3checkpoint with forkhead and ring finger domains
Synonyms-RNF116|RNF196
Cytomap('ARF3')('CHFR')

12q13.12

12q24.33

Type of geneprotein-codingprotein-coding
DescriptionADP-ribosylation factor 3small GTP binding proteinE3 ubiquitin-protein ligase CHFRRING finger protein 196RING-type E3 ubiquitin transferase CHFRcheckpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase
Modification date2020031320200313
UniProtAcc

P61204

.
Ensembl transtripts involved in fusion geneENST00000256682, ENST00000447318, 
ENST00000541959, ENST00000541967, 
Fusion gene scores* DoF score10 X 10 X 5=5006 X 7 X 4=168
# samples 106
** MAII scorelog2(10/500*10)=-2.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/168*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARF3 [Title/Abstract] AND CHFR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARF3(49334731)-CHFR(133463926), # samples:1
ARF3(49334731)-CHFR(133454240), # samples:1
Anticipated loss of major functional domain due to fusion event.ARF3-CHFR seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ARF3-CHFR seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ARF3-CHFR seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneCHFR

GO:0000209

protein polyubiquitination

19182791

TgeneCHFR

GO:0019941

modification-dependent protein catabolic process

19182791



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
ChimerDB4LUADTCGA-55-6712-01AARF3chr12

49334731

-CHFRchr12

133454240

-
ChimerDB4LUADTCGA-55-6712-01AARF3chr12

49334731

-CHFRchr12

133463926

-


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Fusion Gene ORF analysis for ARF3-CHFR

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-5UTRENST00000256682ENST00000266880ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000256682ENST00000315585ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000256682ENST00000432561ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-5UTRENST00000256682ENST00000432561ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000256682ENST00000443047ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000256682ENST00000450056ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000256682ENST00000541837ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-5UTRENST00000447318ENST00000266880ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000447318ENST00000315585ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000447318ENST00000432561ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-5UTRENST00000447318ENST00000432561ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000447318ENST00000443047ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000447318ENST00000450056ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000447318ENST00000541837ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-5UTRENST00000541959ENST00000266880ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000541959ENST00000315585ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000541959ENST00000432561ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-5UTRENST00000541959ENST00000432561ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000541959ENST00000443047ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000541959ENST00000450056ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-5UTRENST00000541959ENST00000541837ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000256682ENST00000537522ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000256682ENST00000537522ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000256682ENST00000541341ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000256682ENST00000541341ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000256682ENST00000541837ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000447318ENST00000537522ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000447318ENST00000537522ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000447318ENST00000541341ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000447318ENST00000541341ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000447318ENST00000541837ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000541959ENST00000537522ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000541959ENST00000537522ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000541959ENST00000541341ARF3chr12

49334731

-CHFRchr12

133454240

-
5CDS-intronENST00000541959ENST00000541341ARF3chr12

49334731

-CHFRchr12

133463926

-
5CDS-intronENST00000541959ENST00000541837ARF3chr12

49334731

-CHFRchr12

133463926

-
Frame-shiftENST00000256682ENST00000266880ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000256682ENST00000315585ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000256682ENST00000443047ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000256682ENST00000450056ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000447318ENST00000266880ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000447318ENST00000315585ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000447318ENST00000443047ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000447318ENST00000450056ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000541959ENST00000266880ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000541959ENST00000315585ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000541959ENST00000443047ARF3chr12

49334731

-CHFRchr12

133454240

-
Frame-shiftENST00000541959ENST00000450056ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-3CDSENST00000541967ENST00000266880ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-3CDSENST00000541967ENST00000315585ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-3CDSENST00000541967ENST00000443047ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-3CDSENST00000541967ENST00000450056ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-5UTRENST00000541967ENST00000266880ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-5UTRENST00000541967ENST00000315585ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-5UTRENST00000541967ENST00000432561ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-5UTRENST00000541967ENST00000432561ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-5UTRENST00000541967ENST00000443047ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-5UTRENST00000541967ENST00000450056ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-5UTRENST00000541967ENST00000541837ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-intronENST00000541967ENST00000537522ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-intronENST00000541967ENST00000537522ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-intronENST00000541967ENST00000541341ARF3chr12

49334731

-CHFRchr12

133454240

-
intron-intronENST00000541967ENST00000541341ARF3chr12

49334731

-CHFRchr12

133463926

-
intron-intronENST00000541967ENST00000541837ARF3chr12

49334731

-CHFRchr12

133463926

-

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 ARF3-CHFR


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 ARF3-CHFR


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/:49334731/:133463926)
- 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
ARF3

P61204

.
FUNCTION: GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP-ribosyltransferase. Involved in protein trafficking; may modulate vesicle budding and uncoating within the Golgi apparatus.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 ARF3-CHFR


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 ARF3-CHFR


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 ARF3-CHFR


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 ARF3-CHFR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0007131Non-Small Cell Lung Carcinoma1CTD_human;UNIPROT
TgeneC0014170Endometrial Neoplasms1CTD_human
TgeneC0024623Malignant neoplasm of stomach1CTD_human
TgeneC0038356Stomach Neoplasms1CTD_human
TgeneC0476089Endometrial Carcinoma1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer1CTD_human