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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:RAB40C-IRF3 (FusionGDB2 ID:71414)

Fusion Gene Summary for RAB40C-IRF3

check button Fusion gene summary
Fusion gene informationFusion gene name: RAB40C-IRF3
Fusion gene ID: 71414
HgeneTgene
Gene symbol

RAB40C

IRF3

Gene ID

57799

3661

Gene nameRAB40C, member RAS oncogene familyinterferon regulatory factor 3
SynonymsRARL|RASL8CIIAE7
Cytomap

16p13.3

19q13.33

Type of geneprotein-codingprotein-coding
Descriptionras-related protein Rab-40CRAR (RAS like GTPASE) likeRAR likeRAS-like GTPaseRAS-like, family 8, member CSOCS box-containing protein RAR3rar-like proteinras-like protein family member 8Cinterferon regulatory factor 3
Modification date2020031320200315
UniProtAcc.

Q14653

Ensembl transtripts involved in fusion geneENST00000248139, ENST00000535977, 
ENST00000538492, ENST00000539661, 
ENST00000377135, ENST00000377139, 
ENST00000442265, ENST00000593922, 
ENST00000596765, ENST00000596822, 
ENST00000597198, ENST00000598808, 
ENST00000599144, ENST00000599223, 
ENST00000600022, ENST00000601291, 
ENST00000309877, ENST00000599680, 
ENST00000600911, 
Fusion gene scores* DoF score11 X 3 X 10=3308 X 5 X 7=280
# samples 139
** MAII scorelog2(13/330*10)=-1.34395440121736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RAB40C [Title/Abstract] AND IRF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRAB40C(640433)-IRF3(50166515), # samples:1
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
TgeneIRF3

GO:0032481

positive regulation of type I interferon production

25636800

TgeneIRF3

GO:0035666

TRIF-dependent toll-like receptor signaling pathway

25636800

TgeneIRF3

GO:0045944

positive regulation of transcription by RNA polymerase II

9660935


check buttonFusion gene breakpoints across RAB40C (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across IRF3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4SKCMTCGA-D3-A3C1-06ARAB40Cchr16

640433

+IRF3chr19

50166515

-


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Fusion Gene ORF analysis for RAB40C-IRF3

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-5UTRENST00000248139ENST00000377135RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000377139RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000442265RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000593922RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000596765RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000596822RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000597198RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000598808RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000599144RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000599223RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000600022RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000248139ENST00000601291RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000377135RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000377139RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000442265RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000593922RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000596765RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000596822RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000597198RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000598808RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000599144RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000599223RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000600022RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000535977ENST00000601291RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000377135RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000377139RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000442265RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000593922RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000596765RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000596822RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000597198RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000598808RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000599144RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000599223RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000600022RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000538492ENST00000601291RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000377135RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000377139RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000442265RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000593922RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000596765RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000596822RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000597198RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000598808RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000599144RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000599223RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000600022RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-5UTRENST00000539661ENST00000601291RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000248139ENST00000309877RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000248139ENST00000599680RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000248139ENST00000600911RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000535977ENST00000309877RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000535977ENST00000599680RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000535977ENST00000600911RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000538492ENST00000309877RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000538492ENST00000599680RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000538492ENST00000600911RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000539661ENST00000309877RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000539661ENST00000599680RAB40Cchr16

640433

+IRF3chr19

50166515

-
5CDS-intronENST00000539661ENST00000600911RAB40Cchr16

640433

+IRF3chr19

50166515

-

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 RAB40C-IRF3


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for RAB40C-IRF3


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/:640433/:50166515)
- 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
.IRF3

Q14653

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: Key transcriptional regulator of type I interferon (IFN)-dependent immune responses which plays a critical role in the innate immune response against DNA and RNA viruses (PubMed:22394562, PubMed:25636800, PubMed:27302953). Regulates the transcription of type I IFN genes (IFN-alpha and IFN-beta) and IFN-stimulated genes (ISG) by binding to an interferon-stimulated response element (ISRE) in their promoters (PubMed:11846977, PubMed:16846591, PubMed:16979567, PubMed:20049431, PubMed:32972995). Acts as a more potent activator of the IFN-beta (IFNB) gene than the IFN-alpha (IFNA) gene and plays a critical role in both the early and late phases of the IFNA/B gene induction (PubMed:16846591, PubMed:16979567, PubMed:20049431). Found in an inactive form in the cytoplasm of uninfected cells and following viral infection, double-stranded RNA (dsRNA), or toll-like receptor (TLR) signaling, is phosphorylated by IKBKE and TBK1 kinases (PubMed:22394562, PubMed:25636800, PubMed:27302953). This induces a conformational change, leading to its dimerization and nuclear localization and association with CREB binding protein (CREBBP) to form dsRNA-activated factor 1 (DRAF1), a complex which activates the transcription of the type I IFN and ISG genes (PubMed:16154084, PubMed:27302953, PubMed:33440148). Can activate distinct gene expression programs in macrophages and can induce significant apoptosis in primary macrophages (PubMed:16846591). In response to Sendai virus infection, is recruited by TOMM70:HSP90AA1 to mitochondrion and forms an apoptosis complex TOMM70:HSP90AA1:IRF3:BAX inducing apoptosis (PubMed:25609812). Key transcription factor regulating the IFN response during SARS-CoV-2 infection (PubMed:33440148). {ECO:0000269|PubMed:16154084, ECO:0000269|PubMed:22394562, ECO:0000269|PubMed:25609812, ECO:0000269|PubMed:25636800, ECO:0000269|PubMed:27302953, ECO:0000269|PubMed:31413131, ECO:0000269|PubMed:32972995, ECO:0000269|PubMed:33440148, ECO:0000303|PubMed:11846977, ECO:0000303|PubMed:16846591, ECO:0000303|PubMed:16979567, ECO:0000303|PubMed:20049431}.

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 RAB40C-IRF3


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 RAB40C-IRF3


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 RAB40C-IRF3


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 RAB40C-IRF3


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