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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:FBXO46-DDX39B (FusionGDB2 ID:29852)

Fusion Gene Summary for FBXO46-DDX39B

check button Fusion gene summary
Fusion gene informationFusion gene name: FBXO46-DDX39B
Fusion gene ID: 29852
HgeneTgene
Gene symbol

FBXO46

DDX39B

Gene ID

23403

7919

Gene nameF-box protein 46DExD-box helicase 39B
Synonyms20D7-FC4|FBXO34L|Fbx46BAT1|D6S81E|UAP56
Cytomap

19q13.32

6p21.33

Type of geneprotein-codingprotein-coding
DescriptionF-box only protein 46spliceosome RNA helicase DDX39B56 kDa U2AF65-associated proteinATP-dependent RNA helicase p47DEAD (Asp-Glu-Ala-Asp) box polypeptide 39BDEAD-box helicase 39BHLA-B-associated transcript 1 proteinnuclear RNA helicase (DEAD family)spliceosome RNA helic
Modification date2020031320200313
UniProtAcc

Q6PJ61

Q13838

Ensembl transtripts involved in fusion geneENST00000317683, ENST00000376177, 
ENST00000396172, ENST00000417556, 
ENST00000458640, ENST00000383508, 
ENST00000400293, ENST00000400295, 
ENST00000400296, ENST00000412106, 
ENST00000412330, ENST00000413678, 
ENST00000414440, ENST00000415382, 
ENST00000415689, ENST00000416863, 
ENST00000430703, ENST00000430784, 
ENST00000431360, ENST00000438578, 
ENST00000441425, ENST00000445218, 
ENST00000446341, ENST00000448296, 
ENST00000449074, ENST00000450987, 
ENST00000453105, ENST00000453138, 
ENST00000453488, ENST00000456476, 
ENST00000456666, ENST00000462421, 
ENST00000463430, ENST00000468089, 
ENST00000470514, ENST00000483957, 
ENST00000489325, ENST00000495391, 
ENST00000546633, ENST00000546637, 
ENST00000547039, ENST00000547489, 
ENST00000548331, ENST00000548340, 
ENST00000548614, ENST00000549374, 
ENST00000550217, ENST00000550435, 
ENST00000551031, ENST00000552288, 
ENST00000552820, 
Fusion gene scores* DoF score14 X 3 X 9=37810 X 4 X 6=240
# samples 1811
** MAII scorelog2(18/378*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/240*10)=-1.12553088208386
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FBXO46 [Title/Abstract] AND DDX39B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFBXO46(46234107)-DDX39B(31499182), # 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
TgeneDDX39B

GO:0000245

spliceosomal complex assembly

18593880

TgeneDDX39B

GO:0006406

mRNA export from nucleus

17190602

TgeneDDX39B

GO:0008380

RNA splicing

18593880

TgeneDDX39B

GO:0010501

RNA secondary structure unwinding

18593880

TgeneDDX39B

GO:0046784

viral mRNA export from host cell nucleus

18974867


check buttonFusion gene breakpoints across FBXO46 (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 DDX39B (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
ChimerDB4STADTCGA-CD-8534-01AFBXO46chr19

46234107

-DDX39Bchr6

31499182

-


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Fusion Gene ORF analysis for FBXO46-DDX39B

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
5UTR-3CDSENST00000317683ENST00000376177FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-3CDSENST00000317683ENST00000396172FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-3CDSENST00000317683ENST00000417556FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-3CDSENST00000317683ENST00000458640FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000383508FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000400293FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000400295FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000400296FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000412106FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000412330FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000413678FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000414440FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000415382FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000415689FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000416863FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000430703FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000430784FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000431360FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000438578FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000441425FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000445218FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000446341FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000448296FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000449074FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000450987FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000453105FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000453138FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000453488FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000456476FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000456666FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000462421FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000463430FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000468089FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000470514FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000483957FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000489325FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000495391FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000546633FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000546637FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000547039FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000547489FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000548331FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000548340FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000548614FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000549374FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000550217FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000550435FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000551031FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000552288FBXO46chr19

46234107

-DDX39Bchr6

31499182

-
5UTR-intronENST00000317683ENST00000552820FBXO46chr19

46234107

-DDX39Bchr6

31499182

-

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 FBXO46-DDX39B


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 FBXO46-DDX39B


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/:46234107/:31499182)
- 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
FBXO46

Q6PJ61

DDX39B

Q13838

FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. {ECO:0000250}.FUNCTION: Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability. {ECO:0000269|PubMed:11675789, ECO:0000269|PubMed:15585580, ECO:0000269|PubMed:15833825, ECO:0000269|PubMed:15998806, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17562711, ECO:0000269|PubMed:17984224, ECO:0000269|PubMed:20844015, ECO:0000269|PubMed:22144908, ECO:0000269|PubMed:23222130, ECO:0000269|PubMed:23299939, ECO:0000269|PubMed:9242493}.; FUNCTION: Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly with [PubMed:23299939] reporting a stimulatory effect. {ECO:0000269|PubMed:23299939, ECO:0000269|PubMed:9242493}.; FUNCTION: (Microbial infection) The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. {ECO:0000269|PubMed:18974867}.

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 FBXO46-DDX39B


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 FBXO46-DDX39B


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 FBXO46-DDX39B


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 FBXO46-DDX39B


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