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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:TRAPPC9-IKBKB (FusionGDB2 ID:93845)

Fusion Gene Summary for TRAPPC9-IKBKB

check button Fusion gene summary
Fusion gene informationFusion gene name: TRAPPC9-IKBKB
Fusion gene ID: 93845
HgeneTgene
Gene symbol

TRAPPC9

IKBKB

Gene ID

83696

3551

Gene nametrafficking protein particle complex 9inhibitor of nuclear factor kappa B kinase subunit beta
SynonymsIBP|IKBKBBP|MRT13|NIBP|T1|TRS120IKK-beta|IKK2|IKKB|IMD15|IMD15A|IMD15B|NFKBIKB
Cytomap

8q24.3

8p11.21

Type of geneprotein-codingprotein-coding
Descriptiontrafficking protein particle complex subunit 9IKK2 binding proteinNIK and IKK-beta binding proteinNIK- and IKBKB-binding proteinTRAPP 120 kDa subunittularik gene 1 proteininhibitor of nuclear factor kappa-B kinase subunit betaI-kappa-B kinase 2I-kappa-B-kinase betainhibitor of kappa light polypeptide gene enhancer in B-cells, kinase betanuclear factor NF-kappa-B inhibitor kinase beta
Modification date2020031320200313
UniProtAcc.

O14920

Ensembl transtripts involved in fusion geneENST00000389327, ENST00000389328, 
ENST00000438773, ENST00000522504, 
ENST00000379708, ENST00000416505, 
ENST00000518983, ENST00000519735, 
ENST00000520810, ENST00000520835, 
ENST00000522147, ENST00000522785, 
Fusion gene scores* DoF score26 X 21 X 11=600611 X 14 X 4=616
# samples 3114
** MAII scorelog2(31/6006*10)=-4.27606435428291
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/616*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TRAPPC9 [Title/Abstract] AND IKBKB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTRAPPC9(141345003)-IKBKB(42181283), # 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
TgeneIKBKB

GO:0006468

protein phosphorylation

15084260|20434986

TgeneIKBKB

GO:0018105

peptidyl-serine phosphorylation

21399639

TgeneIKBKB

GO:0042325

regulation of phosphorylation

26212789

TgeneIKBKB

GO:0045944

positive regulation of transcription by RNA polymerase II

23091055|23453807

TgeneIKBKB

GO:0051092

positive regulation of NF-kappaB transcription factor activity

15790681

TgeneIKBKB

GO:0071356

cellular response to tumor necrosis factor

23091055


check buttonFusion gene breakpoints across TRAPPC9 (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 IKBKB (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
ChiTaRS5.0N/AAW813634TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+


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Fusion Gene ORF analysis for TRAPPC9-IKBKB

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
intron-intronENST00000389327ENST00000379708TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000416505TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000518983TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000519735TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000520810TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000520835TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000522147TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389327ENST00000522785TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000379708TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000416505TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000518983TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000519735TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000520810TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000520835TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000522147TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000389328ENST00000522785TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000379708TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000416505TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000518983TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000519735TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000520810TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000520835TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000522147TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000438773ENST00000522785TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000379708TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000416505TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000518983TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000519735TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000520810TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000520835TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000522147TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+
intron-intronENST00000522504ENST00000522785TRAPPC9chr8

141345003

+IKBKBchr8

42181283

+

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 TRAPPC9-IKBKB


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 TRAPPC9-IKBKB


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/:141345003/:42181283)
- 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
.IKBKB

O14920

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: Serine kinase that plays an essential role in the NF-kappa-B signaling pathway which is activated by multiple stimuli such as inflammatory cytokines, bacterial or viral products, DNA damages or other cellular stresses (PubMed:30337470). Acts as part of the canonical IKK complex in the conventional pathway of NF-kappa-B activation. Phosphorylates inhibitors of NF-kappa-B on 2 critical serine residues. These modifications allow polyubiquitination of the inhibitors and subsequent degradation by the proteasome. In turn, free NF-kappa-B is translocated into the nucleus and activates the transcription of hundreds of genes involved in immune response, growth control, or protection against apoptosis. In addition to the NF-kappa-B inhibitors, phosphorylates several other components of the signaling pathway including NEMO/IKBKG, NF-kappa-B subunits RELA and NFKB1, as well as IKK-related kinases TBK1 and IKBKE (PubMed:11297557, PubMed:20410276). IKK-related kinase phosphorylations may prevent the overproduction of inflammatory mediators since they exert a negative regulation on canonical IKKs. Phosphorylates FOXO3, mediating the TNF-dependent inactivation of this pro-apoptotic transcription factor (PubMed:15084260). Also phosphorylates other substrates including NCOA3, BCL10 and IRS1 (PubMed:17213322). Within the nucleus, acts as an adapter protein for NFKBIA degradation in UV-induced NF-kappa-B activation (PubMed:11297557). Phosphorylates RIPK1 at 'Ser-25' which represses its kinase activity and consequently prevents TNF-mediated RIPK1-dependent cell death (By similarity). Phosphorylates the C-terminus of IRF5, stimulating IRF5 homodimerization and translocation into the nucleus (PubMed:25326418). {ECO:0000250|UniProtKB:O88351, ECO:0000269|PubMed:11297557, ECO:0000269|PubMed:15084260, ECO:0000269|PubMed:17213322, ECO:0000269|PubMed:19716809, ECO:0000269|PubMed:20410276, ECO:0000269|PubMed:20434986, ECO:0000269|PubMed:20797629, ECO:0000269|PubMed:21138416, ECO:0000269|PubMed:25326418, ECO:0000269|PubMed:30337470}.

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 TRAPPC9-IKBKB


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 TRAPPC9-IKBKB


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 TRAPPC9-IKBKB


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 TRAPPC9-IKBKB


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