FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:RPS3-TSKU (FusionGDB2 ID:77914)

Fusion Gene Summary for RPS3-TSKU

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS3-TSKU
Fusion gene ID: 77914
HgeneTgene
Gene symbol

RPS3

TSKU

Gene ID

6188

25987

Gene nameribosomal protein S3tsukushi, small leucine rich proteoglycan
SynonymsS3E2IG4|LRRC54|TSK
Cytomap

11q13.4

11q13.5

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S3IMR-90 ribosomal protein S3small ribosomal subunit protein uS3tsukushinE2-induced gene 4 proteinleucine rich repeat containing 54leucine-rich repeat-containing protein 54tsukushi homologtsukushi small leucine rich proteoglycan homolog
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000529285, ENST00000278572, 
ENST00000524851, ENST00000526608, 
ENST00000527446, ENST00000530164, 
ENST00000531188, ENST00000534440, 
ENST00000333090, ENST00000527881, 
Fusion gene scores* DoF score17 X 19 X 5=16156 X 6 X 4=144
# samples 227
** MAII scorelog2(22/1615*10)=-2.87595873605663
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/144*10)=-1.04064198449735
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPS3 [Title/Abstract] AND TSKU [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPS3(75113490)-TSKU(76506653), # 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
HgeneRPS3

GO:0006979

response to oxidative stress

23911537

HgeneRPS3

GO:0017148

negative regulation of translation

20217897

HgeneRPS3

GO:0031397

negative regulation of protein ubiquitination

19656744

HgeneRPS3

GO:0032079

positive regulation of endodeoxyribonuclease activity

18973764

HgeneRPS3

GO:0042769

DNA damage response, detection of DNA damage

23911537

HgeneRPS3

GO:0045739

positive regulation of DNA repair

23911537

HgeneRPS3

GO:0061481

response to TNF agonist

20041225

HgeneRPS3

GO:0070301

cellular response to hydrogen peroxide

23911537

HgeneRPS3

GO:1901224

positive regulation of NIK/NF-kappaB signaling

20041225

HgeneRPS3

GO:1902546

positive regulation of DNA N-glycosylase activity

15518571

HgeneRPS3

GO:1905053

positive regulation of base-excision repair

18973764

HgeneRPS3

GO:2001235

positive regulation of apoptotic signaling pathway

14988002


check buttonFusion gene breakpoints across RPS3 (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 TSKU (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
ChimerDB4BRCATCGA-A2-A3KC-01ARPS3chr11

75113490

+TSKUchr11

76506653

+
ChimerDB4BRCATCGA-A2-A3KCRPS3chr11

75113490

+TSKUchr11

76506652

+


Top

Fusion Gene ORF analysis for RPS3-TSKU

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
3UTR-5UTRENST00000529285ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
3UTR-5UTRENST00000529285ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
3UTR-5UTRENST00000529285ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
3UTR-5UTRENST00000529285ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000278572ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000278572ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000278572ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000278572ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000524851ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000524851ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000524851ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000524851ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000526608ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000526608ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000526608ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000526608ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000527446ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000527446ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000527446ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000527446ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000530164ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000530164ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000530164ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000530164ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000531188ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000531188ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
5CDS-5UTRENST00000531188ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
5CDS-5UTRENST00000531188ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+
intron-5UTRENST00000534440ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506653

+
intron-5UTRENST00000534440ENST00000333090RPS3chr11

75113490

+TSKUchr11

76506652

+
intron-5UTRENST00000534440ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506653

+
intron-5UTRENST00000534440ENST00000527881RPS3chr11

75113490

+TSKUchr11

76506652

+

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

Top

Fusion Genomic Features for RPS3-TSKU


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)
RPS3chr1175113490+TSKUchr1176506652+1.67E-050.9999833
RPS3chr1175113490+TSKUchr1176506652+1.67E-050.9999833
RPS3chr1175113490+TSKUchr1176506652+1.67E-050.9999833
RPS3chr1175113490+TSKUchr1176506652+1.67E-050.9999833

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.
genomic feature of top 1%

Top

Fusion Protein Features for RPS3-TSKU


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/:75113490/:76506653)
- 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
..
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: 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


Top

Fusion Gene Sequence for RPS3-TSKU


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.

Top

Fusion Gene PPI Analysis for RPS3-TSKU


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


Top

Related Drugs for RPS3-TSKU


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for RPS3-TSKU


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