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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:RPS6KA3-EIF1AY (FusionGDB2 ID:HG6197TG9086)

Fusion Gene Summary for RPS6KA3-EIF1AY

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS6KA3-EIF1AY
Fusion gene ID: hg6197tg9086
HgeneTgene
Gene symbol

RPS6KA3

EIF1AY

Gene ID

6197

9086

Gene nameribosomal protein S6 kinase A3eukaryotic translation initiation factor 1A Y-linked
SynonymsCLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2eIF-4C
Cytomap('RPS6KA3')('EIF1AY')

Xp22.12

Yq11.223

Type of geneprotein-codingprotein-coding
Descriptionribosomal protein S6 kinase alpha-3MAP kinase-activated protein kinase 1bMAPK-activated protein kinase 1bMAPKAP kinase 1bMAPKAPK-1bRSK-2S6K-alpha-3epididymis secretory sperm binding proteininsulin-stimulated protein kinase 1p90-RSK 3ribosomal S6eukaryotic translation initiation factor 1A, Y-chromosomaleIF-1A Y isoformeukaryotic translation initiation factor 1A, Y chromosomeeukaryotic translation initiation factor 4C
Modification date2020032720200313
UniProtAcc.

O14602

Ensembl transtripts involved in fusion geneENST00000379565, ENST00000379548, 
ENST00000479809, ENST00000540702, 
ENST00000544447, 
Fusion gene scores* DoF score15 X 11 X 7=11554 X 4 X 2=32
# samples 194
** MAII scorelog2(19/1155*10)=-2.60382152797247
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: RPS6KA3 [Title/Abstract] AND EIF1AY [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPS6KA3(20284681)-EIF1AY(22744475), # samples:1
Anticipated loss of major functional domain due to fusion event.RPS6KA3-EIF1AY seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
RPS6KA3-EIF1AY seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RPS6KA3-EIF1AY seems lost the major protein functional domain in Hgene partner, which is a kinase 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
HgeneRPS6KA3

GO:0043154

negative regulation of cysteine-type endopeptidase activity involved in apoptotic process

18402937



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
ChimerDB4LIHCTCGA-DD-AADJRPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+


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Fusion Gene ORF analysis for RPS6KA3-EIF1AY

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-intronENST00000379565ENST00000464196RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
Frame-shiftENST00000379565ENST00000361365RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
Frame-shiftENST00000379565ENST00000382772RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000379548ENST00000361365RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000379548ENST00000382772RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000479809ENST00000361365RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000479809ENST00000382772RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000540702ENST00000361365RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000540702ENST00000382772RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000544447ENST00000361365RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-3CDSENST00000544447ENST00000382772RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-intronENST00000379548ENST00000464196RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-intronENST00000479809ENST00000464196RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-intronENST00000540702ENST00000464196RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+
intron-intronENST00000544447ENST00000464196RPS6KA3chrX

20284681

-EIF1AYchrY

22744475

+

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 RPS6KA3-EIF1AY


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)
RPS6KA3chrX20284681-EIF1AYchrY22744475+4.05E-081
RPS6KA3chrX20284681-EIF1AYchrY22744475+4.05E-081


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%

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Fusion Protein Features for RPS6KA3-EIF1AY


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/:20284681/:22744475)
- 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
.EIF1AY

O14602

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: Seems to be required for maximal rate of protein biosynthesis. Enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits (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 RPS6KA3-EIF1AY


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 RPS6KA3-EIF1AY


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 RPS6KA3-EIF1AY


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 RPS6KA3-EIF1AY


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRPS6KA3C0265252Coffin-Lowry syndrome15CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneRPS6KA3C0796225Mental Retardation, X-Linked 192CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneRPS6KA3C0005941Bone Diseases, Developmental1CTD_human
HgeneRPS6KA3C0027626Neoplasm Invasiveness1CTD_human
HgeneRPS6KA3C0027627Neoplasm Metastasis1CTD_human
HgeneRPS6KA3C0033922Psychomotor Disorders1CTD_human
HgeneRPS6KA3C0424230Motor retardation1CTD_human
HgeneRPS6KA3C0751456Developmental Psychomotor Disorders1CTD_human
HgeneRPS6KA3C2239176Liver carcinoma1CTD_human
HgeneRPS6KA3C2931498Mental Retardation, X-Linked 11ORPHANET