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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:RPS9-CLTA (FusionGDB2 ID:78165)

Fusion Gene Summary for RPS9-CLTA

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS9-CLTA
Fusion gene ID: 78165
HgeneTgene
Gene symbol

RPS9

CLTA

Gene ID

6203

1211

Gene nameribosomal protein S9clathrin light chain A
SynonymsS9LCA
Cytomap

19q13.42

9p13.3

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S9small ribosomal subunit protein uS4clathrin light chain Aclathrin, light polypeptide (Lca)
Modification date2020031320200313
UniProtAcc.

P09496

Ensembl transtripts involved in fusion geneENST00000302907, ENST00000391751, 
ENST00000391752, ENST00000391753, 
ENST00000402367, ENST00000441429, 
ENST00000242285, ENST00000345519, 
ENST00000396603, ENST00000433436, 
ENST00000466396, ENST00000470744, 
ENST00000538225, ENST00000540080, 
Fusion gene scores* DoF score15 X 12 X 8=14405 X 4 X 3=60
# samples 155
** MAII scorelog2(15/1440*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPS9 [Title/Abstract] AND CLTA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPS9(54705149)-CLTA(36197547), # 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

check buttonFusion gene breakpoints across RPS9 (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 CLTA (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
ChimerDB4OVTCGA-29-1777RPS9chr19

54705149

+CLTAchr9

36197547

+


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Fusion Gene ORF analysis for RPS9-CLTA

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-intronENST00000302907ENST00000242285RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000345519RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000396603RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000433436RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000466396RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000470744RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000538225RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000302907ENST00000540080RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000242285RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000345519RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000396603RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000433436RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000466396RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000470744RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000538225RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391751ENST00000540080RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000242285RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000345519RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000396603RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000433436RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000466396RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000470744RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000538225RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391752ENST00000540080RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000242285RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000345519RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000396603RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000433436RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000466396RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000470744RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000538225RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000391753ENST00000540080RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000242285RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000345519RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000396603RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000433436RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000466396RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000470744RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000538225RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000402367ENST00000540080RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000242285RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000345519RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000396603RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000433436RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000466396RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000470744RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000538225RPS9chr19

54705149

+CLTAchr9

36197547

+
5CDS-intronENST00000441429ENST00000540080RPS9chr19

54705149

+CLTAchr9

36197547

+

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 RPS9-CLTA


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)
RPS9chr1954705149+CLTAchr936197547+0.0017929890.998207
RPS9chr1954705149+CLTAchr936197547+0.0017929890.998207

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.
genomic feature

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 RPS9-CLTA


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/:54705149/:36197547)
- 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
.CLTA

P09496

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: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Acts as component of the TACC3/ch-TOG/clathrin complex proposed to contribute to stabilization of kinetochore fibers of the mitotic spindle by acting as inter-microtubule bridge (PubMed:15858577, PubMed:21297582). {ECO:0000305|PubMed:15858577, ECO:0000305|PubMed:21297582}.

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 RPS9-CLTA


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 RPS9-CLTA


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 RPS9-CLTA


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 RPS9-CLTA


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