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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:RPS20-LYN (FusionGDB2 ID:77564)

Fusion Gene Summary for RPS20-LYN

check button Fusion gene summary
Fusion gene informationFusion gene name: RPS20-LYN
Fusion gene ID: 77564
HgeneTgene
Gene symbol

RPS20

LYN

Gene ID

6224

4067

Gene nameribosomal protein S20LYN proto-oncogene, Src family tyrosine kinase
SynonymsS20|uS10JTK8|p53Lyn|p56Lyn
Cytomap

8q12.1

8q12.1

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S20small ribosomal subunit protein uS10tyrosine-protein kinase Lynlck/Yes-related novel protein tyrosine kinasev-yes-1 Yamaguchi sarcoma viral related oncogene homolog
Modification date2020032720200327
UniProtAcc.

P0DP58

Ensembl transtripts involved in fusion geneENST00000009589, ENST00000518875, 
ENST00000519606, ENST00000519807, 
ENST00000520490, ENST00000520627, 
ENST00000521262, ENST00000523936, 
ENST00000524349, 		ENST00000420292, 
ENST00000519728, ENST00000520220, 
Fusion gene scores* DoF score25 X 13 X 7=227513 X 14 X 7=1274
# samples 2615
** MAII scorelog2(26/2275*10)=-3.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1274*10)=-3.08633087176042
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RPS20 [Title/Abstract] AND LYN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRPS20(56985737)-LYN(56926147), # 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
TgeneLYN

GO:0006468

protein phosphorylation

11517336

TgeneLYN

GO:0006974

cellular response to DNA damage stimulus

10891478|11517336

TgeneLYN

GO:0018108

peptidyl-tyrosine phosphorylation

7682714|11782428

TgeneLYN

GO:0046777

protein autophosphorylation

7682714

TgeneLYN

GO:0051272

positive regulation of cellular component movement

16467205

TgeneLYN

GO:0070304

positive regulation of stress-activated protein kinase signaling cascade

10891478


check buttonFusion gene breakpoints across RPS20 (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 LYN (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
ChimerDB4LUSCTCGA-66-2756-01ARPS20chr8

56985737

-LYNchr8

56926147

+


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Fusion Gene ORF analysis for RPS20-LYN

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-intronENST00000009589ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000009589ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000009589ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000518875ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000518875ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000518875ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000519606ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000519606ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000519606ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000519807ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000519807ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000519807ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000520490ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000520490ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000520490ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000520627ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000520627ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000520627ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000521262ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000521262ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000521262ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000523936ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000523936ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000523936ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000524349ENST00000420292RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000524349ENST00000519728RPS20chr8

56985737

-LYNchr8

56926147

+
intron-intronENST00000524349ENST00000520220RPS20chr8

56985737

-LYNchr8

56926147

+

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 RPS20-LYN


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 RPS20-LYN


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/:56985737/:56926147)
- 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
.LYN

P0DP58

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: Acts in different tissues through interaction to nicotinic acetylcholine receptors (nAChRs) (PubMed:21252236). The proposed role as modulator of nAChR activity seems to be dependent on the nAChR subtype and stoichiometry, and to involve an effect on nAChR trafficking and its cell surface expression, and on single channel properties of the nAChR inserted in the plasma membrane. Modulates functional properties of nicotinic acetylcholine receptors (nAChRs) to prevent excessive excitation, and hence neurodegeneration. Enhances desensitization by increasing both the rate and extent of desensitization of alpha-4:beta-2-containing nAChRs and slowing recovery from desensitization. Promotes large amplitude ACh-evoked currents through alpha-4:beta-2 nAChRs. Is involved in regulation of the nAChR pentameric assembly in the endoplasmic reticulum. Shifts stoichiometry from high sensitivity alpha-4(2):beta-2(3) to low sensitivity alpha-4(3):beta-2(2) nAChR (By similarity). In vitro modulates alpha-3:beta-4-containing nAChRs. Reduces cell surface expression of (alpha-3:beta-4)(2):beta-4 and (alpha-3:beta-4)(2):alpha-5 nAChRs suggesting an interaction with nAChR alpha-3(-):(+)beta-4 subunit interfaces and an allosteric mode. Corresponding single channel effects characterized by decreased unitary conductance, altered burst proportions and enhanced desensitization/inactivation seem to depend on nAChR alpha:alpha subunit interfaces and are greater in (alpha-3:beta-2)(2):alpha-3 when compared to (alpha-3:beta-2)(2):alpha-5 nAChRs (PubMed:28100642). Prevents plasticity in the primary visual cortex late in life (By similarity). {ECO:0000250|UniProtKB:P0DP60, ECO:0000269|PubMed:21252236, ECO:0000269|PubMed:28100642}.

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 RPS20-LYN


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 RPS20-LYN


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 RPS20-LYN


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 RPS20-LYN


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