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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:RBM39-RPS20 (FusionGDB2 ID:72439)

Fusion Gene Summary for RBM39-RPS20

check button Fusion gene summary
Fusion gene informationFusion gene name: RBM39-RPS20
Fusion gene ID: 72439
HgeneTgene
Gene symbol

RBM39

RPS20

Gene ID

9584

6224

Gene nameRNA binding motif protein 39ribosomal protein S20
SynonymsCAPER|CAPERalpha|FSAP59|HCC1|RNPC2S20|uS10
Cytomap

20q11.22

8q12.1

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 39CAPER alphaRNA-binding region (RNP1, RRM) containing 2coactivator of activating protein-1 and estrogen receptorsepididymis secretory sperm binding proteinfunctional spliceosome-associated protein 59hepatocellular carcinoma prot40S ribosomal protein S20small ribosomal subunit protein uS10
Modification date2020032720200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000253363, ENST00000361162, 
ENST00000528062, ENST00000407261, 
ENST00000397370, ENST00000463098, 
ENST00000519807, ENST00000009589, 
ENST00000524349, ENST00000520490, 
ENST00000520627, ENST00000521262, 
ENST00000523936, ENST00000519606, 
ENST00000518875, 
Fusion gene scores* DoF score17 X 20 X 10=340021 X 12 X 3=756
# samples 2322
** MAII scorelog2(23/3400*10)=-3.88582898008069
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/756*10)=-1.78088271069641
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBM39 [Title/Abstract] AND RPS20 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBM39(34327887)-RPS20(56985693), # 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 RBM39 (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 RPS20 (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/AAV692320RBM39chr20

34327887

-RPS20chr8

56985693

+


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Fusion Gene ORF analysis for RBM39-RPS20

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-3CDSENST00000253363ENST00000519807RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000253363ENST00000009589RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000253363ENST00000524349RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000253363ENST00000520490RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000253363ENST00000520627RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000253363ENST00000521262RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000253363ENST00000523936RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000253363ENST00000519606RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-intronENST00000253363ENST00000518875RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000361162ENST00000519807RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000361162ENST00000009589RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000361162ENST00000524349RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000361162ENST00000520490RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000361162ENST00000520627RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000361162ENST00000521262RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000361162ENST00000523936RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000361162ENST00000519606RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-intronENST00000361162ENST00000518875RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000528062ENST00000519807RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000528062ENST00000009589RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000528062ENST00000524349RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000528062ENST00000520490RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000528062ENST00000520627RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000528062ENST00000521262RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000528062ENST00000523936RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000528062ENST00000519606RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-intronENST00000528062ENST00000518875RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000407261ENST00000519807RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000407261ENST00000009589RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000407261ENST00000524349RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000407261ENST00000520490RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000407261ENST00000520627RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000407261ENST00000521262RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000407261ENST00000523936RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000407261ENST00000519606RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-intronENST00000407261ENST00000518875RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000397370ENST00000519807RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000397370ENST00000009589RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000397370ENST00000524349RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000397370ENST00000520490RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000397370ENST00000520627RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000397370ENST00000521262RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000397370ENST00000523936RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000397370ENST00000519606RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-intronENST00000397370ENST00000518875RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000463098ENST00000519807RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000463098ENST00000009589RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3CDSENST00000463098ENST00000524349RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000463098ENST00000520490RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000463098ENST00000520627RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-5UTRENST00000463098ENST00000521262RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000463098ENST00000523936RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-3UTRENST00000463098ENST00000519606RBM39chr20

34327887

-RPS20chr8

56985693

+
intron-intronENST00000463098ENST00000518875RBM39chr20

34327887

-RPS20chr8

56985693

+

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 RBM39-RPS20


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 RBM39-RPS20


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 RBM39-RPS20


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 RBM39-RPS20


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 RBM39-RPS20


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 RBM39-RPS20


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneRPS20C0009405Hereditary Nonpolyposis Colorectal Neoplasms2CLINGEN
TgeneRPS20C1112155Hereditary non-polyposis colorectal cancer syndrome2CLINGEN
TgeneRPS20C1333990Hereditary Nonpolyposis Colorectal Cancer2CLINGEN
TgeneRPS20C1333991Hereditary Non-Polyposis Colon Cancer Type 22CLINGEN
TgeneRPS20C2936783Colorectal cancer, hereditary nonpolyposis, type 12CLINGEN
TgeneRPS20C3896578Familial Colorectal Cancer Type X1ORPHANET