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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:RIC3-ZNF143 (FusionGDB2 ID:73586)

Fusion Gene Summary for RIC3-ZNF143

check button Fusion gene summary
Fusion gene informationFusion gene name: RIC3-ZNF143
Fusion gene ID: 73586
HgeneTgene
Gene symbol

RIC3

ZNF143

Gene ID

79608

7702

Gene nameRIC3 acetylcholine receptor chaperonezinc finger protein 143
SynonymsAYST720|PRO1385SBF|STAF|pHZ-1
Cytomap

11p15.4

11p15.4

Type of geneprotein-codingprotein-coding
Descriptionprotein RIC-3resistance to inhibitors of cholinesterase 3-like proteinresistant to inhibitor of cholinesterase 3zinc finger protein 143SPH-binding factorhStafselenocysteine tRNA gene transcription-activating factortranscriptional activator Staf
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000396677, ENST00000335425, 
ENST00000343202, ENST00000309737, 
ENST00000530060, ENST00000539720, 
ENST00000425599, ENST00000419822, 
ENST00000396604, ENST00000396602, 
ENST00000530463, ENST00000396597, 
ENST00000299606, 
Fusion gene scores* DoF score2 X 2 X 2=812 X 16 X 8=1536
# samples 215
** MAII scorelog2(2/8*10)=1.32192809488736log2(15/1536*10)=-3.35614381022528
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RIC3 [Title/Abstract] AND ZNF143 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRIC3(8158924)-ZNF143(9530165), # samples:1
Anticipated loss of major functional domain due to fusion event.RIC3-ZNF143 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
RIC3-ZNF143 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneZNF143

GO:0045944

positive regulation of transcription by RNA polymerase II

10893243


check buttonFusion gene breakpoints across RIC3 (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 ZNF143 (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
ChimerDB4UCECTCGA-D1-A1NYRIC3chr11

8158924

-ZNF143chr11

9530165

+


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Fusion Gene ORF analysis for RIC3-ZNF143

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-3CDSENST00000396677ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000396677ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000396677ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000396677ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000396677ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000335425ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000335425ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000335425ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000335425ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000335425ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000343202ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000343202ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000343202ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000343202ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000343202ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000309737ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000309737ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000309737ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000309737ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000309737ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
5UTR-3CDSENST00000530060ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
5UTR-3CDSENST00000530060ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
5UTR-3CDSENST00000530060ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
5UTR-3CDSENST00000530060ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
5UTR-3CDSENST00000530060ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000539720ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000539720ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000539720ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000539720ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
Frame-shiftENST00000539720ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000425599ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000425599ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000425599ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000425599ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000425599ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000419822ENST00000396604RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000419822ENST00000396602RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000419822ENST00000530463RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000419822ENST00000396597RIC3chr11

8158924

-ZNF143chr11

9530165

+
intron-3CDSENST00000419822ENST00000299606RIC3chr11

8158924

-ZNF143chr11

9530165

+

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 RIC3-ZNF143


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)
RIC3chr118158924-ZNF143chr119530165+4.83E-081
RIC3chr118158924-ZNF143chr119530165+4.83E-081

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 RIC3-ZNF143


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 RIC3-ZNF143


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 RIC3-ZNF143


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 RIC3-ZNF143


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 RIC3-ZNF143


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