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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:RBM47-CNOT3 (FusionGDB2 ID:72467)

Fusion Gene Summary for RBM47-CNOT3

check button Fusion gene summary
Fusion gene informationFusion gene name: RBM47-CNOT3
Fusion gene ID: 72467
HgeneTgene
Gene symbol

RBM47

CNOT3

Gene ID

54502

4849

Gene nameRNA binding motif protein 47CCR4-NOT transcription complex subunit 3
SynonymsNET18IDDSADF|LENG2|NOT3|NOT3H
Cytomap

4p14

19q13.42

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 47CCR4-NOT transcription complex subunit 3CCR4-associated factor 3NOT3 (negative regulator of transcription 3, yeast) homologleukocyte receptor cluster member 2
Modification date2020031320200313
UniProtAcc.

O75175

Ensembl transtripts involved in fusion geneENST00000319592, ENST00000381793, 
ENST00000381795, ENST00000295971, 
ENST00000514014, ENST00000515809, 
ENST00000221232, ENST00000358389, 
ENST00000406403, ENST00000496327, 
Fusion gene scores* DoF score25 X 25 X 11=68755 X 5 X 4=100
# samples 355
** MAII scorelog2(35/6875*10)=-4.29593288635442
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBM47 [Title/Abstract] AND CNOT3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBM47(40546438)-CNOT3(54647395), # 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 RBM47 (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 CNOT3 (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-59-2348RBM47chr4

40546438

-CNOT3chr19

54647395

+


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Fusion Gene ORF analysis for RBM47-CNOT3

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
5UTR-3CDSENST00000319592ENST00000221232RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-5UTRENST00000319592ENST00000358389RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-5UTRENST00000319592ENST00000406403RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-intronENST00000319592ENST00000496327RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-3CDSENST00000381793ENST00000221232RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-5UTRENST00000381793ENST00000358389RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-5UTRENST00000381793ENST00000406403RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-intronENST00000381793ENST00000496327RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-3CDSENST00000381795ENST00000221232RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-5UTRENST00000381795ENST00000358389RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-5UTRENST00000381795ENST00000406403RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-intronENST00000381795ENST00000496327RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-3CDSENST00000295971ENST00000221232RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-5UTRENST00000295971ENST00000358389RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-5UTRENST00000295971ENST00000406403RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-intronENST00000295971ENST00000496327RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-3CDSENST00000514014ENST00000221232RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-5UTRENST00000514014ENST00000358389RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-5UTRENST00000514014ENST00000406403RBM47chr4

40546438

-CNOT3chr19

54647395

+
5UTR-intronENST00000514014ENST00000496327RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-3CDSENST00000515809ENST00000221232RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-5UTRENST00000515809ENST00000358389RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-5UTRENST00000515809ENST00000406403RBM47chr4

40546438

-CNOT3chr19

54647395

+
intron-intronENST00000515809ENST00000496327RBM47chr4

40546438

-CNOT3chr19

54647395

+

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 RBM47-CNOT3


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)
RBM47chr440546443-CNOT3chr1954647395+5.14E-091
RBM47chr440546443-CNOT3chr1954647395+5.14E-091

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 RBM47-CNOT3


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
.CNOT3

O75175

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: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. May be involved in metabolic regulation; may be involved in recruitment of the CCR4-NOT complex to deadenylation target mRNAs involved in energy metabolism. Involved in mitotic progression and regulation of the spindle assembly checkpoint by regulating the stability of MAD1L1 mRNA. Can repress transcription and may link the CCR4-NOT complex to transcriptional regulation; the repressive function may involve histone deacetylases. Involved in the maintenance of embryonic stem (ES) cell identity. {ECO:0000269|PubMed:14707134, ECO:0000269|PubMed:22342980, ECO:0000269|PubMed:22367759}.

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 RBM47-CNOT3


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 RBM47-CNOT3


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 RBM47-CNOT3


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 RBM47-CNOT3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRBM47C0087031Juvenile-Onset Still Disease1CTD_human
HgeneRBM47C3495559Juvenile arthritis1CTD_human
HgeneRBM47C3714758Juvenile psoriatic arthritis1CTD_human
HgeneRBM47C4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneRBM47C4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneCNOT3C0033578Prostatic Neoplasms2CTD_human
TgeneCNOT3C0376358Malignant neoplasm of prostate2CTD_human
TgeneCNOT3C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CGI;CTD_human;ORPHANET