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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:CNOT3-KMT2B (FusionGDB2 ID:HG4849TG9757)

Fusion Gene Summary for CNOT3-KMT2B

check button Fusion gene summary
Fusion gene informationFusion gene name: CNOT3-KMT2B
Fusion gene ID: hg4849tg9757
HgeneTgene
Gene symbol

CNOT3

KMT2B

Gene ID

4849

9757

Gene nameCCR4-NOT transcription complex subunit 3lysine methyltransferase 2B
SynonymsIDDSADF|LENG2|NOT3|NOT3HCXXC10|DYT28|HRX2|MLL1B|MLL2|MLL4|TRX2|WBP-7|WBP7
Cytomap('CNOT3')('KMT2B')

19q13.42

19q13.12

Type of geneprotein-codingprotein-coding
DescriptionCCR4-NOT transcription complex subunit 3CCR4-associated factor 3NOT3 (negative regulator of transcription 3, yeast) homologleukocyte receptor cluster member 2histone-lysine N-methyltransferase 2BWW domain binding protein 7histone-lysine N-methyltransferase MLL4lysine (K)-specific methyltransferase 2Bmixed lineage leukemia gene homolog 2myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosoph
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000406403, ENST00000221232, 
ENST00000358389, ENST00000496327, 
Fusion gene scores* DoF score3 X 2 X 2=124 X 4 X 3=48
# samples 34
** MAII scorelog2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CNOT3 [Title/Abstract] AND KMT2B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNOT3(54645195)-KMT2B(36214043), # 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
TgeneKMT2B

GO:0044648

histone H3-K4 dimethylation

25561738

TgeneKMT2B

GO:0097692

histone H3-K4 monomethylation

25561738



check button Fusion gene information
* 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-24-2019-01ACNOT3chr19

54645195

+KMT2Bchr19

36214043

+


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Fusion Gene ORF analysis for CNOT3-KMT2B

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-3UTRENST00000406403ENST00000222270CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
5UTR-3UTRENST00000406403ENST00000420124CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
5UTR-3UTRENST00000406403ENST00000607650CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
5UTR-intronENST00000406403ENST00000341701CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000221232ENST00000222270CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000221232ENST00000420124CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000221232ENST00000607650CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000358389ENST00000222270CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000358389ENST00000420124CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000358389ENST00000607650CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000496327ENST00000222270CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000496327ENST00000420124CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-3UTRENST00000496327ENST00000607650CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-intronENST00000221232ENST00000341701CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-intronENST00000358389ENST00000341701CNOT3chr19

54645195

+KMT2Bchr19

36214043

+
intron-intronENST00000496327ENST00000341701CNOT3chr19

54645195

+KMT2Bchr19

36214043

+

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 CNOT3-KMT2B


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)


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Fusion Protein Features for CNOT3-KMT2B


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/:54645195/:36214043)
- 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
..
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: 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}.

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 CNOT3-KMT2B


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 CNOT3-KMT2B


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 CNOT3-KMT2B


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 CNOT3-KMT2B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCNOT3C0033578Prostatic Neoplasms2CTD_human
HgeneCNOT3C0376358Malignant neoplasm of prostate2CTD_human
HgeneCNOT3C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CGI;CTD_human;ORPHANET
TgeneC4310633DYSTONIA 28, CHILDHOOD-ONSET3GENOMICS_ENGLAND;UNIPROT
TgeneC0013421Dystonia1CTD_human
TgeneC0393588Dystonia, Paroxysmal1CTD_human
TgeneC0393610Dystonia, Diurnal1CTD_human
TgeneC0751093Dystonia, Limb1CTD_human
TgeneC2239176Liver carcinoma1CTD_human