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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:MEX3D-TCF3 (FusionGDB2 ID:53158)

Fusion Gene Summary for MEX3D-TCF3

check button Fusion gene summary
Fusion gene informationFusion gene name: MEX3D-TCF3
Fusion gene ID: 53158
HgeneTgene
Gene symbol

MEX3D

TCF3

Gene ID

399664

83439

Gene namemex-3 RNA binding family member Dtranscription factor 7 like 1
SynonymsMEX-3D|MEX3|OK/SW-cl.4|RKHD1|RNF193|TINOTCF-3|TCF3
Cytomap

19p13.3

2p11.2

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein MEX3DRING finger and KH domain-containing protein 1RING finger protein 193bcl-2 ARE RNA binding proteinring finger (C3HC4 type) and KH domain containing 1ring finger and KH domain containing 1transcription factor 7-like 1HMG box transcription factor 3transcription factor 7-like 1 (T-cell specific, HMG-box)
Modification date2020031320200313
UniProtAcc

Q86XN8

TFPT

Ensembl transtripts involved in fusion geneENST00000388824, ENST00000402693, 
ENST00000395423, ENST00000453954, 
ENST00000588136, ENST00000262965, 
ENST00000344749, 
Fusion gene scores* DoF score4 X 2 X 3=2412 X 15 X 8=1440
# samples 517
** MAII scorelog2(5/24*10)=1.05889368905357
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(17/1440*10)=-3.08246216019197
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MEX3D [Title/Abstract] AND TCF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMEX3D(1567463)-TCF3(1646426), # samples:3
TCF3(1615283)-MEX3D(1556922), # samples:2
Anticipated loss of major functional domain due to fusion event.MEX3D-TCF3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
MEX3D-TCF3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
MEX3D-TCF3 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
TCF3-MEX3D seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
TCF3-MEX3D seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
TCF3-MEX3D seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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

check buttonFusion gene breakpoints across MEX3D (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across TCF3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4ESCATCGA-Q9-A6FU-01AMEX3Dchr19

1567463

-TCF3chr19

1646426

-
ChimerDB4ESCATCGA-Q9-A6FUMEX3Dchr19

1567462

-TCF3chr19

1632404

-
ChimerDB4ESCATCGA-Q9-A6FUMEX3Dchr19

1567462

-TCF3chr19

1646426

-
ChimerDB4ESCATCGA-Q9-A6FUMEX3Dchr19

1567463

-TCF3chr19

1646426

-


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Fusion Gene ORF analysis for MEX3D-TCF3

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
5CDS-intronENST00000388824ENST00000395423MEX3Dchr19

1567463

-TCF3chr19

1646426

-
5CDS-intronENST00000388824ENST00000395423MEX3Dchr19

1567462

-TCF3chr19

1632404

-
5CDS-intronENST00000388824ENST00000395423MEX3Dchr19

1567462

-TCF3chr19

1646426

-
5CDS-intronENST00000388824ENST00000453954MEX3Dchr19

1567463

-TCF3chr19

1646426

-
5CDS-intronENST00000388824ENST00000453954MEX3Dchr19

1567462

-TCF3chr19

1632404

-
5CDS-intronENST00000388824ENST00000453954MEX3Dchr19

1567462

-TCF3chr19

1646426

-
5CDS-intronENST00000388824ENST00000588136MEX3Dchr19

1567463

-TCF3chr19

1646426

-
5CDS-intronENST00000388824ENST00000588136MEX3Dchr19

1567462

-TCF3chr19

1632404

-
5CDS-intronENST00000388824ENST00000588136MEX3Dchr19

1567462

-TCF3chr19

1646426

-
5CDS-intronENST00000402693ENST00000395423MEX3Dchr19

1567463

-TCF3chr19

1646426

-
5CDS-intronENST00000402693ENST00000395423MEX3Dchr19

1567462

-TCF3chr19

1632404

-
5CDS-intronENST00000402693ENST00000395423MEX3Dchr19

1567462

-TCF3chr19

1646426

-
5CDS-intronENST00000402693ENST00000453954MEX3Dchr19

1567463

-TCF3chr19

1646426

-
5CDS-intronENST00000402693ENST00000453954MEX3Dchr19

1567462

-TCF3chr19

1632404

-
5CDS-intronENST00000402693ENST00000453954MEX3Dchr19

1567462

-TCF3chr19

1646426

-
5CDS-intronENST00000402693ENST00000588136MEX3Dchr19

1567463

-TCF3chr19

1646426

-
5CDS-intronENST00000402693ENST00000588136MEX3Dchr19

1567462

-TCF3chr19

1632404

-
5CDS-intronENST00000402693ENST00000588136MEX3Dchr19

1567462

-TCF3chr19

1646426

-
Frame-shiftENST00000388824ENST00000262965MEX3Dchr19

1567462

-TCF3chr19

1632404

-
Frame-shiftENST00000388824ENST00000344749MEX3Dchr19

1567462

-TCF3chr19

1632404

-
Frame-shiftENST00000402693ENST00000262965MEX3Dchr19

1567462

-TCF3chr19

1632404

-
Frame-shiftENST00000402693ENST00000344749MEX3Dchr19

1567462

-TCF3chr19

1632404

-
In-frameENST00000388824ENST00000262965MEX3Dchr19

1567463

-TCF3chr19

1646426

-
In-frameENST00000388824ENST00000262965MEX3Dchr19

1567462

-TCF3chr19

1646426

-
In-frameENST00000388824ENST00000344749MEX3Dchr19

1567463

-TCF3chr19

1646426

-
In-frameENST00000388824ENST00000344749MEX3Dchr19

1567462

-TCF3chr19

1646426

-
In-frameENST00000402693ENST00000262965MEX3Dchr19

1567463

-TCF3chr19

1646426

-
In-frameENST00000402693ENST00000262965MEX3Dchr19

1567462

-TCF3chr19

1646426

-
In-frameENST00000402693ENST00000344749MEX3Dchr19

1567463

-TCF3chr19

1646426

-
In-frameENST00000402693ENST00000344749MEX3Dchr19

1567462

-TCF3chr19

1646426

-

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 MEX3D-TCF3


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.
genomic feature

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 MEX3D-TCF3


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/chr19:1567463/chr19:1646426)
- 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
MEX3D

Q86XN8

TCF3

TFPT

FUNCTION: RNA binding protein, may be involved in post-transcriptional regulatory mechanisms. {ECO:0000250}.253

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
TgeneTCF3chr19:1567462chr19:1646426ENST00000262965119549_60224655.0DomainbHLH
TgeneTCF3chr19:1567462chr19:1646426ENST00000344749119549_60224652.0DomainbHLH
TgeneTCF3chr19:1567462chr19:1646426ENST00000588136019549_60224527.0DomainbHLH
TgeneTCF3chr19:1567463chr19:1646426ENST00000262965119549_60224655.0DomainbHLH
TgeneTCF3chr19:1567463chr19:1646426ENST00000344749119549_60224652.0DomainbHLH
TgeneTCF3chr19:1567463chr19:1646426ENST00000588136019549_60224527.0DomainbHLH
TgeneTCF3chr19:1567462chr19:1646426ENST00000262965119170_17624655.0MotifNuclear localization signal
TgeneTCF3chr19:1567462chr19:1646426ENST00000344749119170_17624652.0MotifNuclear localization signal
TgeneTCF3chr19:1567462chr19:1646426ENST00000588136019170_17624527.0MotifNuclear localization signal
TgeneTCF3chr19:1567463chr19:1646426ENST00000262965119170_17624655.0MotifNuclear localization signal
TgeneTCF3chr19:1567463chr19:1646426ENST00000344749119170_17624652.0MotifNuclear localization signal
TgeneTCF3chr19:1567463chr19:1646426ENST00000588136019170_17624527.0MotifNuclear localization signal
TgeneTCF3chr19:1567462chr19:1646426ENST00000262965119389_42524655.0RegionNote=Leucine-zipper
TgeneTCF3chr19:1567462chr19:1646426ENST00000344749119389_42524652.0RegionNote=Leucine-zipper
TgeneTCF3chr19:1567462chr19:1646426ENST00000588136019389_42524527.0RegionNote=Leucine-zipper
TgeneTCF3chr19:1567463chr19:1646426ENST00000262965119389_42524655.0RegionNote=Leucine-zipper
TgeneTCF3chr19:1567463chr19:1646426ENST00000344749119389_42524652.0RegionNote=Leucine-zipper
TgeneTCF3chr19:1567463chr19:1646426ENST00000588136019389_42524527.0RegionNote=Leucine-zipper

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMEX3Dchr19:1567462chr19:1646426ENST00000388824-13179_240198667.0DomainKH 1
HgeneMEX3Dchr19:1567462chr19:1646426ENST00000388824-13273_334198667.0DomainKH 2
HgeneMEX3Dchr19:1567462chr19:1646426ENST00000402693-12179_240198652.0DomainKH 1
HgeneMEX3Dchr19:1567462chr19:1646426ENST00000402693-12273_334198652.0DomainKH 2
HgeneMEX3Dchr19:1567463chr19:1646426ENST00000388824-13179_240198667.0DomainKH 1
HgeneMEX3Dchr19:1567463chr19:1646426ENST00000388824-13273_334198667.0DomainKH 2
HgeneMEX3Dchr19:1567463chr19:1646426ENST00000402693-12179_240198652.0DomainKH 1
HgeneMEX3Dchr19:1567463chr19:1646426ENST00000402693-12273_334198652.0DomainKH 2
HgeneMEX3Dchr19:1567462chr19:1646426ENST00000388824-13600_640198667.0Zinc fingerRING-type
HgeneMEX3Dchr19:1567462chr19:1646426ENST00000402693-12600_640198652.0Zinc fingerRING-type
HgeneMEX3Dchr19:1567463chr19:1646426ENST00000388824-13600_640198667.0Zinc fingerRING-type
HgeneMEX3Dchr19:1567463chr19:1646426ENST00000402693-12600_640198652.0Zinc fingerRING-type
TgeneTCF3chr19:1567462chr19:1646426ENST0000026296511919_2724655.0MotifNote=9aaTAD
TgeneTCF3chr19:1567462chr19:1646426ENST0000034474911919_2724652.0MotifNote=9aaTAD
TgeneTCF3chr19:1567462chr19:1646426ENST0000058813601919_2724527.0MotifNote=9aaTAD
TgeneTCF3chr19:1567463chr19:1646426ENST0000026296511919_2724655.0MotifNote=9aaTAD
TgeneTCF3chr19:1567463chr19:1646426ENST0000034474911919_2724652.0MotifNote=9aaTAD
TgeneTCF3chr19:1567463chr19:1646426ENST0000058813601919_2724527.0MotifNote=9aaTAD


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Fusion Gene Sequence for MEX3D-TCF3


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 MEX3D-TCF3


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 MEX3D-TCF3


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 MEX3D-TCF3


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