Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:BCL11B-TRDC (FusionGDB2 ID:HG64919TG28526)

Fusion Gene Summary for BCL11B-TRDC

check button Fusion gene summary
Fusion gene informationFusion gene name: BCL11B-TRDC
Fusion gene ID: hg64919tg28526
HgeneTgene
Gene symbol

BCL11B

TRDC

Gene ID

64919

28526

Gene nameBAF chromatin remodeling complex subunit BCL11B
SynonymsATL1|ATL1-alpha|ATL1-beta|ATL1-delta|ATL1-gamma|CTIP-2|CTIP2|IDDFSTA|IMD49|RIT1|ZNF856B|hRIT1-alpha
Cytomap('BCL11B')('TRDC')

14q32.2

Type of geneprotein-coding
DescriptionB-cell lymphoma/leukemia 11BB cell CLL/lymphoma 11BB-cell CLL/lymphoma 11B (zinc finger protein)B-cell CLL/lymphoma 11B/T-cell receptor delta constant region fusion proteinB-cell lymphoma/leukaemia 11BBCL-11BBCL11B, BAF complex componentBCL11B/TRDC
Modification date20200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000345514, ENST00000357195, 
ENST00000443726, 
Fusion gene scores* DoF score6 X 8 X 2=962 X 3 X 2=12
# samples 83
** MAII scorelog2(8/96*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: BCL11B [Title/Abstract] AND TRDC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCL11B(99697681)-TRDC(22931921), # samples:1
BCL11B(99723807)-TRDC(22931918), # samples:1
Anticipated loss of major functional domain due to fusion event.BCL11B-TRDC seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
BCL11B-TRDC seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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 BCL11B (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 TRDC (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
* 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


Top

Fusion Gene ORF analysis for BCL11B-TRDC

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

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
ENST00000357195ENST00000390477BCL11Bchr1499697681-TRDCchr1422931921+0.001483210.99851674
ENST00000357195ENST00000390477BCL11Bchr1499723807-TRDCchr1422931918+0.0008134240.9991866
ENST00000345514ENST00000390477BCL11Bchr1499723807-TRDCchr1422931918+0.001167020.998833

Top

Fusion Genomic Features for BCL11B-TRDC


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)
BCL11Bchr1499697681-TRDCchr1422931923+0.0587294850.9412705
BCL11Bchr1499723807-TRDCchr1422931923+0.0198170060.980183
BCL11Bchr1499697681-TRDCchr1422931923+0.0587294850.9412705
BCL11Bchr1499723807-TRDCchr1422931923+0.0198170060.980183

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.
genomic feature of top 1%

Top

Fusion Protein Features for BCL11B-TRDC


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/chr14:99697681/chr14:22931921)
- 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
TgeneTRDCchr14:99697681chr14:22931921ENST00000390477-14130_15293146.66666666666666TransmembraneHelical
TgeneTRDCchr14:99723807chr14:22931918ENST00000390477-14130_15293146.66666666666666TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13529_5530824.0Compositional biasNote=Glu-rich
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13569_6610824.0Compositional biasNote=Gly-rich
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34529_553213895.0Compositional biasNote=Glu-rich
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34569_661213895.0Compositional biasNote=Gly-rich
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23529_553142824.0Compositional biasNote=Glu-rich
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23569_661142824.0Compositional biasNote=Gly-rich
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24529_553142895.0Compositional biasNote=Glu-rich
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24569_661142895.0Compositional biasNote=Gly-rich
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13221_2510824.0Zinc fingerC2H2-type 1
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13427_4540824.0Zinc fingerC2H2-type 2
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13455_4820824.0Zinc fingerC2H2-type 3
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13796_8230824.0Zinc fingerC2H2-type 4
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13824_8530824.0Zinc fingerC2H2-type 5
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000345514-13854_8840824.0Zinc fingerC2H2-type 6
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34221_251213895.0Zinc fingerC2H2-type 1
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34427_454213895.0Zinc fingerC2H2-type 2
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34455_482213895.0Zinc fingerC2H2-type 3
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34796_823213895.0Zinc fingerC2H2-type 4
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34824_853213895.0Zinc fingerC2H2-type 5
HgeneBCL11Bchr14:99697681chr14:22931921ENST00000357195-34854_884213895.0Zinc fingerC2H2-type 6
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23221_251142824.0Zinc fingerC2H2-type 1
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23427_454142824.0Zinc fingerC2H2-type 2
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23455_482142824.0Zinc fingerC2H2-type 3
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23796_823142824.0Zinc fingerC2H2-type 4
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23824_853142824.0Zinc fingerC2H2-type 5
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000345514-23854_884142824.0Zinc fingerC2H2-type 6
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24221_251142895.0Zinc fingerC2H2-type 1
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24427_454142895.0Zinc fingerC2H2-type 2
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24455_482142895.0Zinc fingerC2H2-type 3
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24796_823142895.0Zinc fingerC2H2-type 4
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24824_853142895.0Zinc fingerC2H2-type 5
HgeneBCL11Bchr14:99723807chr14:22931918ENST00000357195-24854_884142895.0Zinc fingerC2H2-type 6


Top

Fusion Gene Sequence for BCL11B-TRDC


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.

Top

Fusion Gene PPI Analysis for BCL11B-TRDC


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


Top

Related Drugs for BCL11B-TRDC


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for BCL11B-TRDC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBCL11BC4310656IMMUNODEFICIENCY 492CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneBCL11BC0024299Lymphoma1CTD_human
HgeneBCL11BC1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
HgeneBCL11BC3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneBCL11BC4748152INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY, DYSMORPHIC FACIES, AND T-CELL ABNORMALITIES1GENOMICS_ENGLAND