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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:TCOF1-BCOR (FusionGDB2 ID:HG6949TG54880)

Fusion Gene Summary for TCOF1-BCOR

check button Fusion gene summary
Fusion gene informationFusion gene name: TCOF1-BCOR
Fusion gene ID: hg6949tg54880
HgeneTgene
Gene symbol

TCOF1

BCOR

Gene ID

6949

54880

Gene nametreacle ribosome biogenesis factor 1BCL6 corepressor
SynonymsMFD1|TCS|TCS1|treacleANOP2|MAA2|MCOPS2
Cytomap('TCOF1')('BCOR')

5q32-q33.1

Xp11.4

Type of geneprotein-codingprotein-coding
Descriptiontreacle proteinTreacher Collins syndrome proteinTreacher Collins-Franceschetti syndrome 1nucleolar trafficking phosphoproteinBCL-6 corepressorBCL-6 coreceptorBCL-6 interacting corepressorBCL6 interacting corepressor
Modification date2020031320200328
UniProtAcc.

Q6W2J9

Ensembl transtripts involved in fusion geneENST00000323668, ENST00000377797, 
ENST00000439160, ENST00000445265, 
ENST00000451292, ENST00000504761, 
ENST00000513346, ENST00000394269, 
ENST00000506063, 
Fusion gene scores* DoF score20 X 12 X 3=7206 X 12 X 4=288
# samples 218
** MAII scorelog2(21/720*10)=-1.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/288*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TCOF1 [Title/Abstract] AND BCOR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTCOF1(149777992)-BCOR(39994654), # 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
TgeneBCOR

GO:0035518

histone H2A monoubiquitination

16943429

TgeneBCOR

GO:0045892

negative regulation of transcription, DNA-templated

10898795



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
ChiTaRS5.0N/ADL058916TCOF1chr5

149777992

+BCORchrX

39994654

-


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Fusion Gene ORF analysis for TCOF1-BCOR

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-intronENST00000323668ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000323668ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000323668ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000323668ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000323668ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000377797ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000377797ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000377797ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000377797ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000377797ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000439160ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000439160ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000439160ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000439160ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000439160ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000445265ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000445265ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000445265ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000445265ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000445265ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000451292ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000451292ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000451292ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000451292ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000451292ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000504761ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000504761ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000504761ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000504761ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000504761ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000513346ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000513346ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000513346ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000513346ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
5CDS-intronENST00000513346ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000394269ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000394269ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000394269ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000394269ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000394269ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000506063ENST00000342274TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000506063ENST00000378444TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000506063ENST00000378455TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000506063ENST00000378463TCOF1chr5

149777992

+BCORchrX

39994654

-
intron-intronENST00000506063ENST00000397354TCOF1chr5

149777992

+BCORchrX

39994654

-

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 TCOF1-BCOR


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 TCOF1-BCOR


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/:149777992/:39994654)
- 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
.BCOR

Q6W2J9

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 corepressor. May specifically inhibit gene expression when recruited to promoter regions by sequence-specific DNA-binding proteins such as BCL6 and MLLT3. This repression may be mediated at least in part by histone deacetylase activities which can associate with this corepressor. Involved in the repression of TFAP2A; impairs binding of BCL6 and KDM2B to TFAP2A promoter regions. Via repression of TFAP2A acts as a negative regulator of osteo-dentiogenic capacity in adult stem cells; the function implies inhibition of methylation on histone H3 'Lys-4' (H3K4me3) and 'Lys-36' (H3K36me2). {ECO:0000269|PubMed:10898795, ECO:0000269|PubMed:15004558, ECO:0000269|PubMed:18280243, ECO:0000269|PubMed:19578371, ECO:0000269|PubMed:23911289}.

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 TCOF1-BCOR


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 TCOF1-BCOR


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 TCOF1-BCOR


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 TCOF1-BCOR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTCOF1C0265241Franceschetti-Klein syndrome7CLINGEN
HgeneTCOF1C0242387Mandibulofacial Dysostosis5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTCOF1C0152423Congenital small ears1GENOMICS_ENGLAND
HgeneTCOF1C0376634Craniofacial Abnormalities1CTD_human
TgeneC1846265Microphthalmia, syndromic 24CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0023487Acute Promyelocytic Leukemia2ORPHANET
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0022665Kidney Neoplasm1CTD_human
TgeneC0027708Nephroblastoma1CTD_human
TgeneC0029463Osteosarcoma1CTD_human
TgeneC0206651Clear Cell Sarcoma of Soft Tissue1CTD_human
TgeneC0206656Embryonal Rhabdomyosarcoma1CTD_human
TgeneC0334488Clear cell sarcoma of kidney1ORPHANET
TgeneC0740457Malignant neoplasm of kidney1CTD_human
TgeneC0796016Microphthalmia, syndromic 11CTD_human;ORPHANET
TgeneC2930471Bilateral Wilms Tumor1CTD_human