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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:CTCF-TBCD (FusionGDB2 ID:HG10664TG6904)

Fusion Gene Summary for CTCF-TBCD

check button Fusion gene summary
Fusion gene informationFusion gene name: CTCF-TBCD
Fusion gene ID: hg10664tg6904
HgeneTgene
Gene symbol

CTCF

TBCD

Gene ID

10664

6904

Gene nameCCCTC-binding factortubulin folding cofactor D
SynonymsCFAP108|FAP108|MRD21PEBAT|SSD-1|tfcD
Cytomap('CTCF')('TBCD')

16q22.1

17q25.3

Type of geneprotein-codingprotein-coding
Descriptiontranscriptional repressor CTCF11 zinc finger transcriptional repressor11-zinc finger proteinCCCTC-binding factor (zinc finger protein)CTCFL paralogtubulin-specific chaperone Dbeta-tubulin cofactor D
Modification date2020031320200313
UniProtAcc

P49711

.
Ensembl transtripts involved in fusion geneENST00000264010, ENST00000401394, 
Fusion gene scores* DoF score18 X 16 X 10=288019 X 22 X 13=5434
# samples 2628
** MAII scorelog2(26/2880*10)=-3.46948528330122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/5434*10)=-4.27851583327701
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTCF [Title/Abstract] AND TBCD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTCF(67605167)-TBCD(80869634), # 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
HgeneCTCF

GO:0000122

negative regulation of transcription by RNA polymerase II

8649389

HgeneCTCF

GO:0016584

nucleosome positioning

18654629

HgeneCTCF

GO:0045892

negative regulation of transcription, DNA-templated

8649389|18413740

HgeneCTCF

GO:0045893

positive regulation of transcription, DNA-templated

9407128

TgeneTBCD

GO:0006457

protein folding

20740604

TgeneTBCD

GO:0007021

tubulin complex assembly

28158450

TgeneTBCD

GO:0007023

post-chaperonin tubulin folding pathway

11847227

TgeneTBCD

GO:0031115

negative regulation of microtubule polymerization

10831612|20740604



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
ChimerDB4Non-CancerTCGA-IN-8462-11ACTCFchr16

67605167

+TBCDchr17

80869634

+


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Fusion Gene ORF analysis for CTCF-TBCD

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-3CDSENST00000264010ENST00000355528CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-3CDSENST00000401394ENST00000355528CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-intronENST00000264010ENST00000397466CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-intronENST00000264010ENST00000539345CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-intronENST00000264010ENST00000576691CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-intronENST00000401394ENST00000397466CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-intronENST00000401394ENST00000539345CTCFchr16

67605167

+TBCDchr17

80869634

+
5UTR-intronENST00000401394ENST00000576691CTCFchr16

67605167

+TBCDchr17

80869634

+

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 CTCF-TBCD


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)
CTCFchr1667605167+TBCDchr1780869633+2.18E-101
CTCFchr1667605167+TBCDchr1780869633+2.18E-101


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%

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Fusion Protein Features for CTCF-TBCD


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/:67605167/:80869634)
- 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
CTCF

P49711

.
FUNCTION: Chromatin binding factor that binds to DNA sequence specific sites. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Acts as transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor. Plays a critical role in the epigenetic regulation. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region (ICR) mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays an important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X- inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Regulates asynchronous replication of IGF2/H19. Plays a role in the recruitment of CENPE to the pericentromeric/centromeric regions of the chromosome during mitosis (PubMed:26321640). {ECO:0000269|PubMed:11743158, ECO:0000269|PubMed:16815976, ECO:0000269|PubMed:17827499, ECO:0000269|PubMed:18347100, ECO:0000269|PubMed:18413740, ECO:0000269|PubMed:18550811, ECO:0000269|PubMed:18654629, ECO:0000269|PubMed:19322193, ECO:0000269|PubMed:26321640, ECO:0000269|PubMed:8649389, ECO:0000269|PubMed:9591631}.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 CTCF-TBCD


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 CTCF-TBCD


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 CTCF-TBCD


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 CTCF-TBCD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCTCFC3809686MENTAL RETARDATION, AUTOSOMAL DOMINANT 217CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCTCFC0036341Schizophrenia1PSYGENET
HgeneCTCFC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
HgeneCTCFC0376407Granulomatous Slack Skin1CTD_human
HgeneCTCFC1860789Leukemia, Megakaryoblastic, of Down Syndrome1CTD_human
HgeneCTCFC1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
HgeneCTCFC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4310671ENCEPHALOPATHY, PROGRESSIVE, EARLY-ONSET, WITH BRAIN ATROPHY AND THIN CORPUS CALLOSUM4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0025958Microcephaly2CTD_human
TgeneC0036572Seizures2CTD_human;GENOMICS_ENGLAND
TgeneC1956147Microlissencephaly2CTD_human
TgeneC3853041Severe Congenital Microcephaly2CTD_human
TgeneC0008073Developmental Disabilities1CTD_human
TgeneC0020796Profound Mental Retardation1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0023944Locked-In Syndrome1CTD_human
TgeneC0025363Mental Retardation, Psychosocial1CTD_human
TgeneC0029124Optic Atrophy1CTD_human
TgeneC0034372Quadriplegia1CTD_human
TgeneC0035229Respiratory Insufficiency1CTD_human
TgeneC0037769West Syndrome1GENOMICS_ENGLAND
TgeneC0085996Child Development Deviations1CTD_human
TgeneC0085997Child Development Disorders, Specific1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0151786Muscle Weakness1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0235063Respiratory Depression1CTD_human
TgeneC0270715Degenerative Diseases, Central Nervous System1CTD_human
TgeneC0270790Quadriparesis1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0426970Spastic Quadriplegia1CTD_human
TgeneC0431380Cortical Dysplasia1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0524851Neurodegenerative Disorders1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751460Flaccid Quadriplegia1CTD_human
TgeneC0751461Paralysis, Spinal, Quadriplegic1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC0751733Degenerative Diseases, Spinal Cord1CTD_human
TgeneC0917816Mental deficiency1CTD_human
TgeneC1145670Respiratory Failure1CTD_human
TgeneC1955869Malformations of Cortical Development1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC3714756Intellectual Disability1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human