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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:HLA-F-AS1-TSC1 (FusionGDB2 ID:HG285830TG7248)

Fusion Gene Summary for HLA-F-AS1-TSC1

check button Fusion gene summary
Fusion gene informationFusion gene name: HLA-F-AS1-TSC1
Fusion gene ID: hg285830tg7248
HgeneTgene
Gene symbol

HLA-F-AS1

TSC1

Gene ID

285830

7248

Gene nameHLA-F antisense RNA 1TSC complex subunit 1
Synonyms-LAM|TSC
Cytomap('HLA-F-AS1')('TSC1')

6p22.1

9q34.13

Type of genencRNAprotein-coding
DescriptionHLA-F antisense RNA 1 (non-protein coding)hamartintruncated hemartintuberous sclerosis 1 protein
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000458236, 
Fusion gene scores* DoF score2 X 2 X 2=82 X 2 X 2=8
# samples 22
** MAII scorelog2(2/8*10)=1.32192809488736log2(2/8*10)=1.32192809488736
Context

PubMed: HLA-F-AS1 [Title/Abstract] AND TSC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHLA-F-AS1(29716029)-TSC1(135804247), # 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
TgeneTSC1

GO:0006417

regulation of translation

17308101

TgeneTSC1

GO:0032780

negative regulation of ATPase activity

29127155

TgeneTSC1

GO:0032868

response to insulin

16996505

TgeneTSC1

GO:0050821

protein stabilization

11175345

TgeneTSC1

GO:0051492

regulation of stress fiber assembly

10806479

TgeneTSC1

GO:0051894

positive regulation of focal adhesion assembly

10806479

TgeneTSC1

GO:0090630

activation of GTPase activity

10806479



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


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Fusion Gene ORF analysis for HLA-F-AS1-TSC1

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

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Fusion Genomic Features for HLA-F-AS1-TSC1


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 HLA-F-AS1-TSC1


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/:29716029/:135804247)
- 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 HLA-F-AS1-TSC1


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 HLA-F-AS1-TSC1


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 HLA-F-AS1-TSC1


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 HLA-F-AS1-TSC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1854465TUBEROUS SCLEROSIS 1 (disorder)19CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0041341Tuberous Sclerosis11CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneC0265319Fibrous skin tumor of tuberous sclerosis3CTD_human
TgeneC0751674Lymphangioleiomyomatosis3CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC0014544Epilepsy2CTD_human
TgeneC0086237Epilepsy, Cryptogenic2CTD_human
TgeneC0236018Aura2CTD_human
TgeneC0751111Awakening Epilepsy2CTD_human
TgeneC1846385FOCAL CORTICAL DYSPLASIA OF TAYLOR2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1846386Focal Cortical Dysplasia of Taylor, Type IIa2CTD_human
TgeneC1846389Focal Cortical Dysplasia of Taylor, Type IIb2CTD_human
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0006111Brain Diseases1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0009241Cognition Disorders1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0026640Mouth Neoplasms1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0037769West Syndrome1CTD_human
TgeneC0085584Encephalopathies1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0153381Malignant neoplasm of mouth1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0279607Adult Hepatocellular Carcinoma1ORPHANET
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CGI;CTD_human
TgeneC0393698Cryptogenic Infantile Spasms1CTD_human
TgeneC0393699Symptomatic Infantile Spasms1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0546878Nodding spasm1CTD_human
TgeneC0553558Jackknife Seizures1CTD_human
TgeneC0684276Hypsarrhythmia1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC0751776Atypical Inclusion-Body Disease1CTD_human
TgeneC0751777Familial Progressive Myoclonic Epilepsy1CTD_human
TgeneC0751778Myoclonic Epilepsies, Progressive1CTD_human
TgeneC0751779Action Myoclonus-Renal Failure Syndrome1CTD_human
TgeneC0751780Biotin-Responsive Encephalopathy1CTD_human
TgeneC0751781Dentatorubral-Pallidoluysian Atrophy1CTD_human
TgeneC0751782May-White Syndrome1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC1527306spasmus nutans1CTD_human
TgeneC1527366Salaam Seizures1CTD_human
TgeneC2239176Liver carcinoma1CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human