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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:36573)

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: 36573
HgeneTgene
Gene symbol

HLA-F-AS1

TSC1

Gene ID

285830

7248

Gene nameHLA-F antisense RNA 1TSC complex subunit 1
Synonyms-LAM|TSC
Cytomap

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, ENST00000298552, 
ENST00000545250, ENST00000440111, 
ENST00000403810, ENST00000475903, 
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 buttonFusion gene breakpoints across HLA-F-AS1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across TSC1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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/ABF738281HLA-F-AS1chr6

29716029

-TSC1chr9

135804247

+


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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
intron-3CDSENST00000458236ENST00000298552HLA-F-AS1chr6

29716029

-TSC1chr9

135804247

+
intron-3CDSENST00000458236ENST00000545250HLA-F-AS1chr6

29716029

-TSC1chr9

135804247

+
intron-3CDSENST00000458236ENST00000440111HLA-F-AS1chr6

29716029

-TSC1chr9

135804247

+
intron-3CDSENST00000458236ENST00000403810HLA-F-AS1chr6

29716029

-TSC1chr9

135804247

+
intron-5UTRENST00000458236ENST00000475903HLA-F-AS1chr6

29716029

-TSC1chr9

135804247

+

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)

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.

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 HLA-F-AS1-TSC1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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
TgeneTSC1C1854465TUBEROUS SCLEROSIS 1 (disorder)19CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneTSC1C0041341Tuberous Sclerosis11CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneTSC1C0265319Fibrous skin tumor of tuberous sclerosis3CTD_human
TgeneTSC1C0751674Lymphangioleiomyomatosis3CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneTSC1C0014544Epilepsy2CTD_human
TgeneTSC1C0086237Epilepsy, Cryptogenic2CTD_human
TgeneTSC1C0236018Aura2CTD_human
TgeneTSC1C0751111Awakening Epilepsy2CTD_human
TgeneTSC1C1846385FOCAL CORTICAL DYSPLASIA OF TAYLOR2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneTSC1C1846386Focal Cortical Dysplasia of Taylor, Type IIa2CTD_human
TgeneTSC1C1846389Focal Cortical Dysplasia of Taylor, Type IIb2CTD_human
TgeneTSC1C0004352Autistic Disorder1CTD_human
TgeneTSC1C0006111Brain Diseases1CTD_human
TgeneTSC1C0007134Renal Cell Carcinoma1CTD_human
TgeneTSC1C0007137Squamous cell carcinoma1CTD_human
TgeneTSC1C0009241Cognition Disorders1CTD_human
TgeneTSC1C0022333Jacksonian Seizure1CTD_human
TgeneTSC1C0026640Mouth Neoplasms1CTD_human
TgeneTSC1C0036572Seizures1CTD_human
TgeneTSC1C0037769West Syndrome1CTD_human
TgeneTSC1C0085584Encephalopathies1CTD_human
TgeneTSC1C0149958Complex partial seizures1CTD_human
TgeneTSC1C0153381Malignant neoplasm of mouth1CTD_human
TgeneTSC1C0234533Generalized seizures1CTD_human
TgeneTSC1C0234535Clonic Seizures1CTD_human
TgeneTSC1C0270824Visual seizure1CTD_human
TgeneTSC1C0270844Tonic Seizures1CTD_human
TgeneTSC1C0270846Epileptic drop attack1CTD_human
TgeneTSC1C0279607Adult Hepatocellular Carcinoma1ORPHANET
TgeneTSC1C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CGI;CTD_human
TgeneTSC1C0393698Cryptogenic Infantile Spasms1CTD_human
TgeneTSC1C0393699Symptomatic Infantile Spasms1CTD_human
TgeneTSC1C0422850Seizures, Somatosensory1CTD_human
TgeneTSC1C0422852Seizures, Auditory1CTD_human
TgeneTSC1C0422853Olfactory seizure1CTD_human
TgeneTSC1C0422854Gustatory seizure1CTD_human
TgeneTSC1C0422855Vertiginous seizure1CTD_human
TgeneTSC1C0494475Tonic - clonic seizures1CTD_human
TgeneTSC1C0546878Nodding spasm1CTD_human
TgeneTSC1C0553558Jackknife Seizures1CTD_human
TgeneTSC1C0684276Hypsarrhythmia1CTD_human
TgeneTSC1C0751056Non-epileptic convulsion1CTD_human
TgeneTSC1C0751110Single Seizure1CTD_human
TgeneTSC1C0751123Atonic Absence Seizures1CTD_human
TgeneTSC1C0751494Convulsive Seizures1CTD_human
TgeneTSC1C0751495Seizures, Focal1CTD_human
TgeneTSC1C0751496Seizures, Sensory1CTD_human
TgeneTSC1C0751776Atypical Inclusion-Body Disease1CTD_human
TgeneTSC1C0751777Familial Progressive Myoclonic Epilepsy1CTD_human
TgeneTSC1C0751778Myoclonic Epilepsies, Progressive1CTD_human
TgeneTSC1C0751779Action Myoclonus-Renal Failure Syndrome1CTD_human
TgeneTSC1C0751780Biotin-Responsive Encephalopathy1CTD_human
TgeneTSC1C0751781Dentatorubral-Pallidoluysian Atrophy1CTD_human
TgeneTSC1C0751782May-White Syndrome1CTD_human
TgeneTSC1C1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneTSC1C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneTSC1C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneTSC1C1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneTSC1C1527306spasmus nutans1CTD_human
TgeneTSC1C1527366Salaam Seizures1CTD_human
TgeneTSC1C2239176Liver carcinoma1CTD_human
TgeneTSC1C3495874Nonepileptic Seizures1CTD_human
TgeneTSC1C4048158Convulsions1CTD_human
TgeneTSC1C4316903Absence Seizures1CTD_human
TgeneTSC1C4317109Epileptic Seizures1CTD_human
TgeneTSC1C4317123Myoclonic Seizures1CTD_human
TgeneTSC1C4505436Generalized Absence Seizures1CTD_human