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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:TFE3-CYP11A1 (FusionGDB2 ID:HG7030TG1583)

Fusion Gene Summary for TFE3-CYP11A1

check button Fusion gene summary
Fusion gene informationFusion gene name: TFE3-CYP11A1
Fusion gene ID: hg7030tg1583
HgeneTgene
Gene symbol

TFE3

CYP11A1

Gene ID

7030

1583

Gene nametranscription factor binding to IGHM enhancer 3cytochrome P450 family 11 subfamily A member 1
SynonymsRCCP2|RCCX1|TFEA|bHLHe33CYP11A|CYPXIA1|P450SCC
Cytomap('TFE3')('CYP11A1')

Xp11.23

15q24.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor E3class E basic helix-loop-helix protein 33transcription factor E family, member Atranscription factor for IgH enhancertranscription factor for immunoglobulin heavy-chain enhancer 3cholesterol side-chain cleavage enzyme, mitochondrialcholesterol 20-22 desmolasecholesterol monooxygenase (side-chain cleaving)cytochrome P450 11A1cytochrome P450 family 11 subfamily A polypeptide 1cytochrome P450(scc)cytochrome P450, subfamily XIA
Modification date2020032720200313
UniProtAcc

P19532

.
Ensembl transtripts involved in fusion geneENST00000315869, ENST00000487451, 
Fusion gene scores* DoF score9 X 12 X 6=6487 X 4 X 4=112
# samples 128
** MAII scorelog2(12/648*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/112*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TFE3 [Title/Abstract] AND CYP11A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTFE3(48891263)-CYP11A1(74637560), # 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
TgeneCYP11A1

GO:0006700

C21-steroid hormone biosynthetic process

11502818|18182448|21636783

TgeneCYP11A1

GO:0008203

cholesterol metabolic process

21636783



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/AAA368421TFE3chrX

48891263

+CYP11A1chr15

74637560

+


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Fusion Gene ORF analysis for TFE3-CYP11A1

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-5UTRENST00000315869ENST00000268053TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-5UTRENST00000315869ENST00000358632TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-5UTRENST00000315869ENST00000419019TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-5UTRENST00000487451ENST00000268053TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-5UTRENST00000487451ENST00000358632TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-5UTRENST00000487451ENST00000419019TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-intronENST00000315869ENST00000467407TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-intronENST00000315869ENST00000541301TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-intronENST00000487451ENST00000467407TFE3chrX

48891263

+CYP11A1chr15

74637560

+
intron-intronENST00000487451ENST00000541301TFE3chrX

48891263

+CYP11A1chr15

74637560

+

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 TFE3-CYP11A1


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 TFE3-CYP11A1


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/:48891263/:74637560)
- 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
TFE3

P19532

.
FUNCTION: Transcription factor that acts as a master regulator of lysosomal biogenesis and immune response (PubMed:2338243, PubMed:29146937, PubMed:30733432, PubMed:31672913). Specifically recognizes and binds E-box sequences (5'-CANNTG-3'); efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFEB or MITF (By similarity). Involved in the cellular response to amino acid availability by acting downstream of MTOR: in the presence of nutrients, TFE3 phosphorylation by MTOR promotes its cytosolic retention and subsequent inactivation (PubMed:31672913). Upon starvation or lysosomal stress, inhibition of MTOR induces TFE3 dephosphorylation, resulting in nuclear localization and transcription factor activity (PubMed:31672913). In association with TFEB, activates the expression of CD40L in T-cells, thereby playing a role in T-cell-dependent antibody responses in activated CD4(+) T-cells and thymus-dependent humoral immunity (By similarity). Specifically recognizes the MUE3 box, a subset of E-boxes, present in the immunoglobulin enhancer (PubMed:2338243). It also binds very well to a USF/MLTF site (PubMed:2338243). May regulate lysosomal positioning in response to nutrient deprivation by promoting the expression of PIP4P1 (PubMed:29146937). Acts as a positive regulator of browning of adipose tissue by promoting expression of target genes; mTOR-dependent phosphorylation promotes cytoplasmic retention of TFE3 and inhibits browning of adipose tissue (By similarity). Maintains the pluripotent state of embryonic stem cells by promoting the expression of genes such as ESRRB; mTOR-dependent nuclear exclusion promotes exit from pluripotency (By similarity). Required to maintain the naive pluripotent state of hematopoietic stem cell; mTOR-dependent cytoplasmic retention of TFE3 promotes the exit of hematopoietic stem cell from pluripotency (PubMed:30733432). {ECO:0000250|UniProtKB:Q64092, ECO:0000269|PubMed:2338243, ECO:0000269|PubMed:29146937, ECO:0000269|PubMed:30733432, ECO:0000269|PubMed:31672913}.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 TFE3-CYP11A1


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 TFE3-CYP11A1


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 TFE3-CYP11A1


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 TFE3-CYP11A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTFE3C4518356MiT family translocation renal cell carcinoma2ORPHANET
HgeneTFE3C0206657Alveolar Soft Part Sarcoma1ORPHANET
HgeneTFE3C0206732Epithelioid hemangioendothelioma1ORPHANET
TgeneC3151055ADRENAL INSUFFICIENCY, CONGENITAL, WITH 46,XY SEX REVERSAL, PARTIAL OR COMPLETE7GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0001623Adrenal gland hypofunction1CTD_human
TgeneC0014170Endometrial Neoplasms1CTD_human
TgeneC0022333Jacksonian Seizure1CTD_human
TgeneC0036572Seizures1CTD_human
TgeneC0149958Complex partial seizures1CTD_human
TgeneC0234533Generalized seizures1CTD_human
TgeneC0234535Clonic Seizures1CTD_human
TgeneC0238395Male Pseudohermaphroditism1CTD_human
TgeneC0270824Visual seizure1CTD_human
TgeneC0270844Tonic Seizures1CTD_human
TgeneC0270846Epileptic drop attack1CTD_human
TgeneC0342474Lipoid congenital adrenal hyperplasia1CTD_human
TgeneC0422850Seizures, Somatosensory1CTD_human
TgeneC0422852Seizures, Auditory1CTD_human
TgeneC0422853Olfactory seizure1CTD_human
TgeneC0422854Gustatory seizure1CTD_human
TgeneC0422855Vertiginous seizure1CTD_human
TgeneC0476089Endometrial Carcinoma1CTD_human
TgeneC0494475Tonic - clonic seizures1CTD_human
TgeneC0751056Non-epileptic convulsion1CTD_human
TgeneC0751110Single Seizure1CTD_human
TgeneC0751123Atonic Absence Seizures1CTD_human
TgeneC0751494Convulsive Seizures1CTD_human
TgeneC0751495Seizures, Focal1CTD_human
TgeneC0751496Seizures, Sensory1CTD_human
TgeneC275182446, XY Disorders of Sex Development1CTD_human
TgeneC348979346,XY Sex Reversal 31CTD_human
TgeneC3495874Nonepileptic Seizures1CTD_human
TgeneC3496069cocaine use1PSYGENET
TgeneC4048158Convulsions1CTD_human
TgeneC4316903Absence Seizures1CTD_human
TgeneC4317109Epileptic Seizures1CTD_human
TgeneC4317123Myoclonic Seizures1CTD_human
TgeneC4505436Generalized Absence Seizures1CTD_human
TgeneC4707238Inherited isolated adrenal insufficiency due to partial CYP11A1 deficiency1ORPHANET