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TFE3 Gene(Protein Coding)

Transcription Factor Binding To IGHM Enhancer 3

GCID:
GC0XM049028
GIFtS:
53
Genes Participants
UDN Logo

Aliases for TFE3 Gene

Aliases for TFE3 Gene

  • Transcription Factor Binding To IGHM Enhancer 3 2 3 5
  • Class E Basic Helix-Loop-Helix Protein 33 3 4
  • Transcription Factor E Family, Member A 2 3
  • BHLHe33 3 4
  • Transcription Factor For Immunoglobulin Heavy-Chain Enhancer 3 3
  • Transcription Factor For IgH Enhancer 3
  • Transcription Factor E3 3
  • RCCP2 3
  • RCCX1 3
  • TFEA 3

External Ids for TFE3 Gene

Previous GeneCards Identifiers for TFE3 Gene

  • GC0XM047669
  • GC0XM047127
  • GC0XM047912
  • GC0XM048642
  • GC0XM048771
  • GC0XM048886
  • GC0XM046545

Summaries for TFE3 Gene

Entrez Gene Summary for TFE3 Gene

  • This gene encodes a basic helix-loop-helix domain-containing transcription factor that binds MUE3-type E-box sequences in the promoter of genes. The encoded protein promotes the expression of genes downstream of transforming growth factor beta (TGF-beta) signaling. This gene may be involved in chromosomal translocations in renal cell carcinomas and other cancers, resulting in the production of fusion proteins. Translocation partners include PRCC (papillary renal cell carcinoma), NONO (non-POU domain containing, octamer-binding), and ASPSCR1 (alveolar soft part sarcoma chromosome region, candidate 1), among other genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

GeneCards Summary for TFE3 Gene

TFE3 (Transcription Factor Binding To IGHM Enhancer 3) is a Protein Coding gene. Diseases associated with TFE3 include Renal Cell Carcinoma, Xp11-Associated and Alveolar Soft Part Sarcoma. Among its related pathways are Mitophagy - animal and TGF-beta Receptor Signaling (WikiPathways). Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is MITF.

UniProtKB/Swiss-Prot for TFE3 Gene

  • Transcription factor that 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. 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. Specifically recognizes the MUE3 box, a subset of E-boxes, present in the immunoglobulin enhancer. It also binds very well to a USF/MLTF site.

Gene Wiki entry for TFE3 Gene

Additional gene information for TFE3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TFE3 Gene

Genomics for TFE3 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TFE3 Gene

Promoters and enhancers for TFE3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XI049037 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 555.1 +2.4 2386 7 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF2 ZBTB7B YY1 ZNF143 TFE3 PRAF2 OTUD5 RNU6-722P SLC38A5 PLP2 GC0XM049007
GH0XI049071 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 4.7 -29.8 -29835 3.7 PKNOX1 SIN3A YY1 ETS1 GLIS2 ZNF143 KLF7 RUNX3 SP3 YY2 PRAF2 CCDC120 GPKOW TFE3 GC0XP049093 WDR45
GH0XI048933 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 3.4 +105.0 105017 9.7 HDGF FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1 IRF4 ENSG00000279155 PQBP1 WAS OTUD5 SLC35A2 TIMM17B PIM2 TBC1D25 ENSG00000204620 ENSG00000228343
GH0XI049034 Enhancer 0.4 ENCODE 4.6 +8.9 8906 1.1 ZNF518A ZNF697 TFE3 GC0XM049007
GH0XI048667 Enhancer 0.3 FANTOM5 4.3 +375.8 375824 0.2 ZNF341 WAS OTUD5 TFE3 GRIPAP1 PIM2 RBM3 PIR44416
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TFE3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TFE3 gene promoter:

Genomic Locations for TFE3 Gene

Genomic Locations for TFE3 Gene
chrX:49,028,726-49,043,517
(GRCh38/hg38)
Size:
14,792 bases
Orientation:
Minus strand
chrX:48,886,242-48,901,012
(GRCh37/hg19)

Genomic View for TFE3 Gene

Genes around TFE3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TFE3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TFE3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TFE3 Gene

Proteins for TFE3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TFE3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P19532-TFE3_HUMAN
    Recommended name:
    Transcription factor E3
    Protein Accession:
    P19532
    Secondary Accessions:
    • A8MZL6
    • Q5JU74
    • Q92757
    • Q92758
    • Q99964

    Protein attributes for TFE3 Gene

    Size:
    575 amino acids
    Molecular mass:
    61521 Da
    Quaternary structure:
    • Homodimer and heterodimer; with TFEB or MITF.
    SequenceCaution:
    • Sequence=CAA35714.1; Type=Frameshift; Positions=557; Evidence={ECO:0000305}; Sequence=CAA65800.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for TFE3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TFE3 Gene

Protein Expression for TFE3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TFE3 Gene

Other Protein References for TFE3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TFE3 Gene

Domains & Families for TFE3 Gene

Gene Families for TFE3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TFE3 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TFE3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P19532

UniProtKB/Swiss-Prot:

TFE3_HUMAN :
  • Belongs to the MiT/TFE family.
Family:
  • Belongs to the MiT/TFE family.
genes like me logo Genes that share domains with TFE3: view

Function for TFE3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TFE3 Gene

GENATLAS Biochemistry:
transcription factor,binding IGH enhancer motif muE3 (see also RCCPX)
UniProtKB/Swiss-Prot Function:
Transcription factor that 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. 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. Specifically recognizes the MUE3 box, a subset of E-boxes, present in the immunoglobulin enhancer. It also binds very well to a USF/MLTF site.

Gene Ontology (GO) - Molecular Function for TFE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity NAS,ISS --
GO:0005515 protein binding IPI 26168401
genes like me logo Genes that share ontologies with TFE3: view
genes like me logo Genes that share phenotypes with TFE3: view

Human Phenotype Ontology for TFE3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TFE3 Gene

MGI Knock Outs for TFE3:

Animal Model Products

miRNA for TFE3 Gene

miRTarBase miRNAs that target TFE3

Clone Products

  • Addgene plasmids for TFE3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for TFE3 Gene

Localization for TFE3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TFE3 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TFE3 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 2
lysosome 2
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TFE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IMP 21209915
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with TFE3: view

Pathways & Interactions for TFE3 Gene

genes like me logo Genes that share pathways with TFE3: view

Gene Ontology (GO) - Biological Process for TFE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with TFE3: view

No data available for SIGNOR curated interactions for TFE3 Gene

Drugs & Compounds for TFE3 Gene

Products:

  1. Drug

(3) Drugs for TFE3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with TFE3: view

Transcripts for TFE3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TFE3 Gene

(2) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(193) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TFE3 Gene

Transcription factor binding to IGHM enhancer 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for TFE3

Alternative Splicing Database (ASD) splice patterns (SP) for TFE3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1: -
SP2: - - -
SP3: - - -
SP4: - -
SP5: - -
SP6:
SP7:
SP8:

Relevant External Links for TFE3 Gene

GeneLoc Exon Structure for
TFE3
ECgene alternative splicing isoforms for
TFE3

Expression for TFE3 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TFE3 Gene

mRNA expression in normal human tissues for TFE3 Gene
mRNA expression by GTEx for TFE3 GenemRNA expression by BioGPS for TFE3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TFE3 Gene

This gene is overexpressed in Whole Blood (x4.6).

Protein differential expression in normal tissues from HIPED for TFE3 Gene

This gene is overexpressed in Serum (31.7), Placenta (9.2), Urinary Bladder (8.0), and Rectum (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TFE3 Gene



Protein tissue co-expression partners for TFE3 Gene

NURSA nuclear receptor signaling pathways regulating expression of TFE3 Gene:

TFE3

SOURCE GeneReport for Unigene cluster for TFE3 Gene:

Hs.730740

mRNA Expression by UniProt/SwissProt for TFE3 Gene:

P19532-TFE3_HUMAN
Tissue specificity: Ubiquitous in fetal and adult tissues.

Evidence on tissue expression from TISSUES for TFE3 Gene

  • Nervous system(4.6)
  • Blood(4.3)
  • Liver(4.3)
  • Lung(2.9)
  • Kidney(2.7)
  • Muscle(2.3)
  • Lymph node(2.1)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TFE3 Gene

Germ Layers:
  • endoderm
  • mesoderm
Systems:
  • respiratory
  • urinary
Organs:
Thorax:
  • lung
Abdomen:
  • kidney
genes like me logo Genes that share expression patterns with TFE3: view

Orthologs for TFE3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TFE3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TFE3 34 33
  • 97.45 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia TFE3 34 33
  • 92.64 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia TFE3 34 33
  • 91.33 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Tfe3 34 16 33
  • 89.8 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Tfe3 33
  • 89.65 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia TFE3 34
  • 76 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia TFE3 34
  • 67 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia TFE3 34
  • 65 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii tfe3b 34 33
  • 64.72 (n)
 OneToMany
tfe3a 34 33
  • 57 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta Mitf 34
  • 21 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea hlh-30 34
  • 25 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 41 (a)
 OneToMany
Species where no ortholog for TFE3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for TFE3 Gene

ENSEMBL:
Gene Tree for TFE3 (if available)
TreeFam:
Gene Tree for TFE3 (if available)

Paralogs for TFE3 Gene

Paralogs for TFE3 Gene

(3) SIMAP similar genes for TFE3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with TFE3: view

Variants for TFE3 Gene

Sequence variations from dbSNP and Humsavar for TFE3 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000946234 -- 49,037,653(-) C/T intron_variant
rs1001456832 -- 49,045,507(-) G/T upstream_transcript_variant
rs1002431841 -- 49,028,971(-) T/C 3_prime_UTR_variant
rs1002846987 -- 49,040,741(-) C/T intron_variant
rs1002878408 -- 49,041,177(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TFE3 Gene

Variant ID Type Subtype PubMed ID
esv32909 CNV gain+loss 17666407
nsv528292 CNV gain 19592680

Variation tolerance for TFE3 Gene

Residual Variation Intolerance Score: 50.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.25; 25.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TFE3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TFE3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TFE3 Gene

Disorders for TFE3 Gene

MalaCards: The human disease database

(17) MalaCards diseases for TFE3 Gene - From: OMIM, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
renal cell carcinoma, xp11-associated
  • rccx1
alveolar soft part sarcoma
  • asps
epithelioid hemangioendothelioma
  • hemangioendothelioma epithelioid
sarcoma
  • connective and soft tissue neoplasm
waardenburg syndrome, type 2a
  • ws2a
- elite association - COSMIC cancer census association via MalaCards
Search TFE3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TFE3_HUMAN
  • Note=A chromosomal aberration involving TFE3 is found in patients with alveolar soft part sarcoma. Translocation t(X;17)(p11;q25) with ASPSCR1 forms a ASPSCR1-TFE3 fusion protein. {ECO:0000269 PubMed:11358836}.
  • Note=Chromosomal aberrations involving TFE3 are found in patients with papillary renal cell carcinoma. Translocation t(X;1)(p11.2;q21.2) with PRCC; translocation t(X;1)(p11.2;p34) with PSF; inversion inv(X)(p11.2;q12) that fuses NONO to TFE3. {ECO:0000269 PubMed:8872474, ECO:0000269 PubMed:8986805}.

Additional Disease Information for TFE3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TFE3: view

No data available for Genatlas for TFE3 Gene

Publications for TFE3 Gene

  1. The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25. (PMID: 11244503) Ladanyi M … Bridge J (Oncogene 2001) 3 4 22 58
  2. Fusion of a novel gene, RCC17, to the TFE3 gene in t(X;17)(p11.2;q25.3)-bearing papillary renal cell carcinomas. (PMID: 11358836) Heimann P … Vassart G (Cancer research 2001) 3 4 22 58
  3. Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma. (PMID: 9393982) Clark J … Cooper CS (Oncogene 1997) 3 4 22 58
  4. The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene. (PMID: 8872474) Sidhar SK … Cooper CS (Human molecular genetics 1996) 3 4 22 58
  5. The gene encoding human TFE3, a transcription factor that binds the immunoglobulin heavy-chain enhancer, maps to Xp11.22. (PMID: 1685140) Henthorn PS … Puck JM (Genomics 1991) 2 3 22 58

Products for TFE3 Gene

  • Addgene plasmids for TFE3

Sources for TFE3 Gene

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