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Aliases for TFEB Gene

Aliases for TFEB Gene

  • Transcription Factor EB 2 3 5
  • Class E Basic Helix-Loop-Helix Protein 35 3 4
  • BHLHE35 3 4
  • T-Cell Transcription Factor EB 3
  • ALPHATFEB 3
  • TCFEB 3

External Ids for TFEB Gene

Previous GeneCards Identifiers for TFEB Gene

  • GC06M041651
  • GC06M041698
  • GC06M041759
  • GC06M041370

Summaries for TFEB Gene

GeneCards Summary for TFEB Gene

TFEB (Transcription Factor EB) is a Protein Coding gene. Diseases associated with TFEB include Renal Cell Carcinoma, Papillary and Microphthalmia. Among its related pathways are Apoptosis and Autophagy and PI3K-AKT-mTOR signaling pathway and therapeutic opportunities. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and protein dimerization activity. An important paralog of this gene is MITF.

UniProtKB/Swiss-Prot for TFEB 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 TFE3 or MITF. In association with TFE3, 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 and binds the CLEAR-box sequence (5-GTCACGTGAC-3) present in the regulatory region of many lysosomal genes, leading to activate their expression. It thereby plays a central role in expression of lysosomal genes. Acts as a positive regulator of autophagy by promoting expression of genes involved in autophagy. Specifically recognizes the gamma-E3 box, a subset of E-boxes, present in the heavy-chain immunoglobulin enhancer. Plays a role in the signal transduction processes required for normal vascularization of the placenta.

Gene Wiki entry for TFEB Gene

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

Genomics for TFEB Gene

Regulatory Elements for TFEB Gene

Enhancers for TFEB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G041704 1.9 FANTOM5 Ensembl ENCODE dbSUPER 20.5 +29.8 29794 4.9 HDGF PKNOX1 ATF1 WRNIP1 ARID4B SIN3A ZNF2 ZNF48 ZNF143 ZNF207 TFEB PGC UBR2 MDFI TREML3P ENSG00000124593 TREM1 GC06M041708 GC06M041707 GC06P041713
GH06G041711 1.5 Ensembl ENCODE dbSUPER 19.3 +22.8 22780 3.8 HDGF ARNT ARID4B ZNF48 ZNF2 YY1 GLIS2 ZNF143 FOS KDM4B TFEB PGC MDFI GC06P041713 GC06M041707 GC06M041708
GH06G041697 1.2 Ensembl ENCODE dbSUPER 17.5 +37.7 37727 3.0 KLF1 BHLHE40 ZEB2 ATF2 ZNF121 JUND IKZF1 PATZ1 CREB1 FOS TFEB ENSG00000231102 PGC MDFI MED20 GC06M041707 GC06M041708 GC06P041666
GH06G041718 2 FANTOM5 Ensembl ENCODE dbSUPER 9.1 +8.8 8761 17.5 MLX CREB3L1 DMAP1 YBX1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 PGC TFEB ENSG00000124593 ENSG00000231102
GH06G041278 1.8 FANTOM5 Ensembl ENCODE dbSUPER 6.9 +457.1 457060 0.8 HDGF ATF1 CREB3L1 ARNT TCF12 ZNF766 GATA2 ZNF143 MXD4 REST TREM1 USP49 NFYA TFEB TREML2 TREML4 GC06M041280 ENSG00000218809
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TFEB on UCSC Golden Path with GeneCards custom track

Promoters for TFEB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000196875 1459 2001 HDGF PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF766 ZNF207

Genomic Location for TFEB Gene

Chromosome:
6
Start:
41,683,978 bp from pter
End:
41,736,259 bp from pter
Size:
52,282 bases
Orientation:
Minus strand

Genomic View for TFEB Gene

Genes around TFEB on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for TFEB Gene

Proteins for TFEB Gene

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

    Protein Symbol:
    P19484-TFEB_HUMAN
    Recommended name:
    Transcription factor EB
    Protein Accession:
    P19484
    Secondary Accessions:
    • Q709B3
    • Q7Z6P9
    • Q9BRJ5
    • Q9UJD8

    Protein attributes for TFEB Gene

    Size:
    476 amino acids
    Molecular mass:
    52865 Da
    Quaternary structure:
    • Homodimer and heterodimer; with TFE3 or MITF.
    SequenceCaution:
    • Sequence=AAA36730.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAE77681.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for TFEB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TFEB Gene

Post-translational modifications for TFEB Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for TFEB (TFEB)
  • Abcam antibodies for TFEB

No data available for DME Specific Peptides for TFEB Gene

Domains & Families for TFEB Gene

Gene Families for TFEB Gene

Protein Domains for TFEB Gene

Graphical View of Domain Structure for InterPro Entry

P19484

UniProtKB/Swiss-Prot:

TFEB_HUMAN :
  • The leucin zipper region is essential for homo- or heterodimerization and high-affinity DNA binding. DNA binding is mediated by the basic region.
  • Belongs to the MiT/TFE family.
Domain:
  • The leucin zipper region is essential for homo- or heterodimerization and high-affinity DNA binding. DNA binding is mediated by the basic region.
Family:
  • Belongs to the MiT/TFE family.
genes like me logo Genes that share domains with TFEB: view

Function for TFEB Gene

Molecular function for TFEB Gene

GENATLAS Biochemistry:
transcription factor EB,highly recognizing the EB box sequences in the heavy chain immunoglobulin enhancer,murine Tcfeb ortholog
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 TFE3 or MITF. In association with TFE3, 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 and binds the CLEAR-box sequence (5-GTCACGTGAC-3) present in the regulatory region of many lysosomal genes, leading to activate their expression. It thereby plays a central role in expression of lysosomal genes. Acts as a positive regulator of autophagy by promoting expression of genes involved in autophagy. Specifically recognizes the gamma-E3 box, a subset of E-boxes, present in the heavy-chain immunoglobulin enhancer. Plays a role in the signal transduction processes required for normal vascularization of the placenta.

Gene Ontology (GO) - Molecular Function for TFEB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding NAS 2115126
GO:0044212 transcription regulatory region DNA binding IDA 19556463
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with TFEB: view
genes like me logo Genes that share phenotypes with TFEB: view

Animal Models for TFEB Gene

MGI Knock Outs for TFEB:

Animal Model Products

CRISPR Products

miRNA for TFEB Gene

miRTarBase miRNAs that target TFEB

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TFEB Gene

Localization for TFEB Gene

Subcellular locations from UniProtKB/Swiss-Prot for TFEB Gene

Cytoplasm. Nucleus. Note=Mainly present in the cytoplasm (PubMed:23434374). Under aberrant lysosomal storage conditions, it translocates from the cytoplasm to the nucleus (PubMed:23434374). In macrophages, translocates into the nucleus upon live S.enterica infection (PubMed:27184844). {ECO:0000269 PubMed:23434374, ECO:0000269 PubMed:27184844}.

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 TFEB gene
Compartment Confidence
nucleus 5
lysosome 3
mitochondrion 2
cytosol 2
extracellular 1
cytoskeleton 1
endosome 1

Gene Ontology (GO) - Cellular Components for TFEB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 2115126
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 19556463
genes like me logo Genes that share ontologies with TFEB: view

Pathways & Interactions for TFEB Gene

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

Pathways by source for TFEB Gene

2 Cell Signaling Technology pathways for TFEB Gene
1 KEGG pathway for TFEB Gene

Gene Ontology (GO) - Biological Process for TFEB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001892 embryonic placenta development ISS --
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 NAS 2115126
genes like me logo Genes that share ontologies with TFEB: view

No data available for SIGNOR curated interactions for TFEB Gene

Drugs & Compounds for TFEB Gene

(1) Drugs for TFEB Gene - From: Novoseek

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

Transcripts for TFEB Gene

Unigene Clusters for TFEB Gene

Transcription factor EB:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for TFEB Gene

GeneLoc Exon Structure for
TFEB
ECgene alternative splicing isoforms for
TFEB

Expression for TFEB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (x8.0).

Protein differential expression in normal tissues from HIPED for TFEB Gene

This gene is overexpressed in Monocytes (25.3), Blymphocyte (21.8), NK cells (7.0), and Peripheral blood mononuclear cells (6.7).

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



Protein tissue co-expression partners for TFEB Gene

NURSA nuclear receptor signaling pathways regulating expression of TFEB Gene:

TFEB

SOURCE GeneReport for Unigene cluster for TFEB Gene:

Hs.485360

Evidence on tissue expression from TISSUES for TFEB Gene

  • Nervous system(4.5)
  • Kidney(4.4)
  • Lung(4.2)
  • Muscle(2.5)

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

Germ Layers:
  • mesoderm
Systems:
  • urinary
Organs:
Abdomen:
  • kidney
genes like me logo Genes that share expression patterns with TFEB: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for TFEB Gene

Orthologs for TFEB Gene

This gene was present in the common ancestor of animals.

Orthologs for TFEB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TFEB 34 35
  • 99.59 (n)
dog
(Canis familiaris)
Mammalia TFEB 34 35
  • 89.9 (n)
cow
(Bos Taurus)
Mammalia TFEB 34 35
  • 89.82 (n)
mouse
(Mus musculus)
Mammalia Tfeb 34 16 35
  • 88.8 (n)
rat
(Rattus norvegicus)
Mammalia Tfeb 34
  • 88.34 (n)
oppossum
(Monodelphis domestica)
Mammalia TFEB 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TFEB 35
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves TFEB 34 35
  • 79.05 (n)
lizard
(Anolis carolinensis)
Reptilia TFEB 35
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tfeb 34
  • 66.27 (n)
zebrafish
(Danio rerio)
Actinopterygii tfeb 34 35
  • 64.65 (n)
fruit fly
(Drosophila melanogaster)
Insecta Mitf 35
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea hlh-30 35
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 37 (a)
OneToMany
Species where no ortholog for TFEB 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for TFEB Gene

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

Paralogs for TFEB Gene

Paralogs for TFEB Gene

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

Variants for TFEB Gene

Sequence variations from dbSNP and Humsavar for TFEB Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000086416 -- 41,697,274(+) GTGGT(A/G)GCACA intron-variant
rs1000121533 -- 41,701,465(+) GAAAG(A/C)GATGC intron-variant
rs1000228983 -- 41,723,696(+) CCGAC(A/G)GCACA intron-variant, upstream-variant-2KB
rs1000281449 -- 41,723,878(+) CGCCA(C/G)AGTCC intron-variant, upstream-variant-2KB
rs1000286230 -- 41,695,131(+) CTCTC(C/T)GTGCT intron-variant

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

Variant ID Type Subtype PubMed ID
dgv10635n54 CNV loss 21841781
dgv10636n54 CNV gain 21841781
dgv10637n54 CNV gain 21841781
dgv10638n54 CNV loss 21841781
esv2759422 CNV loss 17122850
esv29515 CNV loss 19812545
nsv1114799 CNV deletion 24896259
nsv479034 CNV novel sequence insertion 20440878
nsv526309 CNV loss 19592680
nsv602977 CNV gain 21841781
nsv602988 CNV loss 21841781
nsv7893 CNV gain 18304495

Variation tolerance for TFEB Gene

Residual Variation Intolerance Score: 35.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.37; 42.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TFEB Gene

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

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

Disorders for TFEB Gene

MalaCards: The human disease database

(5) MalaCards diseases for TFEB Gene - From: Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
renal cell carcinoma, papillary
  • renal cell carcinoma
microphthalmia
  • microphthalmos
renal cell carcinoma
  • renal cell carcinoma, clear cell, somatic
childhood kidney cell carcinoma
  • pediatric renal cell carcinoma
hemophagocytic lymphohistiocytosis, familial, 3
  • familial hemophagocytic lymphohistiocytosis 3
- elite association - COSMIC cancer census association via MalaCards
Search TFEB in MalaCards View complete list of genes associated with diseases

Relevant External Links for TFEB

Genetic Association Database (GAD)
TFEB
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TFEB
genes like me logo Genes that share disorders with TFEB: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TFEB Gene

Publications for TFEB Gene

  1. A helix-loop-helix protein related to the immunoglobulin E box- binding proteins. (PMID: 2115126) Carr C.S. … Sharp P.A. (Mol. Cell. Biol. 1990) 2 3 4 22 64
  2. A gene network regulating lysosomal biogenesis and function. (PMID: 19556463) Sardiello M. … Ballabio A. (Science 2009) 3 4 22 64
  3. Regulation of the MiTF/TFE bHLH-LZ transcription factors through restricted spatial expression and alternative splicing of functional domains. (PMID: 15118077) Kuiper R.P. … Geurts van Kessel A. (Nucleic Acids Res. 2004) 3 4 22 64
  4. ZKSCAN3 is a master transcriptional repressor of autophagy. (PMID: 23434374) Chauhan S. … Boyd D.D. (Mol. Cell 2013) 3 4 64
  5. Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. (PMID: 18839057) Lesch K.P. … Jacob C. (J Neural Transm 2008) 3 46 64

Products for TFEB Gene

  • Addgene plasmids for TFEB

Sources for TFEB Gene

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