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TFEB transcription factor EB [ Homo sapiens (human) ]

Gene ID: 7942, updated on 16-Apr-2024

Summary

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Official Symbol
TFEBprovided by HGNC
Official Full Name
transcription factor EBprovided by HGNC
Primary source
HGNC:HGNC:11753
See related
Ensembl:ENSG00000112561 MIM:600744; AllianceGenome:HGNC:11753
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TCFEB; BHLHE35; ALPHATFEB
Summary
Enables DNA-binding transcription factor activity; enzyme binding activity; and transcription cis-regulatory region binding activity. Involved in several processes, including cellular response to amino acid starvation; lysosome localization; and positive regulation of autophagy. Located in cytosol; lysosomal membrane; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 9.7), lymph node (RPKM 8.3) and 25 other tissues See more
Orthologs
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Genomic context

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See TFEB in Genome Data Viewer
Location:
6p21.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41683978..41736223, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41512540..41564779, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41651716..41703961, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41608279-41608859 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:41612529-41613514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41614501-41615485 Neighboring gene MyoD family inhibitor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41625153-41625767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41641529-41642028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41642607-41643108 Neighboring gene nucleophosmin 1 pseudogene 51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41644810-41645324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41645325-41645838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41649993-41650819 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41650820-41651645 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41655149-41656015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41658364-41658864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41673380-41673880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41673881-41674381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24519 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41680541-41681266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41681267-41681990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41690842-41691384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41700542-41701238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17190 Neighboring gene microRNA 10398 Neighboring gene progastricsin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41735161-41736013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17192 Neighboring gene fibroblast growth factor receptor substrate 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. TFEB-dependent lysosome biogenesis is required for senescence. Curnock R, et al. EMBO J, 2023 May 2. PMID 36970883, Free PMC Article
  2. Transcription factor EB regulates phosphatidylinositol-3-phosphate levels that control lysosome positioning in the bladder cancer model. Mathur P, et al. Commun Biol, 2023 Jan 28. PMID 36709383, Free PMC Article
  3. p38 MAPK-dependent phosphorylation of TFEB promotes monocyte-to-macrophage differentiation. Martina JA, et al. EMBO Rep, 2023 Feb 6. PMID 36507874, Free PMC Article
  4. Loss of transcription factor EB dysregulates the G1/S transition and DNA replication in mammary epithelial cells. Slade L, et al. J Biol Chem, 2022 Dec. PMID 36372230, Free PMC Article
  5. TFEB in Alzheimer's disease: From molecular mechanisms to therapeutic implications. Gu Z, et al. Neurobiol Dis, 2022 Oct 15. PMID 36031168

See all (193) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Altered TFEB subcellular localization in nigral neurons of subjects with incidental, sporadic and GBA-related Lewy body diseases.
    Title: Altered TFEB subcellular localization in nigral neurons of subjects with incidental, sporadic and GBA-related Lewy body diseases.
  2. Impaired TFEB-mediated autophagy-lysosome fusion promotes tubular cell cycle G2/M arrest and renal fibrosis by suppressing ATP6V0C expression and interacting with SNAREs.
    Title: Impaired TFEB-mediated autophagy-lysosome fusion promotes tubular cell cycle G2/M arrest and renal fibrosis by suppressing ATP6V0C expression and interacting with SNAREs.
  3. ABCG2 is an itaconate exporter that limits antibacterial innate immunity by alleviating TFEB-dependent lysosomal biogenesis.
    Title: ABCG2 is an itaconate exporter that limits antibacterial innate immunity by alleviating TFEB-dependent lysosomal biogenesis.
  4. A SPLICS reporter reveals [Formula: see text]-synuclein regulation of lysosome-mitochondria contacts which affects TFEB nuclear translocation.
    Title: A SPLICS reporter reveals [Formula: see text]-synuclein regulation of lysosome-mitochondria contacts which affects TFEB nuclear translocation.
  5. TFEB regulates the odontoblastic differentiation of dental pulp stem cells by promoting a positive feedback loop between mitophagy and glycolysis.
    Title: TFEB regulates the odontoblastic differentiation of dental pulp stem cells by promoting a positive feedback loop between mitophagy and glycolysis.
  6. LncRNA XXYLT1-AS2 promotes tumor progression via autophagy inhibition through ubiquitinated degradation of TFEB in hepatocellular carcinoma.
    Title: LncRNA XXYLT1-AS2 promotes tumor progression via autophagy inhibition through ubiquitinated degradation of TFEB in hepatocellular carcinoma.
  7. A candidate prognostic biomarker: TFEB inhibits tumor progression via elevating CDKN1A in bladder cancer.
    Title: A candidate prognostic biomarker: TFEB inhibits tumor progression via elevating CDKN1A in bladder cancer.
  8. FBXL5 promotes lipid accumulation in alcoholic fatty liver disease by promoting the ubiquitination and degradation of TFEB.
    Title: FBXL5 promotes lipid accumulation in alcoholic fatty liver disease by promoting the ubiquitination and degradation of TFEB.
  9. Dissecting the multifaced function of transcription factor EB (TFEB) in human diseases: From molecular mechanism to pharmacological modulation.
    Title: Dissecting the multifaced function of transcription factor EB (TFEB) in human diseases: From molecular mechanism to pharmacological modulation.
  10. Transcription factor EB: A potential integrated network regulator in metabolic-associated cardiac injury.
    Title: Transcription factor EB: A potential integrated network regulator in metabolic-associated cardiac injury.
Submit: New GeneRIF Correction See all GeneRIFs (173)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 activates (and dephosphorylates) TFEB in human macrophages at 24 hours post-treatment with purified HIV-1 virions PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef inhibits TFEB nuclear localization and autophagic flux; HIV-1 Nef is required for anti-autophagy during permissive (ongoing) HIV infection PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in adaptive immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in antibacterial innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to amino acid starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in embryonic placenta development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in humoral immune response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lysosome localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lysosome organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in lysosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of autophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
transcription factor EB
Names
T-cell transcription factor EB
class E basic helix-loop-helix protein 35

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001167827.3 → NP_001161299.2  transcription factor EB isoform 2

    See identical proteins and their annotated locations for NP_001161299.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2, also known as TFEB-A) encodes the longest isoform (2).
    Source sequence(s)
    AJ608786, BC032448
    Consensus CDS
    CCDS64425.1
    UniProtKB/TrEMBL
    B0QYS6, B4DPL3
    Related
    ENSP00000351742.2, ENST00000358871.6
    Conserved Domains (3) summary
    cd00083
    Location:247 → 307
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam11851
    Location:335 → 471
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:18 → 175
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  2. NM_001271943.2 → NP_001258872.1  transcription factor EB isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' exon, which results in a downstream AUG start codon, and also lacks an in-frame coding exon, compared to variant 2. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment, compared to isoform 2.
    Source sequence(s)
    AL365205, AW294760, BC032448, CT000098
    Consensus CDS
    CCDS64424.1
    UniProtKB/TrEMBL
    B1AKB5
    Related
    ENSP00000383998.3, ENST00000406563.7
    Conserved Domains (3) summary
    cd00083
    Location:148 → 208
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam11851
    Location:236 → 372
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:4 → 71
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  3. NM_001271944.2 → NP_001258873.1  transcription factor EB isoform 1

    See identical proteins and their annotated locations for NP_001258873.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon, which results in a downstream AUG start codon, compared to variant 2. The resulting isoform (1) has a shorter N-terminus, compared to isoform 2. Variants 1, 3 and 4 encode the same isoform 1.
    Source sequence(s)
    AL365205, AW294760, BC032448
    Consensus CDS
    CCDS4858.1
    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
    UniProtKB/TrEMBL
    B4DPL3
    Related
    ENSP00000362124.1, ENST00000373033.6
    Conserved Domains (2) summary
    cd00083
    Location:233 → 293
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam15951
    Location:4 → 161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  4. NM_001271945.2 → NP_001258874.1  transcription factor EB isoform 1

    See identical proteins and their annotated locations for NP_001258874.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' exon, which results in a downstream AUG start codon, compared to variant 2. The resulting isoform (1) has a shorter N-terminus, compared to isoform 2. Variants 1, 3 and 4 encode the same isoform 1.
    Source sequence(s)
    BC032448, BU527754
    Consensus CDS
    CCDS4858.1
    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
    UniProtKB/TrEMBL
    B4DPL3
    Related
    ENSP00000384203.4, ENST00000403298.9
    Conserved Domains (2) summary
    cd00083
    Location:233 → 293
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam15951
    Location:4 → 161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  5. NM_007162.3 → NP_009093.1  transcription factor EB isoform 1

    See identical proteins and their annotated locations for NP_009093.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) contains an alternate 5' sequence, which results in a downstream AUG start codon, compared to variant 2. The resulting isoform (1) has a shorter N-terminus, compared to isoform 2. Variants 1, 3 and 4 encode the same isoform 1.
    Source sequence(s)
    BC032448
    Consensus CDS
    CCDS4858.1
    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
    UniProtKB/TrEMBL
    B4DPL3
    Related
    ENSP00000230323.4, ENST00000230323.8
    Conserved Domains (2) summary
    cd00083
    Location:233 → 293
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam15951
    Location:4 → 161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    41683978..41736223 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249411.2 → XP_005249468.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_005249468.1

    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
    UniProtKB/TrEMBL
    B4DPL3
    Related
    ENSP00000503069.1, ENST00000678831.1
    Conserved Domains (2) summary
    cd00083
    Location:233 → 293
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam15951
    Location:4 → 161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  2. XM_047419361.1 → XP_047275317.1  transcription factor EB isoform X1

    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8

  3. XM_006715212.5 → XP_006715275.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_006715275.1

    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
    UniProtKB/TrEMBL
    B4DPL3
    Related
    ENSP00000400276.2, ENST00000419574.6
    Conserved Domains (2) summary
    cd00083
    Location:233 → 293
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    pfam15951
    Location:4 → 161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    41512540..41564779 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356422.1 → XP_054212397.1  transcription factor EB isoform X1

    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8

  2. XM_054356421.1 → XP_054212396.1  transcription factor EB isoform X1

    UniProtKB/Swiss-Prot
    P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P19484.3 GenPept UniProtKB/Swiss-Prot:P19484

Gene LinkOut

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