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TFEB transcription factor EB [ Homo sapiens (human) ]

Gene ID: 7942, updated on 27-Nov-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 antibacterial innate immune response; cellular response to amino acid starvation; and positive regulation of transcription by RNA polymerase II. Located in cytosol and lysosomal membrane. Is active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in spleen (RPKM 9.7), lymph node (RPKM 8.3) and 25 other tissues See more
Orthologs
mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41683978..41736223, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41512540..41564779, complement)
RS_2024_09 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. Renal Cell Carcinoma With Chromosome 6p Amplification Including the TFEB Gene: A Novel Mechanism of Tumor Pathogenesis? Williamson SR, et al. Am J Surg Pathol, 2017 Mar. PMID 28009604
  2. Autophagy-Dependent Increased ADAM10 Mature Protein Induced by TFEB Overexpression Is Mediated Through PPARα. Wang H, et al. Mol Neurobiol, 2021 May. PMID 33417226, Free PMC Article
  3. Iron promotes α-synuclein aggregation and transmission by inhibiting TFEB-mediated autophagosome-lysosome fusion. Xiao Y, et al. J Neurochem, 2018 Apr. PMID 29364516
  4. The important role of TFEB in autophagy-lysosomal pathway and autophagy-related diseases: a systematic review. Song TT, et al. Eur Rev Med Pharmacol Sci, 2021 Feb. PMID 33629334
  5. Coxsackievirus B3 targets TFEB to disrupt lysosomal function. Mohamud Y, et al. Autophagy, 2021 Dec. PMID 33691586, Free PMC Article

See all (224) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Overexpression of RBM4 promotes acute myeloid leukemia cell differentiation by regulating alternative splicing of TFEB.
    Title: Overexpression of RBM4 promotes acute myeloid leukemia cell differentiation by regulating alternative splicing of TFEB.
  2. Lactylation stabilizes TFEB to elevate autophagy and lysosomal activity.
    Title: Lactylation stabilizes TFEB to elevate autophagy and lysosomal activity.
  3. TFEB/3 Govern Repair Schwann Cell Generation and Function Following Peripheral Nerve Injury.
    Title: TFEB/3 Govern Repair Schwann Cell Generation and Function Following Peripheral Nerve Injury.
  4. TFEB alleviates periodontitis by activating autophagy and inhibiting inflammation.
    Title: TFEB alleviates periodontitis by activating autophagy and inhibiting inflammation.
  5. Transcription factor EB (TFEB) interaction with RagC is disrupted during enterovirus D68 infection.
    Title: Transcription factor EB (TFEB) interaction with RagC is disrupted during enterovirus D68 infection.
  6. TFEB safeguards trophoblast syncytialization in humans and mice.
    Title: TFEB safeguards trophoblast syncytialization in humans and mice.
  7. Muscle-bone cross-talk through the FNIP1-TFEB-IGF2 axis is associated with bone metabolism in human and mouse.
    Title: Muscle-bone cross-talk through the FNIP1-TFEB-IGF2 axis is associated with bone metabolism in human and mouse.
  8. Transcription factor EB-mediated autophagy affects cell migration and inhibits apoptosis to promote endometriosis.
    Title: Transcription factor EB-mediated autophagy affects cell migration and inhibits apoptosis to promote endometriosis.
  9. TFEB regulates dendritic cell antigen presentation to modulate immune balance in asthma.
    Title: TFEB regulates dendritic cell antigen presentation to modulate immune balance in asthma.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (182)

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)

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 lysosome organization IDA
Inferred from Direct Assay
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
located_in 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_2024_08

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

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