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    TFEB transcription factor EB [ Homo sapiens (human) ]

    Gene ID: 7942, updated on 12-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 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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    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 Variation Viewer (GRCh37.p13)

    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
    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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