U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    TFEB transcription factor EB [ Homo sapiens (human) ]

    Gene ID: 7942, updated on 17-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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

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

    NCBI Reference Sequences (RefSeq)

    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_001167827.3NP_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:247307
      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:335471
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:18175
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    2. NM_001271943.2NP_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:148208
      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:236372
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:471
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    3. NM_001271944.2NP_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:233293
      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:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    4. NM_001271945.2NP_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:233293
      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:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    5. NM_007162.3NP_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:233293
      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:4161
      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_005249411.2XP_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:233293
      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:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
    2. XM_047419361.1XP_047275317.1  transcription factor EB isoform X1

      UniProtKB/Swiss-Prot
      P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
      UniProtKB/TrEMBL
      B4DPL3
    3. XM_006715212.5XP_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:233293
      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:4161
      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_054356422.1XP_054212397.1  transcription factor EB isoform X1

      UniProtKB/Swiss-Prot
      P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
      UniProtKB/TrEMBL
      B4DPL3
    2. XM_054356421.1XP_054212396.1  transcription factor EB isoform X1

      UniProtKB/Swiss-Prot
      P19484, Q709B3, Q7Z6P9, Q9BRJ5, Q9UJD8
      UniProtKB/TrEMBL
      B4DPL3