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tfeb transcription factor EB [ Danio rerio (zebrafish) ]

Gene ID: 562289, updated on 2-Nov-2024

Summary

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Official Symbol
tfebprovided by ZNC
Official Full Name
transcription factor EBprovided by ZNC
Primary source
ZFIN:ZDB-GENE-090807-3
See related
Ensembl:ENSDARG00000010794 AllianceGenome:ZFIN:ZDB-GENE-090807-3
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within central nervous system myelination. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; head; immature eye; mesoderm; and pronephros. Orthologous to human TFEB (transcription factor EB). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See tfeb in Genome Data Viewer
Location:
chromosome: 11
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (22292010..22361212, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (22130909..22200632, complement)

Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137496650 Neighboring gene uncharacterized LOC103911838 Neighboring gene transmembrane protein 183A Neighboring gene PTPRF interacting protein alpha 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Lysosomal dysfunction and impaired autophagy underlie the pathogenesis of amyloidogenic light chain-mediated cardiotoxicity. Guan J, et al. EMBO Mol Med, 2014 Nov. PMID 25319546, Free PMC Article
  2. Oligodendrocyte development and myelin sheath formation are regulated by the antagonistic interaction between the Rag-Ragulator complex and TFEB. Bouchard EL, et al. Glia, 2024 Feb. PMID 37767930,
  3. Embryonic expression of zebrafish MiT family genes tfe3b, tfeb, and tfec. Lister JA, et al. Dev Dyn, 2011 Nov. PMID 21932325, Free PMC Article
  4. Disruption of Cxcr3 chemotactic signaling alters lysosomal function and renders macrophages more microbicidal. Sommer F, et al. Cell Rep, 2021 Apr 13. PMID 33852860
  5. AMPK promotes induction of the tumor suppressor FLCN through activation of TFEB independently of mTOR. Collodet C, et al. FASEB J, 2019 Nov. PMID 31404503, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Oligodendrocyte development and myelin sheath formation are regulated by the antagonistic interaction between the Rag-Ragulator complex and TFEB.
    Title: Oligodendrocyte development and myelin sheath formation are regulated by the antagonistic interaction between the Rag-Ragulator complex and TFEB.
  2. Loss of Tfeb function is sufficient to restore myelination in RagA mutants, indicating that hyperactive Tfeb represses myelination. Conversely, tfeb(-/-) single mutants exhibit ectopic myelin, further indicating that Tfeb represses myelination during development.
    Title: The Lysosomal Transcription Factor TFEB Represses Myelination Downstream of the Rag-Ragulator Complex.
  3. The zebrafish genome contain two mitf (mitfa and mitfb), two tfe3 (tfe3a and tfe3b), and single tfeb and tfec genes.
    Title: Embryonic expression of zebrafish MiT family genes tfe3b, tfeb, and tfec.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within central nervous system myelination IGI
Inferred from Genetic Interaction
more info
 PubMed 
acts_upstream_of_or_within humoral immune response IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
transcription factor EB

NCBI Reference Sequences (RefSeq)

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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_001257192.1 → NP_001244121.1  transcription factor EB

    See identical proteins and their annotated locations for NP_001244121.1

    Status: PROVISIONAL

    Source sequence(s)
    JN105112
    UniProtKB/TrEMBL
    G5CIM3
    Conserved Domains (3) summary
    cd00083
    Location:243 → 303
    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:332 → 489
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:4 → 168
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007122.7 Reference GRCz11 Primary Assembly

    Range
    22292010..22361212 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005172885.5 → XP_005172942.1  transcription factor EB isoform X2

    UniProtKB/TrEMBL
    A0A8M2BKN6, E7FEM8
    Related
    ENSDARP00000023719.6, ENSDART00000006580.8
    Conserved Domains (3) summary
    cd00083
    Location:241 → 301
    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:330 → 487
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:4 → 168
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  2. XM_005172883.5 → XP_005172940.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_005172940.1

    UniProtKB/TrEMBL
    A0A2R8RRI1, A0A8M2BK79
    Related
    ENSDARP00000156744.1, ENSDART00000180688.1
    Conserved Domains (3) summary
    cd00083
    Location:243 → 303
    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:332 → 489
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:4 → 168
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  3. XM_005172884.5 → XP_005172941.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_005172941.1

    UniProtKB/TrEMBL
    A0A2R8RRI1, A0A8M2BK79
    Conserved Domains (3) summary
    cd00083
    Location:243 → 303
    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:332 → 489
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:4 → 168
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

  4. XM_021479638.2 → XP_021335313.1  transcription factor EB isoform X3

    UniProtKB/TrEMBL
    A0A8M9Q799
    Conserved Domains (3) summary
    cd00083
    Location:183 → 243
    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:388 → 429
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:7 → 108
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
Nucleotide Protein Strain
Heading Accession and Version

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