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    Tfeb transcription factor EB [ Rattus norvegicus (Norway rat) ]

    Gene ID: 316214, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Tfebprovided by RGD
    Official Full Name
    transcription factor EBprovided by RGD
    Primary source
    RGD:1309583
    See related
    EnsemblRapid:ENSRNOG00000014666 AllianceGenome:RGD:1309583
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Tcfeb
    Summary
    Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including cellular response to amino acid starvation; defense response to bacterium; and positive regulation of metabolic process. Predicted to act upstream of or within lysosome organization and positive regulation of DNA-templated transcription. Predicted to be located in cytosol and lysosomal membrane. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human TFEB (transcription factor EB). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 57.8), Spleen (RPKM 43.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tfeb in Genome Data Viewer
    Location:
    9q12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (20696440..20752265, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (13198890..13254726, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (15208141..15264101, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene forkhead box P4 Neighboring gene MyoD family inhibitor Neighboring gene uncharacterized LOC134480340 Neighboring gene uncharacterized LOC102554309 Neighboring gene progastricsin Neighboring gene prickle planar cell polarity protein 4 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Increase of transcription factor EB (TFEB) and lysosomes in rat DRG neurons and their transportation to the central nerve terminal in dorsal horn after nerve injury. Jung J, et al. Neuroscience, 2016 Jan 28. PMID 26601776
    2. Lysosomal autophagy promotes recovery in rats with acute knee injury through TFEB mediation. Xia Q, et al. J Orthop Surg Res, 2020 Feb 21. PMID 32085781, Free PMC Article
    3. Transcription factor EB (TFEB) promotes autophagy in early brain injury after subarachnoid hemorrhage in rats. Lu W, et al. Neurosurg Rev, 2024 Oct 8. PMID 39375262
    4. TFEB ameliorates autophagy flux disturbance induced by PBDE-47 via up-regulating autophagy-lysosome fusion. Tang H, et al. J Hazard Mater, 2022 May 15. PMID 35739666
    5. Impaired TFEB activation and mitophagy as a cause of PPP3/calcineurin inhibitor-induced pancreatic β-cell dysfunction. Park K, et al. Autophagy, 2023 May. PMID 36217215, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Estrogen Receptor-Related Orphan Receptors Regulate Autophagy through TFEB.
      Title: The Estrogen Receptor-Related Orphan Receptors Regulate Autophagy through TFEB.
    2. Transcription factor EB (TFEB) promotes autophagy in early brain injury after subarachnoid hemorrhage in rats.
      Title: Transcription factor EB (TFEB) promotes autophagy in early brain injury after subarachnoid hemorrhage in rats.
    3. 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.
    4. TFEB regulates cellular labile iron and prevents ferroptosis in a TfR1-dependent manner.
      Title: TFEB regulates cellular labile iron and prevents ferroptosis in a TfR1-dependent manner.
    5. Transcription factor EB (TFEB) improves ventricular remodeling after myocardial infarction by inhibiting Wnt/beta-catenin signaling pathway.
      Title: Transcription factor EB (TFEB) improves ventricular remodeling after myocardial infarction by inhibiting Wnt/β-catenin signaling pathway.
    6. Impaired TFEB activation and mitophagy as a cause of PPP3/calcineurin inhibitor-induced pancreatic beta-cell dysfunction.
      Title: Impaired TFEB activation and mitophagy as a cause of PPP3/calcineurin inhibitor-induced pancreatic β-cell dysfunction.
    7. Phosphorylation of STAT3 at Tyr705 contributes to TFEB-mediated autophagy-lysosomal pathway dysfunction and leads to ischemic injury in rats.
      Title: Phosphorylation of STAT3 at Tyr705 contributes to TFEB-mediated autophagy-lysosomal pathway dysfunction and leads to ischemic injury in rats.
    8. The inhibition of TRPML1/TFEB leads to lysosomal biogenesis disorder, contributes to developmental fluoride neurotoxicity.
      Title: The inhibition of TRPML1/TFEB leads to lysosomal biogenesis disorder, contributes to developmental fluoride neurotoxicity.
    9. TFEB-Mediated Lysosomal Restoration Alleviates High Glucose-Induced Cataracts Via Attenuating Oxidative Stress.
      Title: TFEB-Mediated Lysosomal Restoration Alleviates High Glucose-Induced Cataracts Via Attenuating Oxidative Stress.
    10. TFEB ameliorates autophagy flux disturbance induced by PBDE-47 via up-regulating autophagy-lysosome fusion.
      Title: TFEB ameliorates autophagy flux disturbance induced by PBDE-47 via up-regulating autophagy-lysosome fusion.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC116240

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in antibacterial innate immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to amino acid starvation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to starvation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in defense response to Gram-negative bacterium ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in embryonic placenta development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in humoral immune response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of lysosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    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_001025707.2 → NP_001020878.2  transcription factor EB

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A6JII2, A6JII3
      Related
      ENSRNOP00000096641.2, ENSRNOT00000112521.2

    2. NM_001432203.1 → NP_001419132.1  transcription factor EB

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A6JII2, A6JII3

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      20696440..20752265 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083486.2 → XP_038939414.1  transcription factor EB isoform X2

      UniProtKB/TrEMBL
      A6JII2, A6JII3
      Conserved Domains (3) summary
      cd18927
      Location:226 → 316
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
      pfam11851
      Location:321 → 473
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 162
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    2. XM_006244442.4 → XP_006244504.1  transcription factor EB isoform X2

      Related
      ENSRNOP00000037517.7, ENSRNOT00000039102.7
      Conserved Domains (3) summary
      cd18927
      Location:226 → 316
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
      pfam11851
      Location:321 → 473
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 162
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    3. XM_039083488.2 → XP_038939416.1  transcription factor EB isoform X2

      UniProtKB/TrEMBL
      A6JII2, A6JII3
      Conserved Domains (3) summary
      cd18927
      Location:226 → 316
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
      pfam11851
      Location:321 → 473
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 162
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    4. XM_006244446.5 → XP_006244508.1  transcription factor EB isoform X2

      See identical proteins and their annotated locations for XP_006244508.1

      UniProtKB/TrEMBL
      A6JII2, A6JII3
      Conserved Domains (3) summary
      cd18927
      Location:226 → 316
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
      pfam11851
      Location:321 → 473
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 162
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    5. XM_063267087.1 → XP_063123157.1  transcription factor EB isoform X1

      UniProtKB/TrEMBL
      A6JII2
    Nucleotide Protein Strain
    Heading Accession and Version

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