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    Tfeb transcription factor EB [ Mus musculus (house mouse) ]

    Gene ID: 21425, updated on 19-Sep-2021

    Summary

    Official Symbol
    Tfebprovided by MGI
    Official Full Name
    transcription factor EBprovided by MGI
    Primary source
    MGI:MGI:103270
    See related
    Ensembl:ENSMUSG00000023990
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Tcfeb; bHLHe3; bHLHe35
    Expression
    Broad expression in spleen adult (RPKM 26.0), colon adult (RPKM 13.7) and 21 other tissues See more
    Orthologs
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    Genomic context

    See Tfeb in Genome Data Viewer
    Location:
    17 C; 17 23.99 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (48047962..48103341)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (47737037..47792416)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (47873986..47929365)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 46579 Neighboring gene progastricsin (pepsinogen C) Neighboring gene MyoD family inhibitor Neighboring gene predicted gene, 25201

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within autophagy IEA
    Inferred from Electronic Annotation
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in embryonic placenta development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in humoral immune response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within immune system process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lysosome localization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in lysosome organization 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of gene expression 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
    PubMed 
    involved_in regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    located_in lysosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    colocalizes_with nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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_001161722.1NP_001155194.1  transcription factor EB isoform b

      See identical proteins and their annotated locations for NP_001155194.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode isoform b.
      Source sequence(s)
      AC113536, AC124830, AK078755, BC064789
      Consensus CDS
      CCDS50133.1
      UniProtKB/Swiss-Prot
      Q9R210
      UniProtKB/TrEMBL
      Q6P203, Q8C5F1
      Related
      ENSMUSP00000084151.4, ENSMUST00000086932.10
      Conserved Domains (3) summary
      pfam11851
      Location:320472
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18927
      Location:225315
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
    2. NM_001161723.1NP_001155195.1  transcription factor EB isoform b

      See identical proteins and their annotated locations for NP_001155195.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode isoform b.
      Source sequence(s)
      AC113536, AC124830, AK078755, BC064789
      Consensus CDS
      CCDS50133.1
      UniProtKB/Swiss-Prot
      Q9R210
      UniProtKB/TrEMBL
      Q6P203, Q8C5F1
      Related
      ENSMUSP00000108913.2, ENSMUST00000113288.8
      Conserved Domains (3) summary
      pfam11851
      Location:320472
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18927
      Location:225315
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
    3. NM_011549.3NP_035679.3  transcription factor EB isoform a

      See identical proteins and their annotated locations for NP_035679.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC113536, AK146016, BC064789
      Consensus CDS
      CCDS28856.1
      UniProtKB/Swiss-Prot
      Q9R210
      UniProtKB/TrEMBL
      Q3UKG7, Q6P203
      Related
      ENSMUSP00000024786.8, ENSMUST00000024786.14
      Conserved Domains (3) summary
      cd00083
      Location:291351
      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:379531
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:63219
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      48047962..48103341
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006524007.5XP_006524070.1  transcription factor EB isoform X1

      See identical proteins and their annotated locations for XP_006524070.1

      UniProtKB/Swiss-Prot
      Q9R210
      Conserved Domains (3) summary
      pfam11851
      Location:320472
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18927
      Location:225315
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
    2. XM_006524006.4XP_006524069.1  transcription factor EB isoform X1

      See identical proteins and their annotated locations for XP_006524069.1

      UniProtKB/Swiss-Prot
      Q9R210
      Conserved Domains (3) summary
      pfam11851
      Location:320472
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18927
      Location:225315
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
    3. XM_006524004.1XP_006524067.1  transcription factor EB isoform X2

      Conserved Domains (3) summary
      pfam11851
      Location:355507
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:39196
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18927
      Location:260350
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
    4. XM_006524003.4XP_006524066.2  transcription factor EB isoform X1

      See identical proteins and their annotated locations for XP_006524066.2

      UniProtKB/Swiss-Prot
      Q9R210
      Conserved Domains (3) summary
      pfam11851
      Location:320472
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18927
      Location:225315
      bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins
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