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    tfe3b transcription factor binding to IGHM enhancer 3b [ Danio rerio (zebrafish) ]

    Gene ID: 564996, updated on 17-Sep-2024

    Summary

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    Official Symbol
    tfe3bprovided by ZNC
    Official Full Name
    transcription factor binding to IGHM enhancer 3bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-010919-3
    See related
    Ensembl:ENSDARG00000019457 AllianceGenome:ZFIN:ZDB-GENE-010919-3
    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
    Also known as
    zK13A21.9; si:dkey-13a21.9
    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. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within humoral immune response; positive regulation of transcription, DNA-templated; and regulation of osteoclast differentiation. Predicted to be active in nucleus. Is expressed in several structures, including digestive system; ionocyte; lens placode; polster; and sensory system. Human ortholog(s) of this gene implicated in renal cell carcinoma. Orthologous to human TFE3 (transcription factor binding to IGHM enhancer 3). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See tfe3b in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (25504250..25526392)
    105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (25266636..25283053)

    Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene opsin 1 (cone pigments), long-wave-sensitive, 2 Neighboring gene G protein nucleolar 3 like Neighboring gene si:dkey-245f22.3 Neighboring gene CXXC finger protein 1b

    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. Duplicate mitf genes in zebrafish: complementary expression and conservation of melanogenic potential. Lister JA, et al. Dev Biol, 2001 Sep 15. PMID 11543618
    2. Embryonic expression of zebrafish MiT family genes tfe3b, tfeb, and tfec. Lister JA, et al. Dev Dyn, 2011 Nov. PMID 21932325, Free PMC Article
    3. Disruption of Cxcr3 chemotactic signaling alters lysosomal function and renders macrophages more microbicidal. Sommer F, et al. Cell Rep, 2021 Apr 13. PMID 33852860
    4. A lysosomal regulatory circuit essential for the development and function of microglia. Iyer H, et al. Sci Adv, 2022 Sep 2. PMID 36044568, Free PMC Article
    5. CD44a functions as a regulator of p53 signaling, apoptosis and autophagy in the antibacterial immune response. Cao L, et al. Commun Biol, 2022 Aug 30. PMID 36042265, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    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 DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    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
    		  
    acts_upstream_of_or_within regulation of osteoclast differentiation 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 E3b

    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_001045066.1 → NP_001038531.1  transcription factor E3b

      See identical proteins and their annotated locations for NP_001038531.1

      Status: PROVISIONAL

      Source sequence(s)
      AL844847
      UniProtKB/TrEMBL
      Q7SZX8
      Related
      ENSDARP00000008774.6, ENSDART00000011250.7
      Conserved Domains (3) summary
      cd00083
      Location:224 → 284
      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:312 → 450
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 144
      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
      25504250..25526392
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005169305.5 → XP_005169362.1  transcription factor E3b isoform X1

      UniProtKB/TrEMBL
      A0A8M2BGL1, F1R1N1, X1WFJ2
      Related
      ENSDARP00000128996.1, ENSDART00000154213.3
      Conserved Domains (3) summary
      cd00083
      Location:224 → 284
      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:312 → 450
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 144
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    2. XM_005169306.5 → XP_005169363.1  transcription factor E3b isoform X2

      UniProtKB/TrEMBL
      A0A8M2BGP5
      Conserved Domains (3) summary
      cd00083
      Location:222 → 282
      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:310 → 448
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 144
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    3. XM_009306036.4 → XP_009304311.1  transcription factor E3b isoform X3

      UniProtKB/TrEMBL
      A0A8M3B427
      Conserved Domains (3) summary
      cd00083
      Location:220 → 280
      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:308 → 446
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 144
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    4. XM_005169307.5 → XP_005169364.1  transcription factor E3b isoform X4

      UniProtKB/TrEMBL
      A0A8M2BGM5
      Conserved Domains (3) summary
      cd00083
      Location:218 → 278
      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:306 → 444
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 144
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    5. XM_005169308.5 → XP_005169365.1  transcription factor E3b isoform X5

      UniProtKB/TrEMBL
      A0A8M2BH69
      Conserved Domains (3) summary
      cd00083
      Location:216 → 276
      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:304 → 442
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:4 → 144
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394822.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      126772..137592
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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