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    bHLH39 basic helix-loop-helix (bHLH) DNA-binding superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 824865, updated on 18-Sep-2024

    Summary

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    Official Symbol
    bHLH39
    Official Full Name
    basic helix-loop-helix (bHLH) DNA-binding superfamily protein
    Primary source
    TAIR:AT3G56980
    Locus tag
    AT3G56980
    See related
    Araport:AT3G56980
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    basic helix-loop-helix 39; BHLH039; OBP3-RESPONSIVE GENE 3; ORG3; T8M16.8
    Summary
    Encodes a member of the basic helix-loop-helix transcription factor protein.
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    Genomic context

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    See bHLH39 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    2
    Sequence:
    Chromosome: 3; NC_003074.8 (21086390..21087710, complement)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene small and basic intrinsic protein 2;1 Neighboring gene ncRNA Neighboring gene phosphatidyl inositol monophosphate 5 kinase 4 Neighboring gene basic helix-loop-helix (bHLH) DNA-binding superfamily protein Neighboring gene embryo sac development arrest 7 Neighboring gene nucleolar essential protein-like protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia. Omidbakhshfard MA, et al. PLoS Genet, 2018 Jul. PMID 29985961, Free PMC Article
    2. Dissection of iron signaling and iron accumulation by overexpression of subgroup Ib bHLH039 protein. Naranjo-Arcos MA, et al. Sci Rep, 2017 Sep 7. PMID 28883478, Free PMC Article
    3. Iron assimilation and transcription factor controlled synthesis of riboflavin in plants. Vorwieger A, et al. Planta, 2007 Jun. PMID 17260143
    4. Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis. Hong S, et al. Plant Physiol, 2013 Feb. PMID 23250624, Free PMC Article
    5. Iron deficiency-mediated stress regulation of four subgroup Ib BHLH genes in Arabidopsis thaliana. Wang HY, et al. Planta, 2007 Sep. PMID 17516080

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The authors provide evidence that subgroup transcription factor bHLH039 transcription factor is involved in FIT transcriptional regulation.
      Title: Dissection of iron signaling and iron accumulation by overexpression of subgroup Ib bHLH039 protein.
    2. Study identified ORG3 as a direct downstream, and positively regulated target of GRF9. Genetic analysis of grf9 org3 and GRF9ox org3 double mutants reveals that both transcription factors act in a regulatory cascade to control the final leaf dimensions by restricting cell number in the developing leaf in Arabidopsis thaliana.
      Title: GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia.
    3. Data indicate that steady-state mRNA abundance for three representative Fe homeostasis genes, IRT1, bHLH39, and FER1, oscillated in light/dark (LD) cycles or warm/cold environmental cycles.
      Title: Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis.
    4. up-regulated by iron deficiency in roots and leaves
      Title: Iron deficiency-mediated stress regulation of four subgroup Ib BHLH genes in Arabidopsis thaliana.
    5. AtbHLH38 and AtbHLH39 are induced under iron deficiency. They are involved in the iron deficiency induced synthesis and excretion of riboflavin or vitamin B2. [AtbHLH39]
      Title: Iron assimilation and transcription factor controlled synthesis of riboflavin in plants.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_115557.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to iron ion starvation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within multicellular organismal-level iron ion homeostasis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of DNA-templated transcription TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    basic helix-loop-helix (bHLH) DNA-binding superfamily protein
    NP_191257.1
    • BHLH039; FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: regulation of transcription; LOCATED IN: nucleus; EXPRESSED IN: 7 plant structures; EXPRESSED DURING: LP.06 six leaves visible, LP.04 four leaves visible, LP.10 ten leaves visible, LP.08 eight leaves visible, LP.12 twelve leaves visible; CONTAINS InterPro DOMAIN/s: Achaete-scute transcription factor related (InterPro:IPR015660), Helix-loop-helix DNA-binding domain (InterPro:IPR001092), Helix-loop-helix DNA-binding (InterPro:IPR011598); BEST Arabidopsis thaliana protein match is: basic helix-loop-helix (bHLH) DNA-binding superfamily protein (TAIR:AT3G56970.1); Has 485 Blast hits to 485 proteins in 65 species: Archae - 0; Bacteria - 0; Metazoa - 76; Fungi - 7; Plants - 402; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003074.8 Reference assembly

      Range
      21086390..21087710 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_115557.3 → NP_191257.1  basic helix-loop-helix (bHLH) DNA-binding superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_191257.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9M1K0
      UniProtKB/TrEMBL
      A0A5S9XLS0, A0A654FIJ9
      Conserved Domains (1) summary
      cd18914
      Location:77 → 153
      bHLH_AtORG2_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana OBP3-responsive gene 2 (ORG2), 3 (ORG3) and similar proteins
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9M1K0.1

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