PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G56970.1
Common NameBHLH038, bHLH38, EN8, F24I3.50, ORG2
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family bHLH
Protein Properties Length: 253aa    MW: 28714.2 Da    PI: 5.7006
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G56970.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   1 rrrahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 
                  ++ +hn+ Er RR++iN+ f+ Lr++lP  +   +skKls  e++ k  +YI +Lq
                  6789*************************66...*******************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088814.96471123IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000836.24E-1572128No hitNo description
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
PfamPF000105.3E-1472124IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474596.54E-1772139IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.4E-1277129IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0010106Biological Processcellular response to iron ion starvation
GO:0055072Biological Processiron ion homeostasis
GO:0090575Cellular ComponentRNA polymerase II transcription factor complex
GO:0000977Molecular FunctionRNA polymerase II regulatory region sequence-specific DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 253 aa     Download sequence    Send to blast
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G56970-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Roots. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the basic helix-loop-helix transcription factor family protein.
Function -- GeneRIF ? help Back to Top
  1. AtbHLH38 and AtbHLH39 are induced under iron deficiency. They are involved in the iron deficiency induced synthesis and excretion of riboflavin or vitamin B2. [AtbHLH38]
    [PMID: 17260143]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by OBP3, auxin and salicylic acid (SA). Repressed by jasmonic acid (JA), UV LIGHT, and heat treatments. Up regulated by iron deficiency in roots and leaves, as well as by nickel, high zinc or high copper treatments. Repressed by high iron, low copper and low zinc treatments. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:12887587, ECO:0000269|PubMed:17516080}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G07640 (A), AT3G55370 (A)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9M1K1
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G56970
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4885760.0AF488576.1 Arabidopsis thaliana clone bHLH038 putative bHLH transcription factor mRNA, complete cds.
GenBankAK2215420.0AK221542.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL07-73-C01.
GenBankBT0264190.0BT026419.1 Arabidopsis thaliana At3g56970 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_191256.10.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
SwissprotQ9M1K10.0ORG2_ARATH; Transcription factor ORG2
STRINGAT3G56970.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP28261129
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  2. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
  3. Kang HG,Foley RC,Oñate-Sánchez L,Lin C,Singh KB
    Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid.
    Plant J., 2003. 35(3): p. 362-72
  4. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  5. Bailey PC, et al.
    Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.
    Plant Cell, 2003. 15(11): p. 2497-502
  6. Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK
    Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes.
    Plant J., 2004. 38(2): p. 366-79
  7. Fujita Y, et al.
    AREB1 Is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis.
    Plant Cell, 2005. 17(12): p. 3470-88
  8. Yoine M,Ohto MA,Onai K,Mita S,Nakamura K
    The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis.
    Plant J., 2006. 47(1): p. 49-62
  9. Tran LS, et al.
    Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis.
    Plant J., 2007. 49(1): p. 46-63
  10. Vorwieger A, et al.
    Iron assimilation and transcription factor controlled synthesis of riboflavin in plants.
    Planta, 2007. 226(1): p. 147-58
  11. Wang HY, et al.
    Iron deficiency-mediated stress regulation of four subgroup Ib BHLH genes in Arabidopsis thaliana.
    Planta, 2007. 226(4): p. 897-908
  12. Yuan Y, et al.
    FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis.
    Cell Res., 2008. 18(3): p. 385-97
  13. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
  14. Ivanov R,Brumbarova T,Bauer P
    Fitting into the harsh reality: regulation of iron-deficiency responses in dicotyledonous plants.
    Mol Plant, 2012. 5(1): p. 27-42
  15. Wang N, et al.
    Requirement and functional redundancy of Ib subgroup bHLH proteins for iron deficiency responses and uptake in Arabidopsis thaliana.
    Mol Plant, 2013. 6(2): p. 503-13
  16. Sivitz AB,Hermand V,Curie C,Vert G
    Arabidopsis bHLH100 and bHLH101 control iron homeostasis via a FIT-independent pathway.
    PLoS ONE, 2012. 7(9): p. e44843
  17. Matsuoka K, et al.
    Gibberellin-induced expression of Fe uptake-related genes in Arabidopsis.
    Plant Cell Physiol., 2014. 55(1): p. 87-98
  18. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  19. Li X,Zhang H,Ai Q,Liang G,Yu D
    Two bHLH Transcription Factors, bHLH34 and bHLH104, Regulate Iron Homeostasis in Arabidopsis thaliana.
    Plant Physiol., 2016. 170(4): p. 2478-93
  20. Shen C, et al.
    Involvement of endogenous salicylic acid in iron-deficiency responses in Arabidopsis.
    J. Exp. Bot., 2016. 67(14): p. 4179-93
  21. Liang G,Zhang H,Li X,Ai Q,Yu D
    bHLH transcription factor bHLH115 regulates iron homeostasis in Arabidopsis thaliana.
    J. Exp. Bot., 2017. 68(7): p. 1743-1755
  22. Ezer D, et al.
    The G-Box Transcriptional Regulatory Code in Arabidopsis.
    Plant Physiol., 2017. 175(2): p. 628-640
  23. Kailasam S,Wang Y,Lo JC,Chang HF,Yeh KC
    S-Nitrosoglutathione works downstream of nitric oxide to mediate iron-deficiency signaling in Arabidopsis.
    Plant J., 2018. 94(1): p. 157-168
  24. Kurt F,Filiz E
    Genome-wide and comparative analysis of bHLH38, bHLH39, bHLH100 and bHLH101 genes in Arabidopsis, tomato, rice, soybean and maize: insights into iron (Fe) homeostasis.
    Biometals, 2018. 31(4): p. 489-504