Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G56980.1
Common NameBHLH039, bHLH39, EN9, F24I3.60, ORG3
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: 258aa    MW: 29003.8 Da    PI: 6.9125
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G56980.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  ++ +hn+ Er RR++iNs f+ Lr++lP +  ++skKls  +++ +  +YI +Lq
                  6789*************************8..7*******************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088814.44976128IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.57E-1677146IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000838.10E-1577132No hitNo description
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
PfamPF000102.3E-1377129IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003532.9E-1282134IPR011598Myc-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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009015anatomyportion of vascular tissue
PO:0009025anatomyvascular leaf
PO:0025022anatomycollective leaf structure
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 258 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G56980-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in vascular tissues. Detected in roots. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:18296723}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the basic helix-loop-helix transcription factor 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.
    [PMID: 17260143]
  2. up-regulated by iron deficiency in roots and leaves
    [PMID: 17516080]
  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.
    [PMID: 23250624]
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). 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: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 Q9M1K0
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G56980
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4885770.0AF488577.1 Arabidopsis thaliana clone bHLH039 putative bHLH transcription factor mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_191257.10.0transcription factor ORG3
SwissprotQ9M1K00.0ORG3_ARATH; Transcription factor ORG3
TrEMBLD7LVM11e-166D7LVM1_ARALL; OBP3-responsive gene 3
STRINGAT3G56980.10.0(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. M
    Changes in gene expression in response to altered SHL transcript levels.
    Plant Mol. Biol., 2003. 53(6): p. 805-20
  8. S
    ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis.
    Plant J., 2004. 38(3): p. 381-95
  9. Zhao C,Craig JC,Petzold HE,Dickerman AW,Beers EP
    The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl.
    Plant Physiol., 2005. 138(2): p. 803-18
  10. 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
  11. 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
  12. Osuna D, et al.
    Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings.
    Plant J., 2007. 49(3): p. 463-91
  13. 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
  14. Vorwieger A, et al.
    Iron assimilation and transcription factor controlled synthesis of riboflavin in plants.
    Planta, 2007. 226(1): p. 147-58
  15. Sottosanto JB,Saranga Y,Blumwald E
    Impact of AtNHX1, a vacuolar Na+/H+ antiporter, upon gene expression during short- and long-term salt stress in Arabidopsis thaliana.
    BMC Plant Biol., 2007. 7: p. 18
  16. 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
  17. 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
  18. Wenzel CL,Hester Q,Mattsson J
    Identification of genes expressed in vascular tissues using NPA-induced vascular overgrowth in Arabidopsis.
    Plant Cell Physiol., 2008. 49(3): p. 457-68
  19. Krishnaswamy SS, et al.
    Transcriptional profiling of pea ABR17 mediated changes in gene expression in Arabidopsis thaliana.
    BMC Plant Biol., 2008. 8: p. 91
  20. Gong W, et al.
    The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.
    Mol Plant, 2008. 1(1): p. 27-41
  21. 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
  22. 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
  23. 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
  24. Hong S,Kim SA,Guerinot ML,McClung CR
    Reciprocal interaction of the circadian clock with the iron homeostasis network in Arabidopsis.
    Plant Physiol., 2013. 161(2): p. 893-903
  25. 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