Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G02340.1
Common NameBHLH26, EN68, FBI1, HFR1, REP1, RSF1, T6A9_13, T6A9.4
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: 292aa    MW: 33615 Da    PI: 7.5839
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G02340.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH  10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  rrR +++ +++ +L++l+P++      K +K+++L k++eY+k+Lq
                  666679**************9.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088813.802134183IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.69E-10135188No hitNo description
SMARTSM003535.3E-9139189IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000104.3E-7144184IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474598.11E-14144194IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009585Biological Processred, far-red light phototransduction
GO:0009642Biological Processresponse to light intensity
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0009785Biological Processblue light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003712Molecular Functiontranscription cofactor activity
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000293anatomyguard cell
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 292 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 AtlasAT1G02340-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1.
UniProtAtypical bHLH transcription factor that regulates photomorphogenesis through modulation of phytochrome (e.g. PHYA) and cryptochrome signalings (Ref.4, PubMed:11090209, PubMed:10995393, PubMed:19482971). Suppresses the transcriptional regulation activity of PIF4 by forming non-DNA-binding heterodimer. {ECO:0000269|PubMed:10995393, ECO:0000269|PubMed:11090209, ECO:0000269|PubMed:19482971, ECO:0000269|Ref.4}.
Function -- GeneRIF ? help Back to Top
  1. in addition to their independent functions in phyA signaling, LAF1 and HFR1 also cooperate post-translationally to stabilize each other through inhibition of ubiquitination by COP1, thereby enhancing phyA photoresponses
    [PMID: 17699755]
  2. CKII-mediated phosphorylation represents an important post-translational modification influencing the stability and signaling activity of Arabidopsis HFR1
    [PMID: 18556661]
  3. HFR1, which is fine-tuned by cry1, is crucial for regulating global gene expression in cry1-mediated early blue light signaling.
    [PMID: 18974779]
  4. OWL1 interacts with the basic helix-loop-helix HFR1 (LONG HYPOCOTYL IN FAR-RED) transcription factor. Both proteins are involved in the agravitropic response under far-red light.
    [PMID: 19808946]
  5. The HLH and the adjacent C-terminal domain are required for biological activity of HFR1.
    [PMID: 21205034]
  6. HY5 transmits phyA signals through an FHY1/FHL-independent pathway but it may also modulate FHY1/FHL signal through its interaction with HFR1 and LAF1.
    [PMID: 23503597]
  7. HFR1 prevents PIF1 from binding to its target genes and antagonistically regulates PIF1-mediated gene expression. HFR1 and PIF1 are the major transcription regulators responsible for light-directed Transcriptome changes in seed germination.
    [PMID: 24179122]
  8. light inactivates DET1, elevating HFR1 to sequester PIF1's suppression on seed germination
    [PMID: 25775589]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Twofold induction by far-red light and 14-fold suppression by red light.
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 AT1G26945 (R), AT2G46970 (A), AT4G16780 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G29910(A), AT4G16780(R), AT5G13930(R)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT1G02340HFR1 interacts with another molecule of HFR1.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G02340, AT1G26945
IntActSearch Q9FE22
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Partially blind to far-red (FR). Impaired inhibition of hypocotyl elongation and cotyledons expansion under continuous FR light conditions. {ECO:0000269|PubMed:19482971}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G02340
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF2882870.0AF288287.1 Aarabidopsis thaliana reduced phytochrome signaling 1 (REP1) mRNA, complete cds.
GenBankAF3231820.0AF323182.1 Arabidopsis thaliana basic helix-loop-helix FBI1 protein (FBI1) mRNA, complete cds.
GenBankAF3242450.0AF324245.1 Arabidopsis thaliana bHLH-like protein HFR1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_563650.10.0transcription factor HFR1
SwissprotQ9FE220.0HFR1_ARATH; Transcription factor HFR1
TrEMBLR0GQW81e-156R0GQW8_9BRAS; Uncharacterized protein (Fragment)
STRINGAT1G02340.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP25816128
Publications ? help Back to Top
  1. Fankhauser C,Chory J
    RSF1, an Arabidopsis locus implicated in phytochrome A signaling.
    Plant Physiol., 2000. 124(1): p. 39-45
  2. Fairchild CD,Schumaker MA,Quail PH
    HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction.
    Genes Dev., 2000. 14(18): p. 2377-91
  3. Soh MS,Kim YM,Han SJ,Song PS
    REP1, a basic helix-loop-helix protein, is required for a branch pathway of phytochrome A signaling in arabidopsis.
    Plant Cell, 2000. 12(11): p. 2061-74
  4. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  5. Spiegelman JI, et al.
    Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography.
    Plant Cell, 2000. 12(12): p. 2485-2498
  6. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
  7. Kim YM,Woo JC,Song PS,Soh MS
    HFR1, a phytochrome A-signalling component, acts in a separate pathway from HY5, downstream of COP1 in Arabidopsis thaliana.
    Plant J., 2002. 30(6): p. 711-9
  8. Wang H, et al.
    Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis.
    Plant J., 2002. 32(5): p. 723-33
  9. 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
  10. Yamashino T, et al.
    A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(6): p. 619-29
  11. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  12. Yang KY,Kim YM,Lee S,Song PS,Soh MS
    Overexpression of a mutant basic helix-loop-helix protein HFR1, HFR1-deltaN105, activates a branch pathway of light signaling in Arabidopsis.
    Plant Physiol., 2003. 133(4): p. 1630-42
  13. Duek PD,Elmer MV,van Oosten VR,Fankhauser C
    The degradation of HFR1, a putative bHLH class transcription factor involved in light signaling, is regulated by phosphorylation and requires COP1.
    Curr. Biol., 2004. 14(24): p. 2296-301
  14. Yang J, et al.
    Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis.
    Plant Cell, 2005. 17(3): p. 804-21
  15. Jang IC,Yang JY,Seo HS,Chua NH
    HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling.
    Genes Dev., 2005. 19(5): p. 593-602
  16. Yang J, et al.
    Repression of light signaling by Arabidopsis SPA1 involves post-translational regulation of HFR1 protein accumulation.
    Plant J., 2005. 43(1): p. 131-41
  17. Sessa G, et al.
    A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis.
    Genes Dev., 2005. 19(23): p. 2811-5
  18. Kang X,Ni M
    Arabidopsis SHORT HYPOCOTYL UNDER BLUE1 contains SPX and EXS domains and acts in cryptochrome signaling.
    Plant Cell, 2006. 18(4): p. 921-34
  19. Hyun Y,Lee I
    KIDARI, encoding a non-DNA Binding bHLH protein, represses light signal transduction in Arabidopsis thaliana.
    Plant Mol. Biol., 2006. 61(1-2): p. 283-96
  20. Yang J,Wang H
    The central coiled-coil domain and carboxyl-terminal WD-repeat domain of Arabidopsis SPA1 are responsible for mediating repression of light signaling.
    Plant J., 2006. 47(4): p. 564-76
  21. Jang IC,Yang SW,Yang JY,Chua NH
    Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling.
    Genes Dev., 2007. 21(16): p. 2100-11
  22. Park HJ,Ding L,Dai M,Lin R,Wang H
    Multisite phosphorylation of Arabidopsis HFR1 by casein kinase II and a plausible role in regulating its degradation rate.
    J. Biol. Chem., 2008. 283(34): p. 23264-73
  23. Zhang XN, et al.
    HFR1 is crucial for transcriptome regulation in the cryptochrome 1-mediated early response to blue light in Arabidopsis thaliana.
    PLoS ONE, 2008. 3(10): p. e3563
  24. Yang SW,Jang IC,Henriques R,Chua NH
    FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis transcription factors LAF1 and HFR1 to transmit phytochrome A signals for inhibition of hypocotyl elongation.
    Plant Cell, 2009. 21(5): p. 1341-59
  25. Lorrain S,Trevisan M,Pradervand S,Fankhauser C
    Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.
    Plant J., 2009. 60(3): p. 449-61
  26. 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
  27. Kneissl J,Wachtler V,Chua NH,Bolle C
    OWL1: an Arabidopsis J-domain protein involved in perception of very low light fluences.
    Plant Cell, 2009. 21(10): p. 3212-25
  28. Hornitschek P,Lorrain S,Zoete V,Michielin O,Fankhauser C
    Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers.
    EMBO J., 2009. 28(24): p. 3893-902
  29. Zhang LY, et al.
    Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis.
    Plant Cell, 2009. 21(12): p. 3767-80
  30. Mara CD,Huang T,Irish VF
    The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling.
    Plant Cell, 2010. 22(3): p. 690-702
  31. Pokhilko A, et al.
    Ubiquitin ligase switch in plant photomorphogenesis: A hypothesis.
    J. Theor. Biol., 2011. 270(1): p. 31-41
  32. Galstyan A,Cifuentes-Esquivel N,Bou-Torrent J,Martinez-Garcia JF
    The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors.
    Plant J., 2011. 66(2): p. 258-67
  33. Foreman J, et al.
    Light receptor action is critical for maintaining plant biomass at warm ambient temperatures.
    Plant J., 2011. 65(3): p. 441-52
  34. Zhao R, et al.
    The Arabidopsis Ca(2+) -dependent protein kinase CPK12 negatively regulates abscisic acid signaling in seed germination and post-germination growth.
    New Phytol., 2011. 192(1): p. 61-73
  35. Bu Q,Castillon A,Chen F,Zhu L,Huq E
    Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis.
    Plant Mol. Biol., 2011. 77(4-5): p. 501-11
  36. Jang IC,Niu QW,Deng S,Zhao P,Chua NH
    Enhancing protein stability with retained biological function in transgenic plants.
    Plant J., 2012. 72(2): p. 345-54
  37. Li W,Dai L,Wang GL
    PUB13, a U-box/ARM E3 ligase, regulates plant defense, cell death, and flowering time.
    Plant Signal Behav, 2012. 7(8): p. 898-900
  38. Rolauffs S,Fackendahl P,Sahm J,Fiene G,Hoecker U
    Arabidopsis COP1 and SPA genes are essential for plant elongation but not for acceleration of flowering time in response to a low red light to far-red light ratio.
    Plant Physiol., 2012. 160(4): p. 2015-27
  39. Hong SY, et al.
    A competitive peptide inhibitor KIDARI negatively regulates HFR1 by forming nonfunctional heterodimers in Arabidopsis photomorphogenesis.
    Mol. Cells, 2013. 35(1): p. 25-31
  40. Jang IC,Henriques R,Chua NH
    Three transcription factors, HFR1, LAF1 and HY5, regulate largely independent signaling pathways downstream of phytochrome A.
    Plant Cell Physiol., 2013. 54(6): p. 907-16
  41. Shi H, et al.
    HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis.
    Plant Cell, 2013. 25(10): p. 3770-84
  42. Liu Y,Liu Q,Yan Q,Shi L,Fang Y
    Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model.
    Mol. Biol. Cell, 2014. 25(8): p. 1366-73
  43. 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
  44. Shi H, et al.
    Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(12): p. 3817-22