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 AT3G46640.1
Common NameF12A12.160, LUX, PCL1
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 G2-like
Protein Properties Length: 323aa    MW: 34648.9 Da    PI: 5.6716
Description G2-like family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G46640.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
      G2-like   1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 
                  +prl+Wtp+LH+rFv++v++L G+++A+Pkti++lm+v+gLt+e+v+SHLQkYRl
                  59*******************.********************************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129410.252139200IPR017930Myb domain
TIGRFAMsTIGR015571.6E-23145197IPR006447Myb domain, plants
PfamPF002495.6E-8147196IPR001005SANT/Myb domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0042753Biological Processpositive regulation of circadian rhythm
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
Sequence ? help Back to Top
Protein Sequence    Length: 323 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5lxu_A9e-36144200157Transcription factor LUX
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.479510.0flower| root| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G46640-
Functional Description ? help Back to Top
Source Description
TAIREncodes a myb family transcription factor with a single Myb DNA-binding domain (type SHAQKYF) that is unique to plants and is essential for circadian rhythms, specifically for transcriptional regulation within the circadian clock. LUX is required for normal rhythmic expression of multiple clock outputs in both constant light and darkness. It is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter.
UniProtTranscription factor that is essential for the generation of the circadian clock oscillation. Is necessary for activation of CCA1 and LHY expression. Is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter. Directly regulates the expression of PRR9, a major component of the morning transcriptional feedback circuit, by binding specific sites on PRR9 promoter. Binds to its own promoter, inducing a negative auto-regulatory feedback loop within the core clock. Binds to ELF3 and associates with ELF4 in a diurnal complex which is required for the expression of the growth-promoting transcription factors PIF4 and PIF5 and subsequent hypocotyl growth in the early evening. {ECO:0000269|PubMed:16006522, ECO:0000269|PubMed:16164597, ECO:0000269|PubMed:21236673, ECO:0000269|PubMed:21753751, ECO:0000269|PubMed:22311777}.
Function -- GeneRIF ? help Back to Top
  1. LUX ARRHYTHMO (LUX) encodes a Myb domain protein essential for circadian rhythms. [LUX]
    [PMID: 16006522]
  2. The PCL1 gene is the clock oscillator gene essential to the generation of clock oscillation in the higher plant. [PCL1]
    [PMID: 16164597]
  3. The in vitro Dna-binding specificity of LUX, its role in the expression of PRR9, and its feedback properties are reported.
    [PMID: 21236673]
  4. identification of a protein complex composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)--that directly regulates plant growth
    [PMID: 21753751]
  5. Transcriptional co-regulators PRR9, PRR7 and PRR5 inhibit morning loops LHY and CCA1 expression by binding to their promoters.
    [PMID: 24267177]
  6. Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.
    [PMID: 24954045]
  7. Data identified proteins that associate with the evening complex composed of EARLY FLOWERING 4 (ELF4), EARLY FLOWERING 3 (ELF3), and LUX ARRHYTHMO (LUX).
    [PMID: 26545401]
  8. mutations in the core clock component LUX ARRHYTHMO (LUX) disrupt circadian regulation of stomata under free running and Pseudomonas syringae challenge conditions as well as defense signaling mediated by salicylic and jasmonic acid, leading to compromised disease resistance.
    [PMID: 31186426]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Circadian oscillation with peaks at subjective dusk. {ECO:0000269|PubMed:16006522, ECO:0000269|PubMed:16164597, ECO:0000269|PubMed:17132630, ECO:0000269|PubMed:21753751}.
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 AT1G01060 (R), AT2G46830 (R), AT3G46640 (R), AT5G10140 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G01060(A), AT1G22770(R), AT2G40080(R), AT2G46830(A), AT3G46640(R), AT5G61380(R)
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Mutant plant flowering lacks a photoperiodic response. {ECO:0000269|PubMed:16006522, ECO:0000269|PubMed:16164597}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G46640
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2065760.0AB206576.1 Arabidopsis thaliana PCL1 gene for PHYTOCLOCK 1, complete cds.
GenBankAK2276860.0AK227686.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL14-26-J19.
GenBankAL1333140.0AL133314.1 Arabidopsis thaliana DNA chromosome 3, BAC clone F12A12.
GenBankBT0064250.0BT006425.1 Arabidopsis thaliana At3g46640 gene, complete cds.
GenBankCP0026860.0CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001030823.10.0Homeodomain-like superfamily protein
RefseqNP_190248.10.0Homeodomain-like superfamily protein
SwissprotQ9SNB40.0PCL1_ARATH; Transcription factor LUX
TrEMBLF4J9590.0F4J959_ARATH; Homeodomain-like superfamily protein
STRINGAT3G46640.30.0(Arabidopsis thaliana)
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. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  3. Hazen SP, et al.
    LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(29): p. 10387-92
  4. Onai K,Ishiura M
    PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock.
    Genes Cells, 2005. 10(10): p. 963-72
  5. Salom
    Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period.
    Plant Cell, 2006. 18(1): p. 55-69
  6. Murakami M,Tago Y,Yamashino T,Mizuno T
    Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa.
    Plant Cell Physiol., 2007. 48(1): p. 110-21
  7. Abe M,Fujiwara M,Kurotani K,Yokoi S,Shimamoto K
    Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP).
    Plant Cell Physiol., 2008. 49(3): p. 420-32
  8. Bieniawska Z, et al.
    Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
    Plant Physiol., 2008. 147(1): p. 263-79
  9. Helfer A, et al.
    LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock.
    Curr. Biol., 2011. 21(2): p. 126-33
  10. Dai S, et al.
    BROTHER OF LUX ARRHYTHMO is a component of the Arabidopsis circadian clock.
    Plant Cell, 2011. 23(3): p. 961-72
  11. Nusinow DA, et al.
    The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth.
    Nature, 2011. 475(7356): p. 398-402
  12. Chow BY,Helfer A,Nusinow DA,Kay SA
    ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock.
    Plant Signal Behav, 2012. 7(2): p. 170-3
  13. Sellaro R,Pac
    Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling.
    Mol Plant, 2012. 5(3): p. 619-28
  14. Herrero E, et al.
    EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock.
    Plant Cell, 2012. 24(2): p. 428-43
  15. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  16. Mizuno N,Nitta M,Sato K,Nasuda S
    A wheat homologue of PHYTOCLOCK 1 is a candidate gene conferring the early heading phenotype to einkorn wheat.
    Genes Genet. Syst., 2012. 87(6): p. 357-67
  17. Higham CF,Husmeier D
    A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana.
    BMC Bioinformatics, 2013. 14 Suppl 10: p. S3
  18. Chow BY, et al.
    Transcriptional regulation of LUX by CBF1 mediates cold input to the circadian clock in Arabidopsis.
    Curr. Biol., 2014. 24(13): p. 1518-24
  19. 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
  20. Huang H, et al.
    Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry.
    Mol. Cell Proteomics, 2016. 15(1): p. 201-17
  21. Huang H, et al.
    PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis.
    Elife, 2016. 5: p. e13292
  22. Zhang C, et al.
    LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis.
    Nat Commun, 2019. 10(1): p. 2543