Plant Transcription Factor Database
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Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G46970.1
Common NameBHLH124, EN110, F14M4.20, PIL1
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: 416aa    MW: 46579.7 Da    PI: 9.4395
Description phytochrome interacting factor 3-like 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G46970.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   h+  Er+RRd+ N+++  L++llP++      K +Ka+ L +A++Y++ Lq
                  59999*********************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.83E-17227304IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000839.57E-12227283No hitNo description
PROSITE profilePS5088815.332229278IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000107.6E-10233279IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.5E-11235284IPR011598Myc-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:0009641Biological Processshade avoidance
GO:0010017Biological Processred or far-red light signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA 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: 416 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.364250.0flower| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasAT2G46970
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Etiolated seedlings. {ECO:0000269|PubMed:12826627}.
Functional Description ? help Back to Top
Source Description
TAIRencodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family.
UniProtTranscription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. {ECO:0000269|PubMed:14668869, ECO:0000269|PubMed:16565297, ECO:0000269|PubMed:16891401}.
Function -- GeneRIF ? help Back to Top
  1. PIL1 is a direct target of phytochrome signaling and plays a key role in response to long-term shade in Arabidopsis.
    [PMID: 16565297]
  2. PIL1 is necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.
    [PMID: 16891401]
  3. These data suggest that the second-phase decline in robustness of PIL1 derepression is an indirect consequence of the global developmental transition from the etiolated to the de-etiolated state.
    [PMID: 18296722]
  4. PIL1 plays a role as a decelerator of growth during early shade avoidance.
    [PMID: 24895419]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Expressed with a circadian rhythm showing peaks during the light period. Up-regulated by simulated shade in light-grown plants, in a phytochrome-dependent manner; low red/far-red ratio (R/FR) light, but repressed by a high R/FR light. Rapidly down-regulated after seedling deetiolation. {ECO:0000269|PubMed:14668869, ECO:0000269|PubMed:16565297, ECO:0000269|PubMed:16891401}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G02340(A), AT2G46790(A)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q8L5W8
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G46970
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY9548400.0AY954840.1 Arabidopsis thaliana hypothetical protein (At2g46970) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_182220.20.0transcription factor PIL1
SwissprotQ8L5W80.0PIL1_ARATH; Transcription factor PIL1
TrEMBLD7LFX40.0D7LFX4_ARALL; Putative uncharacterized protein
STRINGAT2G46970.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP25816128
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. Makino S,Matsushika A,Kojima M,Yamashino T,Mizuno T
    The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants.
    Plant Cell Physiol., 2002. 43(1): p. 58-69
  3. Matsushika A,Makino S,Kojima M,Yamashino T,Mizuno T
    The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants.
    Plant Cell Physiol., 2002. 43(1): p. 118-22
  4. Fowler S,Thomashow MF
    Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway.
    Plant Cell, 2002. 14(8): p. 1675-90
  5. Xiao YL,Malik M,Whitelaw CA,Town CD
    Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis.
    Plant Physiol., 2002. 130(4): p. 2118-28
  6. 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
  7. 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
  8. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  9. 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
  10. Ito S, et al.
    Characterization of the APRR9 pseudo-response regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(11): p. 1237-45
  11. Devlin PF,Yanovsky MJ,Kay SA
    A genomic analysis of the shade avoidance response in Arabidopsis.
    Plant Physiol., 2003. 133(4): p. 1617-29
  12. Salter MG,Franklin KA,Whitelam GC
    Gating of the rapid shade-avoidance response by the circadian clock in plants.
    Nature, 2003. 426(6967): p. 680-3
  13. Tepperman JM, et al.
    Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation.
    Plant J., 2004. 38(5): p. 725-39
  14. 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
  15. Roig-Villanova I,Bou J,Sorin C,Devlin PF,Martínez-García JF
    Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis.
    Plant Physiol., 2006. 141(1): p. 85-96
  16. Khanna R, et al.
    Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation.
    Plant Cell, 2006. 18(9): p. 2157-71
  17. Franklin KA,Whitelam GC
    Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
    Nat. Genet., 2007. 39(11): p. 1410-3
  18. Hwang YS,Quail PH
    Phytochrome-regulated PIL1 derepression is developmentally modulated.
    Plant Cell Physiol., 2008. 49(4): p. 501-11
  19. Davi
    Transcriptional factor interaction: a central step in DELLA function.
    Curr. Opin. Genet. Dev., 2008. 18(4): p. 295-303
  20. Rehrauer H, et al.
    AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.
    Plant Physiol., 2010. 152(2): p. 487-99
  21. Yang R, et al.
    Assembly of synthetic locked phycocyanobilin derivatives with phytochrome in vitro and in vivo in Ceratodon purpureus and Arabidopsis.
    Plant Cell, 2012. 24(5): p. 1936-51
  22. Wang H, et al.
    CONSTANS-LIKE 7 regulates branching and shade avoidance response in Arabidopsis.
    J. Exp. Bot., 2013. 64(4): p. 1017-24
  23. Choi H, et al.
    The homeodomain-leucine zipper ATHB23, a phytochrome B-interacting protein, is important for phytochrome B-mediated red light signaling.
    Physiol Plant, 2014. 150(2): p. 308-20
  24. Li L, et al.
    PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade.
    Mol Plant, 2014. 7(10): p. 1582-5
  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
  26. Qiu Y, et al.
    HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.
    Plant Cell, 2015. 27(5): p. 1409-27