PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G46970.1
Common NameBHLH124, EN110, F14M4.20, PIL1
Organism
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
1HLH38.12.8e-12233279455
                  HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   h+  Er+RRd+ N+++  L++llP++      K +Ka+ L +A++Y++ Lq
  AT2G46970.1 233 VHKLYERKRRDEFNKKMRALQDLLPNC-----YKDDKASLLDEAIKYMRTLQ 279
                  59999*********************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.109.5E-17226289IPR011598Myc-type, 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
MEAKPLASSS SEPNMISPSS NIKPKLKDED YMELVCENGQ ILAKIRRPKN NGSFQKQRRQ  60
SLLDLYETEY SEGFKKNIKI LGDTQVVPVS QSKPQQDKET NEQMNNNKKK LKSSKIEFER  120
NVSKSNKCVE SSTLIDVSAK GPKNVEVTTA PPDEQSAAVG RSTELYFASS SKFSRGTSRD  180
LSCCSLKRKY GDIEEEESTY LSNNSDDESD DAKTQVHART RKPVTKRKRS TEVHKLYERK  240
RRDEFNKKMR ALQDLLPNCY KDDKASLLDE AIKYMRTLQL QVQMMSMGNG LIRPPTMLPM  300
GHYSPMGLGM HMGAAATPTS IPQFLPMNVQ ATGFPGMNNA PPQMLSFLNH PSGLIPNTPI  360
FSPLENCSQP FVVPSCVSQT QATSFTQFPK SASASNLEDA MQYRGSNGFS YYRSPN
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1226241RKRSTEVHKLYERKRR
2237242ERKRRD
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
AtGenExpressAT2G46970
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
SourceLink
PlantRegMapAT2G46970.1
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
PlantRegMapRetrieveRetrieve
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
MalvidsOGEM139371725
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
    [PMID:11118137]
  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
    [PMID:11828023]
  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
    [PMID:11828029]
  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
    [PMID:12172015]
  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
    [PMID:12481096]
  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
    [PMID:12679534]
  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
    [PMID:12826627]
  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
    [PMID:12897250]
  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
    [PMID:14600211]
  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
    [PMID:14634162]
  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
    [PMID:14645734]
  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
    [PMID:14668869]
  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
    [PMID:15144375]
  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
    [PMID:16322556]
  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
    [PMID:16565297]
  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
    [PMID:16891401]
  17. Franklin KA,Whitelam GC
    Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
    Nat. Genet., 2007. 39(11): p. 1410-3
    [PMID:17965713]
  18. Hwang YS,Quail PH
    Phytochrome-regulated PIL1 derepression is developmentally modulated.
    Plant Cell Physiol., 2008. 49(4): p. 501-11
    [PMID:18296722]
  19. Davi
    Transcriptional factor interaction: a central step in DELLA function.
    Curr. Opin. Genet. Dev., 2008. 18(4): p. 295-303
    [PMID:18590820]
  20. Rehrauer H, et al.
    AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.
    Plant Physiol., 2010. 152(2): p. 487-99
    [PMID:20032078]
  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
    [PMID:22582099]
  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
    [PMID:23314820]
  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
    [PMID:23964902]
  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
    [PMID:24895419]
  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
    [PMID:25750178]
  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
    [PMID:25944101]