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 462895392
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Eragrostideae; Eragrostidinae; Eragrostis
Family bHLH
Protein Properties Length: 174aa    MW: 19045 Da    PI: 7.9783
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
462895392genomeTefView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
        HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                 hn  E+rRR+riN+++  L++l+P++      K +Ka++L +A+eY+k+Lq
                6*************************7.....5******************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
SuperFamilySSF474595.63E-20102165IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.063105154IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000836.21E-19108159No hitNo description
PfamPF000103.0E-14109155IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003537.3E-18111160IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 174 aa     Download sequence    Send to blast
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3'). {ECO:0000269|PubMed:10466729, ECO:0000269|PubMed:10797009}.
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV treatment. {ECO:0000269|PubMed:12679534}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9696891e-81EU969689.1 Zea mays clone 334086 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001131794.19e-56uncharacterized protein LOC100193167
RefseqXP_008658091.19e-56putative HLH DNA-binding domain superfamily protein isoform X1
RefseqXP_008658092.15e-56putative HLH DNA-binding domain superfamily protein isoform X2
SwissprotO805362e-29PIF3_ARATH; Transcription factor PIF3
TrEMBLA0A1D6NUL63e-54A0A1D6NUL6_MAIZE; Transcription factor SPATULA
TrEMBLB4FE222e-54B4FE22_MAIZE; BHLH transcription factor
STRINGGRMZM2G017349_P014e-55(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36930.19e-22bHLH family protein
Publications ? help Back to Top
  1. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
  2. Zhong S, et al.
    Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(11): p. 3913-20
  3. Van Buskirk EK,Reddy AK,Nagatani A,Chen M
    Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark.
    Plant Physiol., 2014. 165(2): p. 595-607
  4. Zhao Y,Zhou J,Xing D
    Phytochrome B-mediated activation of lipoxygenase modulates an excess red light-induced defence response in Arabidopsis.
    J. Exp. Bot., 2014. 65(17): p. 4907-18
  5. Zhang D,Jing Y,Jiang Z,Lin R
    The Chromatin-Remodeling Factor PICKLE Integrates Brassinosteroid and Gibberellin Signaling during Skotomorphogenic Growth in Arabidopsis.
    Plant Cell, 2014. 26(6): p. 2472-2485
  6. Wang Y, et al.
    Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(28): p. 10359-64
  7. Zhu L,Huq E
    Suicidal co-degradation of the phytochrome interacting factor 3 and phytochrome B in response to light.
    Mol Plant, 2014. 7(12): p. 1709-11
  8. Adams E,Diaz C,Hong JP,Shin R
    14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs.
    Int J Mol Sci, 2014. 15(12): p. 22801-14
  9. Horvath DP, et al.
    RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.
    New Phytol., 2015. 207(1): p. 196-210
  10. Geilen K,Böhmer M
    Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana.
    Sci Rep, 2015. 5: p. 13369
  11. Galvão VC,Collani S,Horrer D,Schmid M
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana.
    Plant J., 2015. 84(5): p. 949-62
  12. Yue J, et al.
    TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis.
    Plant Physiol., 2016. 170(3): p. 1381-97
  13. Eprintsev AT,Fedorin DN,Sazonova OV,Igamberdiev AU
    Light inhibition of fumarase in Arabidopsis leaves is phytochrome A-dependent and mediated by calcium.
    Plant Physiol. Biochem., 2016. 102: p. 161-6
  14. Soy J, et al.
    Molecular convergence of clock and photosensory pathways through PIF3-TOC1 interaction and co-occupancy of target promoters.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(17): p. 4870-5
  15. Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ
    Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
    New Phytol., 2016. 211(3): p. 967-79
  16. Yoo J,Cho MH,Lee SW,Bhoo SH
    Phytochrome-interacting ankyrin repeat protein 2 modulates phytochrome A-mediated PIF3 phosphorylation in light signal transduction.
    J. Biochem., 2016. 160(4): p. 243-249
  17. Kumar I,Swaminathan K,Hudson K,Hudson ME
    Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling.
    J. Exp. Bot., 2016. 67(14): p. 4231-40
  18. Li K, et al.
    DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis.
    Nat Commun, 2016. 7: p. 11868
  19. Jeong AR, et al.
    New Constitutively Active Phytochromes Exhibit Light-Independent Signaling Activity.
    Plant Physiol., 2016. 171(4): p. 2826-40
  20. Martin G,Soy J,Monte E
    Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.
    Front Plant Sci, 2016. 7: p. 962
  21. Yu Y,Huang R
    Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 57
  22. Zentella R, et al.
    The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA.
    Nat. Chem. Biol., 2017. 13(5): p. 479-485
  23. Ling JJ,Li J,Zhu D,Deng XW
    Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(13): p. 3539-3544
  24. Kasulin L, et al.
    A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.
    Mol. Ecol., 2017. 26(13): p. 3389-3404
  25. Shor E,Paik I,Kangisser S,Green R,Huq E
    PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis.
    New Phytol., 2017. 215(1): p. 217-228
  26. Ni W, et al.
    PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.
    Nat Commun, 2017. 8: p. 15236
  27. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
  28. Paik I,Kathare PK,Kim JI,Huq E
    Expanding Roles of PIFs in Signal Integration from Multiple Processes.
    Mol Plant, 2017. 10(8): p. 1035-1046
  29. Dong J, et al.
    Light-Dependent Degradation of PIF3 by SCFEBF1/2 Promotes a Photomorphogenic Response in Arabidopsis.
    Curr. Biol., 2017. 27(16): p. 2420-2430.e6
  30. Jiang B, et al.
    PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(32): p. E6695-E6702
  31. Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B
    PhiReX: a programmable and red light-regulated protein expression switch for yeast.
    Nucleic Acids Res., 2017. 45(15): p. 9193-9205
  32. Liu X, et al.
    EIN3 and PIF3 Form an Interdependent Module That Represses Chloroplast Development in Buried Seedlings.
    Plant Cell, 2017. 29(12): p. 3051-3067
  33. Wang Y,Li J,Deng XW,Zhu D
    Arabidopsis noncoding RNA modulates seedling greening during deetiolation.
    Sci China Life Sci, 2018. 61(2): p. 199-203
  34. Ma Q,Wang X,Sun J,Mao T
    Coordinated Regulation of Hypocotyl Cell Elongation by Light and Ethylene through a Microtubule Destabilizing Protein.
    Plant Physiol., 2018. 176(1): p. 678-690
  35. Qiu Y, et al.
    Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B.
    Nat Commun, 2017. 8(1): p. 1905
  36. Xin X, et al.
    Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3.
    J. Exp. Bot., 2018. 69(3): p. 423-439