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 Seita.1G357300.1.p
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria
Family bHLH
Protein Properties Length: 109aa    MW: 12336.1 Da    PI: 10.1586
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Seita.1G357300.1.pgenomeJGIView 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*************************8.....7******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474595.1E-2043104IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088817.9814695IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000833.99E-1349100No hitNo description
PfamPF000105.7E-155096IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
SMARTSM003532.0E-1852101IPR011598Myc-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: 109 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}.
UniProtTranscription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269|PubMed:10225997, ECO:0000269|Ref.8}.
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV treatment. {ECO:0000269|PubMed:12679534}.
UniProtINDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269|PubMed:11245574}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0333821e-122BT033382.1 Zea mays full-length cDNA clone ZM_BFb0041N16 mRNA, complete cds.
GenBankBT0640561e-122BT064056.1 Zea mays full-length cDNA clone ZM_BFc0135E23 mRNA, complete cds.
GenBankKJ7269881e-122KJ726988.1 Zea mays clone pUT3689 bHLH transcription factor (bHLH168) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004954276.18e-65transcription factor SPATULA isoform X1
RefseqXP_022682068.12e-65transcription factor SPATULA isoform X2
SwissprotO805366e-27PIF3_ARATH; Transcription factor PIF3
SwissprotQ9FUA41e-27SPT_ARATH; Transcription factor SPATULA
TrEMBLA0A368PTP72e-72A0A368PTP7_SETIT; Uncharacterized protein
STRINGSi017762m3e-64(Setaria italica)
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
AT4G36930.12e-23bHLH 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. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
  8. 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
  9. Moubayidin L,Ostergaard L
    Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development.
    Curr. Biol., 2014. 24(22): p. 2743-8
  10. 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
  11. 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
  12. Geilen K,Böhmer M
    Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana.
    Sci Rep, 2015. 5: p. 13369
  13. 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
  14. Yue J, et al.
    TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis.
    Plant Physiol., 2016. 170(3): p. 1381-97
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. Li K, et al.
    DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis.
    Nat Commun, 2016. 7: p. 11868
  21. Jeong AR, et al.
    New Constitutively Active Phytochromes Exhibit Light-Independent Signaling Activity.
    Plant Physiol., 2016. 171(4): p. 2826-40
  22. 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
  23. Pfannebecker KC,Lange M,Rupp O,Becker A
    Seed Plant-Specific Gene Lineages Involved in Carpel Development.
    Mol. Biol. Evol., 2017. 34(4): p. 925-942
  24. Yu Y,Huang R
    Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 57
  25. Zentella R, et al.
    The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA.
    Nat. Chem. Biol., 2017. 13(5): p. 479-485
  26. 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
  27. 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
  28. Zumajo-Cardona C,Ambrose BA,Pabón-Mora N
    Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae).
    Evodevo, 2017. 8: p. 5
  29. Reyes-Olalde JI, et al.
    The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium.
    PLoS Genet., 2017. 13(4): p. e1006726
  30. 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
  31. Ni W, et al.
    PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.
    Nat Commun, 2017. 8: p. 15236
  32. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. Wu M, et al.
    SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis.
    Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385