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 Rsa1.0_02246.1_g00005.1
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family bHLH
Protein Properties Length: 447aa    MW: 50387.2 Da    PI: 8.9321
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02246.1_g00005.1genomeRGDView 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  ErrRRdriN+++  L+el+P++     +K +Ka+iLe+A++Y+ksLq
                              6**************************.....9******************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
PROSITE profilePS5088819.244305354IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474595.89E-21308378IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000836.35E-11308359No hitNo description
PfamPF000102.7E-16309355IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.4E-19311360IPR011598Myc-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: 447 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting negatively in the phytochrome B signaling pathway. May regulate the expression of a subset of genes involved in cell expansion by binding to the G-box motif (By similarity). Activated by CRY1 and CRY2 in response to low blue light (LBL) by direct binding at chromatin on E-box variant 5'-CA[CT]GTG-3' to stimulate specific gene expression to adapt global physiology (e.g. hypocotyl elongation in low blue light) (PubMed:26724867). {ECO:0000250|UniProtKB:Q84LH8, ECO:0000269|PubMed:26724867}.
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV treatment. Follow a free-running robust circadian rhythm, with higher levels during the light phase. Rapidly induced by light in etiolated plants. Sixfold induction by both red and far-red light. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:12826627}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018473360.10.0PREDICTED: LOW QUALITY PROTEIN: transcription factor PIF4-like
SwissprotQ8W2F31e-143PIF4_ARATH; Transcription factor PIF4
TrEMBLA0A3N6QAU00.0A0A3N6QAU0_BRACR; Uncharacterized protein
STRINGBra000283.1-P0.0(Brassica rapa)
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
AT2G43010.21e-132phytochrome interacting factor 4
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. Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I
    Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development.
    Plant Signal Behav, 2014.
  3. Karayekov E,Sellaro R,Legris M,Yanovsky MJ,Casal JJ
    Heat shock-induced fluctuations in clock and light signaling enhance phytochrome B-mediated Arabidopsis deetiolation.
    Plant Cell, 2013. 25(8): p. 2892-906
  4. Wigge PA
    Ambient temperature signalling in plants.
    Curr. Opin. Plant Biol., 2013. 16(5): p. 661-6
  5. Oh S,Montgomery BL
    Phytochrome-induced SIG2 expression contributes to photoregulation of phytochrome signalling and photomorphogenesis in Arabidopsis thaliana.
    J. Exp. Bot., 2013. 64(18): p. 5457-72
  6. Mizuno T, et al.
    Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana.
    Plant Cell Physiol., 2014. 55(5): p. 958-76
  7. Zhiponova MK, et al.
    Helix-loop-helix/basic helix-loop-helix transcription factor network represses cell elongation in Arabidopsis through an apparent incoherent feed-forward loop.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(7): p. 2824-9
  8. Oh E, et al.
    Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl.
    Elife, 2015.
  9. Hayes S,Velanis CN,Jenkins GI,Franklin KA
    UV-B detected by the UVR8 photoreceptor antagonizes auxin signaling and plant shade avoidance.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(32): p. 11894-9
  10. Di C, et al.
    Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.
    Plant J., 2014. 80(5): p. 848-61
  11. Dornbusch T,Michaud O,Xenarios I,Fankhauser C
    Differentially phased leaf growth and movements in Arabidopsis depend on coordinated circadian and light regulation.
    Plant Cell, 2014. 26(10): p. 3911-21
  12. Delker C, et al.
    The DET1-COP1-HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis.
    Cell Rep, 2014. 9(6): p. 1983-9
  13. de Montaigu A, et al.
    Natural diversity in daily rhythms of gene expression contributes to phenotypic variation.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(3): p. 905-10
  14. Kong W,Li Y,Zhang M,Jin F,Li J
    A Novel Arabidopsis microRNA promotes IAA biosynthesis via the indole-3-acetaldoxime pathway by suppressing superroot1.
    Plant Cell Physiol., 2015. 56(4): p. 715-26
  15. Seaton DD, et al.
    Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature.
    Mol. Syst. Biol., 2015. 11(1): p. 776
  16. Filo J, et al.
    Gibberellin driven growth in elf3 mutants requires PIF4 and PIF5.
    Plant Signal Behav, 2015. 10(3): p. e992707
  17. Mizuno T,Kitayama M,Takayama C,Yamashino T
    Insight into a Physiological Role for the EC Night-Time Repressor in the Arabidopsis Circadian Clock.
    Plant Cell Physiol., 2015. 56(9): p. 1738-47
  18. Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T
    Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94
  19. Geilen K,Böhmer M
    Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana.
    Sci Rep, 2015. 5: p. 13369
  20. 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
  21. Huang M,Hu Y,Liu X,Li Y,Hou X
    Arabidopsis LEAFY COTYLEDON1 Mediates Postembryonic Development via Interacting with PHYTOCHROME-INTERACTING FACTOR4.
    Plant Cell, 2015. 27(11): p. 3099-111
  22. Miyazaki Y, et al.
    Enhancement of hypocotyl elongation by LOV KELCH PROTEIN2 production is mediated by auxin and phytochrome-interacting factors in Arabidopsis thaliana.
    Plant Cell Rep., 2016. 35(2): p. 455-67
  23. Shimizu H,Torii K,Araki T,Endo M
    Importance of epidermal clocks for regulation of hypocotyl elongation through PIF4 and IAA29.
    Plant Signal Behav, 2016. 11(2): p. e1143999
  24. 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
  25. Fernández V,Takahashi Y,Le Gourrierec J,Coupland G
    Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days.
    Plant J., 2016. 86(5): p. 426-40
  26. Shahnejat-Bushehri S,Tarkowska D,Sakuraba Y,Balazadeh S
    Arabidopsis NAC transcription factor JUB1 regulates GA/BR metabolism and signalling.
    Nat Plants, 2016. 2: p. 16013
  27. Quint M, et al.
    Molecular and genetic control of plant thermomorphogenesis.
    Nat Plants, 2016. 2: p. 15190
  28. Li K, et al.
    DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis.
    Nat Commun, 2016. 7: p. 11868
  29. Choi H,Oh E
    PIF4 Integrates Multiple Environmental and Hormonal Signals for Plant Growth Regulation in Arabidopsis.
    Mol. Cells, 2016. 39(8): p. 587-93
  30. 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
  31. Press MO,Lanctot A,Queitsch C
    PIF4 and ELF3 Act Independently in Arabidopsis thaliana Thermoresponsive Flowering.
    PLoS ONE, 2016. 11(8): p. e0161791
  32. Liu G, et al.
    Local Transcriptional Control of YUCCA Regulates Auxin Promoted Root-Growth Inhibition in Response to Aluminium Stress in Arabidopsis.
    PLoS Genet., 2016. 12(10): p. e1006360
  33. Di DW, et al.
    Functional roles of Arabidopsis CKRC2/YUCCA8 gene and the involvement of PIF4 in the regulation of auxin biosynthesis by cytokinin.
    Sci Rep, 2016. 6: p. 36866
  34. Kim JH,Lee HJ,Jung JH,Lee S,Park CM
    HOS1 Facilitates the Phytochrome B-Mediated Inhibition of PIF4 Function during Hypocotyl Growth in Arabidopsis.
    Mol Plant, 2017. 10(2): p. 274-284
  35. Zhu JY,Oh E,Wang T,Wang ZY
    TOC1-PIF4 interaction mediates the circadian gating of thermoresponsive growth in Arabidopsis.
    Nat Commun, 2016. 7: p. 13692
  36. Hayes S, et al.
    UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis.
    Curr. Biol., 2017. 27(1): p. 120-127
  37. Gangappa SN,Berriri S,Kumar SV
    PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis.
    Curr. Biol., 2017. 27(2): p. 243-249
  38. Gangappa SN,Kumar SV
    DET1 and HY5 Control PIF4-Mediated Thermosensory Elongation Growth through Distinct Mechanisms.
    Cell Rep, 2017. 18(2): p. 344-351
  39. Zentella R, et al.
    The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA.
    Nat. Chem. Biol., 2017. 13(5): p. 479-485
  40. Gray JA,Shalit-Kaneh A,Chu DN,Hsu PY,Harmer SL
    The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size.
    Plant Physiol., 2017. 173(4): p. 2308-2322
  41. Wang L, et al.
    PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(17): p. E3555-E3562
  42. Kim JH,Lee HJ,Park CM
    HOS1 acts as a key modulator of hypocotyl photomorphogenesis.
    Plant Signal Behav, 2017. 12(5): p. e1315497
  43. 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
  44. Ritter A, et al.
    The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis.
    Nat Commun, 2017. 8: p. 15235
  45. Jégu T, et al.
    The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility.
    Genome Biol., 2017. 18(1): p. 114
  46. 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
  47. Hwang G, et al.
    PIF4 Promotes Expression of LNG1 and LNG2 to Induce Thermomorphogenic Growth in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 1320
  48. Zhang B, et al.
    BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance.
    Elife, 2018.
  49. Sakuraba Y,Bülbül S,Piao W,Choi G,Paek NC
    Arabidopsis EARLY FLOWERING3 increases salt tolerance by suppressing salt stress response pathways.
    Plant J., 2017. 92(6): p. 1106-1120
  50. Ibañez C, et al.
    Brassinosteroids Dominate Hormonal Regulation of Plant Thermomorphogenesis via BZR1.
    Curr. Biol., 2018. 28(2): p. 303-310.e3
  51. Sun Z, et al.
    Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4.
    PLoS Genet., 2018. 14(3): p. e1007247
  52. Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS
    Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana.
    Plant Cell Rep., 2018. 37(6): p. 901-912
  53. Tasset C, et al.
    POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana.
    PLoS Genet., 2018. 14(3): p. e1007280
  54. Huai J, et al.
    SEUSS and PIF4 Coordinately Regulate Light and Temperature Signaling Pathways to Control Plant Growth.
    Mol Plant, 2018. 11(7): p. 928-942
  55. Zhao X, et al.
    COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressing CCA1 and PIF4 expression in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2018. 115(45): p. 11631-11636
  56. Qiu Y,Li M,Kim RJ,Moore CM,Chen M
    Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA.
    Nat Commun, 2019. 10(1): p. 140