PlantTFDB
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_09028.1_g00002.1
Organism
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: 378aa    MW: 42727.7 Da    PI: 7.6422
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_09028.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH56.45.4e-18250295454
                              HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHH CS
                      HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksL 54 
                               hn  ErrRRdriN+++ +L+el+P++     +K +Ka+iL +A++Y+ksL
  Rsa1.0_09028.1_g00002.1 250 VHNLSERRRRDRINERMKTLQELIPHC-----TKTDKASILDEAIDYMKSL 295
                              6**************************.....9****************99 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474592.75E-20244308IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.102.9E-20244302IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088819.213246295IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000832.70E-10249300No hitNo description
PfamPF000101.9E-15250295IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003539.5E-19252301IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009704Biological Processde-etiolation
GO:0010161Biological Processred light signaling pathway
GO:0010244Biological Processresponse to low fluence blue light stimulus by blue low-fluence system
GO:0010600Biological Processregulation of auxin biosynthetic process
GO:0010928Biological Processregulation of auxin mediated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 378 aa     Download sequence    Send to blast
MDYQDWNFEK NYKLSNSRRS TRAQDELVEL LWRDGEVVLQ SQTNREQTQA QTEKYDHHQE  60
TLRSNNFLED QETVSWIQYP PDEDPFIAAD FSSHFFSTAN PLEKPATEIF KHDAGPDPPD  120
QVMPPPKFWL MDSSSGVKQL GKEQYSVVTV GPSHCGSNQP HNNLDVSMSH DRNKTVVERL  180
YHNAGSSSGG SSGCSFGKNI KEIASGQSIT TNRKRKIIMD TDESLSQSDA ILNKSNQRSG  240
STRRSRAAEV HNLSERRRRD RINERMKTLQ ELIPHCTKTD KASILDEAID YMKSLRLQVQ  300
VTWMGSRMAG AAVAPMVFPG VQPQMQSPVQ FPRFPVMDPS AIQNNPGLVC GNPVQTKFSP  360
SGLIDAWAYS HTCRPRLR
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1254259ERRRRD
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00606ChIP-seqTransfer from AT2G43010Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_09028.1_g00002.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009142152.10.0PREDICTED: transcription factor PIF4 isoform X1
SwissprotQ8W2F31e-162PIF4_ARATH; Transcription factor PIF4
TrEMBLA0A078GWP90.0A0A078GWP9_BRANA; BnaC01g40470D protein
STRINGBra037742.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM34682561
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G43010.11e-160phytochrome 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
    [PMID:20219281]
  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.
    [PMID:23838958]
  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
    [PMID:23933882]
  4. Wigge PA
    Ambient temperature signalling in plants.
    Curr. Opin. Plant Biol., 2013. 16(5): p. 661-6
    [PMID:24021869]
  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
    [PMID:24078666]
  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
    [PMID:24500967]
  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
    [PMID:24505057]
  8. Oh E, et al.
    Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl.
    Elife, 2015.
    [PMID:24867218]
  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
    [PMID:25071218]
  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
    [PMID:25256571]
  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
    [PMID:25281688]
  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
    [PMID:25533339]
  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
    [PMID:25548158]
  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
    [PMID:25552472]
  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
    [PMID:25600997]
  16. Filo J, et al.
    Gibberellin driven growth in elf3 mutants requires PIF4 and PIF5.
    Plant Signal Behav, 2015. 10(3): p. e992707
    [PMID:25738547]
  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
    [PMID:26108788]
  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
    [PMID:26193333]
  19. Geilen K,Böhmer M
    Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana.
    Sci Rep, 2015. 5: p. 13369
    [PMID:26293691]
  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
    [PMID:26466761]
  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
    [PMID:26566918]
  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
    [PMID:26601822]
  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
    [PMID:26829165]
  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
    [PMID:27105120]
  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
    [PMID:27117775]
  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
    [PMID:27249348]
  27. Quint M, et al.
    Molecular and genetic control of plant thermomorphogenesis.
    Nat Plants, 2016. 2: p. 15190
    [PMID:27250752]
  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
    [PMID:27282989]
  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
    [PMID:27432188]
  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
    [PMID:27458465]
  31. Press MO,Lanctot A,Queitsch C
    PIF4 and ELF3 Act Independently in Arabidopsis thaliana Thermoresponsive Flowering.
    PLoS ONE, 2016. 11(8): p. e0161791
    [PMID:27564448]
  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
    [PMID:27716807]
  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
    [PMID:27827441]
  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
    [PMID:27890635]
  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
    [PMID:27966533]
  36. Hayes S, et al.
    UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis.
    Curr. Biol., 2017. 27(1): p. 120-127
    [PMID:27989670]
  37. Gangappa SN,Berriri S,Kumar SV
    PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis.
    Curr. Biol., 2017. 27(2): p. 243-249
    [PMID:28041792]
  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
    [PMID:28076780]
  39. Zentella R, et al.
    The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA.
    Nat. Chem. Biol., 2017. 13(5): p. 479-485
    [PMID:28244988]
  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
    [PMID:28254761]
  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
    [PMID:28396418]
  42. Kim JH,Lee HJ,Park CM
    HOS1 acts as a key modulator of hypocotyl photomorphogenesis.
    Plant Signal Behav, 2017. 12(5): p. e1315497
    [PMID:28426369]
  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
    [PMID:28440582]
  44. Ritter A, et al.
    The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis.
    Nat Commun, 2017. 8: p. 15235
    [PMID:28492275]
  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
    [PMID:28619072]
  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
    [PMID:28711729]
  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
    [PMID:28791042]
  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.
    [PMID:28826468]
  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
    [PMID:29032592]
  50. Ibañez C, et al.
    Brassinosteroids Dominate Hormonal Regulation of Plant Thermomorphogenesis via BZR1.
    Curr. Biol., 2018. 28(2): p. 303-310.e3
    [PMID:29337075]
  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
    [PMID:29522510]
  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
    [PMID:29541883]
  53. Tasset C, et al.
    POWERDRESS-mediated histone deacetylation is essential for thermomorphogenesis in Arabidopsis thaliana.
    PLoS Genet., 2018. 14(3): p. e1007280
    [PMID:29547672]
  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
    [PMID:29729397]
  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
    [PMID:30352855]
  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
    [PMID:30635559]