PlantTFDB
Plant Transcription Factor Database
v5.0
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_00197.1_g00013.1
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: 507aa    MW: 55227.5 Da    PI: 5.6784
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00197.1_g00013.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH52.68.5e-17328374455
                              HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                      HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                               hn  ErrRRdriN+++  L+el+P++      K++Ka++L +A+eY+ksLq
  Rsa1.0_00197.1_g00013.1 328 VHNLSERRRRDRINEKMRALQELIPNC-----NKVDKASMLDEAIEYLKSLQ 374
                              6*************************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000836.37E-18320378No hitNo description
Gene3DG3DSA:4.10.280.105.7E-21321382IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474595.76E-21321387IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.584324373IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000103.5E-14328374IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003533.3E-18330379IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009704Biological Processde-etiolation
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0010017Biological Processred or far-red light signaling pathway
GO:0031539Biological Processpositive regulation of anthocyanin metabolic process
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0042802Molecular Functionidentical protein binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 507 aa     Download sequence    Send to blast
MPLFELFRLT NTKFESAQDN NPSPPVDEVV ELVWENGQIS TQTQSNRSRN IPPPPPPGQE  60
SSSRAREIVN GSKTTMVEEI PMSVPSLMTG LSQDDDLVPW LNPHHQSLDG YCSDFLHDVS  120
PVAVDEQESE DAFPLFQRRD NGNESAPPAD STSLQFNGFQ SHSLYGSGRA RDPPVSQPAK  180
PDPSTSNKPG LINFSHFLRT AASAKTNDSP PGSKEKSPQC PPNVFQTRVL GAKEVLNESV  240
MPKDNQKACL VSEDSNRKDQ ESEKAVVCSS VGSGNSPSES PLKRKHPPDV QDIECHSEDV  300
EGESGDGRKE AAPSRTGMGS KRSRSAEVHN LSERRRRDRI NEKMRALQEL IPNCNKVDKA  360
SMLDEAIEYL KSLQLQVQFM SMASGYYMPP VMFPPGMGHH YQAAAMAMGM GMPYAMGLPD  420
INRGGPSVNN APQFQFPGMQ QPVTMALPRV SAGGLFGSST VEMNKSGDGS TRDLPGTNDQ  480
TTTKSNNGLK PIKRKQASPP DQFCGSS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1332337ERRRRD
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00081ChIP-seqTransfer from AT1G09530Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00197.1_g00013.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018443444.10.0PREDICTED: transcription factor PIF3-like isoform X1
SwissprotO805360.0PIF3_ARATH; Transcription factor PIF3
TrEMBLA0A397Z2330.0A0A397Z233_BRACM; Uncharacterized protein
STRINGBra020017.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM76652739
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G09530.20.0phytochrome interacting factor 3
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. 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
    [PMID:24599595]
  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
    [PMID:24769533]
  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
    [PMID:24916071]
  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
    [PMID:24920333]
  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
    [PMID:24982146]
  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
    [PMID:25281666]
  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
    [PMID:25501334]
  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
    [PMID:25711503]
  10. 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]
  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
    [PMID:26466761]
  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
    [PMID:26704640]
  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
    [PMID:26949024]
  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
    [PMID:27071129]
  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
    [PMID:27105120]
  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
    [PMID:27143545]
  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
    [PMID:27262126]
  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
    [PMID:27282989]
  19. Jeong AR, et al.
    New Constitutively Active Phytochromes Exhibit Light-Independent Signaling Activity.
    Plant Physiol., 2016. 171(4): p. 2826-40
    [PMID:27325667]
  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
    [PMID:27458465]
  21. Yu Y,Huang R
    Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 57
    [PMID:28174592]
  22. 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]
  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
    [PMID:28292892]
  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
    [PMID:28316114]
  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
    [PMID:28440582]
  26. Ni W, et al.
    PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3.
    Nat Commun, 2017. 8: p. 15236
    [PMID:28492231]
  27. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
    [PMID:28687557]
  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
    [PMID:28711729]
  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
    [PMID:28736168]
  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
    [PMID:28739888]
  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
    [PMID:28911120]
  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
    [PMID:29114016]
  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
    [PMID:29143279]
  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
    [PMID:29167353]
  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
    [PMID:29199270]
  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
    [PMID:29244171]