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 676723124
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family bHLH
Protein Properties Length: 642aa    MW: 70107.9 Da    PI: 8.0243
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676723124genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH51.81.4e-16449495455
                HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
        HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                 hn  ErrRRdriN+++  L+el+P++      K++Ka++L +A+eY+ksLq
  676723124 449 VHNLSERRRRDRINEKMRALQELIPNC-----NKVDKASMLDEAIEYLKSLQ 495
                5*************************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000831.33E-17441499No hitNo description
SuperFamilySSF474591.1E-19442510IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.584445494IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000104.7E-14449495IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.108.3E-20449508IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.7E-18451500IPR011598Myc-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: 642 aa     Download sequence    Send to blast
MQRTLALPCN RDRRCVQRVL ATIWSPSPSC ASGLSPSLSA PPTFSPLLPL CSLQLTLCIW  60
IDVLLMLRGS RFLSSPPTLI PSTPFSQDQV SVRDSVCQPN TMPLFELFRL TNAKLDSAQD  120
KTPSPPVDEV VELVWENGQI STQSQSSRSR NIPLSQSIHQ GSFSRAREIG NGSKTTMVDE  180
IPMSVPSLMT GLSQDDDLVP WLNHHQSLDG YCSDFLHDVS PVTANEQESD MAVNQNVFPL  240
IQRRNNGNES APAASSSQFN GFQSRSLYGS DRARDPVSQP AKPDRFTQTQ EPLVNSNKPG  300
LINFSHFLRP ATLAKTNNPH GSKEKSPQSP PNVFQTRVLK AKNSEDKVLN ESVASAMPKD  360
NQKACMISED SGRKDQESEK AVVCSSVGSG NSLDGPSESP SLSLKRKHSD VQDIDCHSED  420
VEGESGDGRK EAAPSRTGMG SKRSRSAEVH NLSERRRRDR INEKMRALQE LIPNCNKVDK  480
ASMLDEAIEY LKSLQLQVQR NVTLTNNLNT IIIQIMSMAS GYYMPPVMFP PGMGHYQAAA  540
MAMGMGVPYA MGLPDMSRGG PSVNHGPQFQ VPGMQQPVAM AIPRVSGGGF FTGSSTMEMK  600
KSDDGSTRDL SGTKDQTTTR SNNSLKPTKR KQASSDQFCG SS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1453458ERRRRD
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
PlantRegMap676723124
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1001660.0AF100166.1 Arabidopsis thaliana phytochrome interacting factor 3 (PIF3) mRNA, complete cds.
GenBankAK1172550.0AK117255.1 Arabidopsis thaliana At1g09530 mRNA for putative transcription factor BHLH8, complete cds, clone: RAFL16-81-C24.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006417565.10.0transcription factor PIF3
SwissprotO805360.0PIF3_ARATH; Transcription factor PIF3
TrEMBLA0A1J3CK880.0A0A1J3CK88_NOCCA; Transcription factor PIF3 (Fragment)
STRINGXP_006417565.10.0(Eutrema salsugineum)
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]