PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Rsa1.0_00166.1_g00023.1

Common Name

RsLFY1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

LFY

Protein Properties

Length: 415aa MW: 46239.9 Da PI: 7.021

Description

LFY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00166.1_g00023.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FLO_LFY	616.5	4.9e-188	1	391	1	386
FLO_LFY 1 mdpeafsaslfkwdpraaaaapparlleeaa..vseapleaaaaaaarklreleelfkayGvryltvakiaelGftvstLvdmkde 84 mdpe f++ lf+w+p a+++++++ + ++++p++ ++aa ++l +le lf yGvr++t+akiaelGft+stLv+mkde Rsa1.0_00166.1_g00023.1 1 MDPEGFTSGLFRWNPTRAMVQQQQQQPPPVPppQQQPPATPQTAAFGMRLGGLEGLFGPYGVRFYTAAKIAELGFTASTLVGMKDE 86 9***********7666544333222222200233334455666666677******************************* PP FLO_LFY 85 elddlmkslseifrldllvGeryGikaavraerrrlee..eeaekkrrkll.....sedeetaldalsqeglseepvqeeke.aag 162 el+d+m+sls+ifr++llvGeryG+kaavraerrrl+e ee+ ++rr+ll + +++aldalsqeglse+pv++ ++ +a+ Rsa1.0_00166.1_g00023.1 87 ELEDMMNSLSHIFRWELLVGERYGVKAAVRAERRRLQEeeEEEYSRRRHLLlsaagDSGTHHALDALSQEGLSEDPVHQLEHtDAA 172 ********************************99443445677777768744344556***********995551444 PP FLO_LFY 163 sggeglgeaelvaaeekkseeekkkaskkkqkrkkkkelkseededeeeeededeegsgedge...erqrehPfivtepgevargk 245 +++ g +e+ +++ kk + +++++k+ ++++++d+ +e e+d+d++g+g +g erqrehPfivtepgevargk Rsa1.0_00166.1_g00023.1 173 GNNAVGGYWEAGQTK------MKKPQ--QRRRKKQVVTSVETDDDMNEGEDDDDGNGNGGGGVlgiERQREHPFIVTEPGEVARGK 250 444444555544333......22222..23333444333333333333344444444333333445**************** PP FLO_LFY 246 knGLDYLfdLyeqCrefLlqvqkiakerGekcPtkvtnqvfryakkagasyinkPkmrhYvhCYalhcLdeeasnalrrafkerge 331 knGLDYLf+LyeqCrefL+qvq+iak+rGekcPtkvtnqvfryakk+gasyinkPkmrhYvhCYalhcLdeeasnalrrafkerge Rsa1.0_00166.1_g00023.1 251 KNGLDYLFHLYEQCREFLVQVQTIAKDRGEKCPTKVTNQVFRYAKKSGASYINKPKMRHYVHCYALHCLDEEASNALRRAFKERGE 336 ********************************************************************************** PP FLO_LFY 332 nvGawrqacykplvaiaarqgwdidavfnahprLsiWYvPtkLrqLChlerskas 386 nvG+wrqacykplv+ia r+gwdidavfnahprLsiWYvPtkLrqLChler++a+ Rsa1.0_00166.1_g00023.1 337 NVGSWRQACYKPLVDIACRHGWDIDAVFNAHPRLSIWYVPTKLRQLCHLERNNAV 391 *************************************************9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF01698	5.8E-197	1	390	IPR002910	Floricaula/leafy protein

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010077	Biological Process	maintenance of inflorescence meristem identity
GO:0010582	Biological Process	floral meristem determinacy
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0031490	Molecular Function	chromatin DNA binding
GO:0042803	Molecular Function	protein homodimerization activity
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0043621	Molecular Function	protein self-association

Sequence ? help Back to Top
Protein Sequence Length: 415 aa Download sequence Send to blast
MDPEGFTSGL FRWNPTRAMV QQQQQQPPPV PPPQQQPPAT PQTAAFGMRL GGLEGLFGPY 60 GVRFYTAAKI AELGFTASTL VGMKDEELED MMNSLSHIFR WELLVGERYG VKAAVRAERR 120 RLQEEEEEEY SRRRHLLLSA AGDSGTHHAL DALSQEGLSE DPVHQLEHTD AAGNNAVGGY 180 WEAGQTKMKK PQQRRRKKQV VTSVETDDDM NEGEDDDDGN GNGGGGVLGI ERQREHPFIV 240 TEPGEVARGK KNGLDYLFHL YEQCREFLVQ VQTIAKDRGE KCPTKVTNQV FRYAKKSGAS 300 YINKPKMRHY VHCYALHCLD EEASNALRRA FKERGENVGS WRQACYKPLV DIACRHGWDI 360 DAVFNAHPRL SIWYVPTKLR QLCHLERNNA VAAASALVGN GISCTGSSAS GGFGV

Sequence ? help Back to Top

Protein Sequence Length: 415 aa Download sequence Send to blast

MDPEGFTSGL FRWNPTRAMV QQQQQQPPPV PPPQQQPPAT PQTAAFGMRL GGLEGLFGPY  60
GVRFYTAAKI AELGFTASTL VGMKDEELED MMNSLSHIFR WELLVGERYG VKAAVRAERR  120
RLQEEEEEEY SRRRHLLLSA AGDSGTHHAL DALSQEGLSE DPVHQLEHTD AAGNNAVGGY  180
WEAGQTKMKK PQQRRRKKQV VTSVETDDDM NEGEDDDDGN GNGGGGVLGI ERQREHPFIV  240
TEPGEVARGK KNGLDYLFHL YEQCREFLVQ VQTIAKDRGE KCPTKVTNQV FRYAKKSGAS  300
YINKPKMRHY VHCYALHCLD EEASNALRRA FKERGENVGS WRQACYKPLV DIACRHGWDI  360
DAVFNAHPRL SIWYVPTKLR QLCHLERNNA VAAASALVGN GISCTGSSAS GGFGV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2vy1_A	1e-126	228	411	1	183	PROTEIN LEAFY
2vy2_A	1e-126	228	411	1	183	PROTEIN LEAFY
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	190	198	PQQRRRKKQ

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that promotes early floral meristem identity in synergy with APETALA1. Is required subsequently for the transition of an inflorescence meristem into a floral meristem, by an immediate upstream regulation of the ABC classes of floral homeotic genes. Activates directly APETALA1, CAULIFLOWER and AGAMOUS, and indirectly APETALA3 and PISTILLATA with the cooperation of UFO. {ECO:0000269\|PubMed:8565821, ECO:0000269\|PubMed:9783581, ECO:0000269\|Ref.6}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00095	SELEX	Transfer from AT5G61850	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00166.1_g00023.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Positively regulated by CAULIFLOWER and APETALA1. Down-regulated by TFL1.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB449248	0.0	AB449248.1 Raphanus sativus RsLFY1 mRNA for leafy-like protein, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018437915.1	0.0	PREDICTED: protein LEAFY-like
Swissprot	Q00958	0.0	LFY_ARATH; Protein LEAFY
TrEMBL	B7XD69	0.0	B7XD69_RAPSA; Leafy-like protein
STRING	Bra029305.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7907	28	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G61850.1	0.0	floral meristem identity control protein LEAFY (LFY)

Publications ? help Back to Top
Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula). PLoS ONE, 2012. 7(8): p. e42839 [PMID:22916167] Yang C, et al. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr. Biol., 2013. 23(14): p. 1324-9 [PMID:23810531] Lei HJ, et al. Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry. Gene, 2013. 531(2): p. 158-67 [PMID:24055423] Yu Y, et al. MlWRKY12, a novel Miscanthus transcription factor, participates in pith secondary cell wall formation and promotes flowering. Plant Sci., 2013. 212: p. 1-9 [PMID:24094048] Niwa M,Endo M,Araki T Florigen is involved in axillary bud development at multiple stages in Arabidopsis. Plant Signal Behav, 2013. 8(11): p. e27167 [PMID:24305631] Fu J, et al. Photoperiodic control of FT-like gene ClFT initiates flowering in Chrysanthemum lavandulifolium. Plant Physiol. Biochem., 2014. 74: p. 230-8 [PMID:24316581] Risseeuw E, et al. An activated form of UFO alters leaf development and produces ectopic floral and inflorescence meristems. PLoS ONE, 2013. 8(12): p. e83807 [PMID:24376756] Yang Z, et al. Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines. Mol. Biol. Rep., 2014. 41(2): p. 1117-25 [PMID:24381105] Chandler JW,Werr W Arabidopsis floral phytomer development: auxin response relative to biphasic modes of organ initiation. J. Exp. Bot., 2014. 65(12): p. 3097-110 [PMID:24744428] Yamaguchi N, et al. Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science, 2014. 344(6184): p. 638-41 [PMID:24812402] Leal Valentim F, et al. A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network. PLoS ONE, 2015. 10(2): p. e0116973 [PMID:25719734] Chen Z, et al. Overexpression of AtAP1M3 regulates flowering time and floral development in Arabidopsis and effects key flowering-related genes in poplar. Transgenic Res., 2015. 24(4): p. 705-15 [PMID:25820621] Müller-Xing R,Schubert D,Goodrich J Non-inductive conditions expose the cryptic bract of flower phytomeres in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(4): p. e1010868 [PMID:25924005] Ma X, et al. CYCLIN-DEPENDENT KINASE G2 regulates salinity stress response and salt mediated flowering in Arabidopsis thaliana. Plant Mol. Biol., 2015. 88(3): p. 287-99 [PMID:25948280] Wang C,Dehesh K From retrograde signaling to flowering time. Plant Signal Behav, 2015. 10(6): p. e1022012 [PMID:26098376] Kusters E,Della Pina S,Castel R,Souer E,Koes R Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures. Development, 2015. 142(16): p. 2822-31 [PMID:26220938] Andrés F, et al. Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE. Plant Physiol., 2015. 169(3): p. 2187-99 [PMID:26417007] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Yu Y, et al. WRKY71 accelerates flowering via the direct activation of FLOWERING LOCUS T and LEAFY in Arabidopsis thaliana. Plant J., 2016. 85(1): p. 96-106 [PMID:26643131] Fu X, et al. CHD3 chromatin-remodeling factor PICKLE regulates floral transition partially via modulating LEAFY expression at the chromatin level in Arabidopsis. Sci China Life Sci, 2016. 59(5): p. 516-28 [PMID:27056257] Yamaguchi N,Wu MF,Winter CM,Wagner D LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. Plants (Basel), 2014. 3(2): p. 251-65 [PMID:27135503] Xu C,Yu Y,Zhang Y,Li Y,Wei S Gibberellins are involved in effect of near-null magnetic field on Arabidopsis flowering. Bioelectromagnetics, 2017. 38(1): p. 1-10 [PMID:27598690] Tang M, et al. An ortholog of LEAFY in Jatropha curcas regulates flowering time and floral organ development. Sci Rep, 2016. 6: p. 37306 [PMID:27869146] Wendell M, et al. Thermoperiodic Control of Floral Induction Involves Modulation of the Diurnal FLOWERING LOCUS T Expression Pattern. Plant Cell Physiol., 2017. 58(3): p. 466-477 [PMID:28028164] Monniaux M, et al. Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta. New Phytol., 2017. 216(2): p. 549-561 [PMID:28098947] Guo WY,Cui YM,Wang TT,Yu DY,Huang F Functional analysis of flower development related gene GsLFY from Glycine soja. Yi Chuan, 2017. 39(1): p. 56-65 [PMID:28115306] Dhakate P,Tyagi S,Singh A,Singh A Functional characterization of a novel Brassica LEAFY homolog from Indian mustard: Expression pattern and gain-of-function studies. Plant Sci., 2017. 258: p. 29-44 [PMID:28330561] Yang T,Du MF,Guo YH,Liu X Two LEAFY homologs ILFY1 and ILFY2 control reproductive and vegetative developments in Isoetes L. Sci Rep, 2017. 7(1): p. 225 [PMID:28331204] Goslin K, et al. Transcription Factor Interplay between LEAFY and APETALA1/CAULIFLOWER during Floral Initiation. Plant Physiol., 2017. 174(2): p. 1097-1109 [PMID:28385730] Serrano-Mislata A, et al. Regulatory interplay between LEAFY, APETALA1/CAULIFLOWER and TERMINAL FLOWER1: New insights into an old relationship. Plant Signal Behav, 2017. 12(10): p. e1370164 [PMID:28873010] Zhang GZ, et al. Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis. Plant Cell Rep., 2017. 36(12): p. 1995-2006 [PMID:29027578] Zhao W, et al. CsLFY is required for shoot meristem maintenance via interaction with WUSCHEL in cucumber (Cucumis sativus). New Phytol., 2018. 218(1): p. 344-356 [PMID:29274285] Dotto M,Gómez MS,Soto MS,Casati P UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana. Plant Cell Environ., 2018. 41(6): p. 1394-1406 [PMID:29447428] 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]