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

Carubv10028602m

Common Name

CARUB_v10028602mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

LFY

Protein Properties

Length: 423aa MW: 46624.3 Da PI: 7.1121

Description

LFY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10028602m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FLO_LFY	625.7	8e-191	1	391	1	386
FLO_LFY 1 mdpeafsaslfkwdpraaaaapparlleeaavseapleaaaaaaarklreleelfkayGvryltvakiaelGftvstLvdmkdeelddlmksls 94 mdpe f++ lf+w+p a++++p + + + ++++p++ ++aa ++l +le lf ayG+r++t+akiaelGft+stLv+mkdeel+++m+sls Carubv10028602m 1 MDPEGFTSGLFRWNPMRAMVQAPPPVPP-SPQQQQPVTPQTAAFGMRLGGLEGLFGAYGIRFYTAAKIAELGFTASTLVGMKDEELEEMMNSLS 93 9***********77776665555544.44556666777888888899***************************************** PP FLO_LFY 95 eifrldllvGeryGikaavraerrrlee..eeaekkrrkll.....sedeetaldalsqeglseepvqeekeaagsggeglgeaelvaaeekks 181 +ifr++llvGeryGikaavraerrrl+e ee++++rr+ll + +++aldalsqeglseepvq++ ++ ++g++g g ++ a ++k Carubv10028602m 94 HIFRWELLVGERYGIKAAVRAERRRLQEeeEEESSRRRHLLlsaagDSGTHHALDALSQEGLSEEPVQQQDQTDAAGNNGGGGSGYWEAGQAK- 186 **********************99544456778887778844344556************9777666666665666666655322. PP FLO_LFY 182 eeekkkaskkkqkrkkkkelkseededeeeeededeeg.....sgedgeerqrehPfivtepgevargkknGLDYLfdLyeqCrefLlqvqkia 270 kk++ + +++ kk ++ e+d+d +e ed+d+++ +g g+erqrehPfivtepgevargkknGLDYLf+LyeqCrefLlqvq+ia Carubv10028602m 187 --MKKQQ-Q-RRR-KKPMVASVETDDDGNEGEDDDGMDngnggGGGMGTERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCREFLLQVQTIA 275 ..22222.2.222.22222233334444443333333312222556677***************************************** PP FLO_LFY 271 kerGekcPtkvtnqvfryakkagasyinkPkmrhYvhCYalhcLdeeasnalrrafkergenvGawrqacykplvaiaarqgwdidavfnahpr 364 k+rGekcPtkvtnqvfryakk+gasyinkPkmrhYvhCYalhcLde+asnalrr+fkergenvG+wrqacykplv+ia r+gwdidavfnahpr Carubv10028602m 276 KDRGEKCPTKVTNQVFRYAKKSGASYINKPKMRHYVHCYALHCLDEDASNALRRSFKERGENVGSWRQACYKPLVNIACRHGWDIDAVFNAHPR 369 ****************************************************************************************** PP FLO_LFY 365 LsiWYvPtkLrqLChlerskas 386 LsiWYvPtkLrqLChler++a+ Carubv10028602m 370 LSIWYVPTKLRQLCHLERNNAV 391 ****************9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF01698	1.1E-200	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: 423 aa Download sequence Send to blast
MDPEGFTSGL FRWNPMRAMV QAPPPVPPSP QQQQPVTPQT AAFGMRLGGL EGLFGAYGIR 60 FYTAAKIAEL GFTASTLVGM KDEELEEMMN SLSHIFRWEL LVGERYGIKA AVRAERRRLQ 120 EEEEEESSRR RHLLLSAAGD SGTHHALDAL SQEGLSEEPV QQQDQTDAAG NNGGGGSGYW 180 EAGQAKMKKQ QQRRRKKPMV ASVETDDDGN EGEDDDGMDN GNGGGGGMGT ERQREHPFIV 240 TEPGEVARGK KNGLDYLFHL YEQCREFLLQ VQTIAKDRGE KCPTKVTNQV FRYAKKSGAS 300 YINKPKMRHY VHCYALHCLD EDASNALRRS FKERGENVGS WRQACYKPLV NIACRHGWDI 360 DAVFNAHPRL SIWYVPTKLR QLCHLERNNA VAAAAALVGG GISCTGSSTS GRGGCGGDEL 420 RF*

Sequence ? help Back to Top

Protein Sequence Length: 423 aa Download sequence Send to blast

MDPEGFTSGL FRWNPMRAMV QAPPPVPPSP QQQQPVTPQT AAFGMRLGGL EGLFGAYGIR  60
FYTAAKIAEL GFTASTLVGM KDEELEEMMN SLSHIFRWEL LVGERYGIKA AVRAERRRLQ  120
EEEEEESSRR RHLLLSAAGD SGTHHALDAL SQEGLSEEPV QQQDQTDAAG NNGGGGSGYW  180
EAGQAKMKKQ QQRRRKKPMV ASVETDDDGN EGEDDDGMDN GNGGGGGMGT ERQREHPFIV  240
TEPGEVARGK KNGLDYLFHL YEQCREFLLQ VQTIAKDRGE KCPTKVTNQV FRYAKKSGAS  300
YINKPKMRHY VHCYALHCLD EDASNALRRS FKERGENVGS WRQACYKPLV NIACRHGWDI  360
DAVFNAHPRL SIWYVPTKLR QLCHLERNNA VAAAAALVGG GISCTGSSTS GRGGCGGDEL  420
RF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2vy1_A	1e-136	228	422	1	194	PROTEIN LEAFY
2vy2_A	1e-136	228	422	1	194	PROTEIN LEAFY
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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	Carubv10028602m

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	DQ471932	0.0	DQ471932.1 Brassica juncea cultivar Varuna LEAFY transcription factor mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006282313.1	0.0	protein LEAFY isoform X2
Swissprot	Q00958	0.0	LFY_ARATH; Protein LEAFY
TrEMBL	R0F1N9	0.0	R0F1N9_9BRAS; Uncharacterized protein
STRING	XP_006282313.1	0.0	(Capsella rubella)

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)

Link Out ? help Back to Top
Phytozome	Carubv10028602m
Entrez Gene	17876585

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]