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

AT3G09600.1

Common Name

F11F8.19, LCL5, RVE8

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

MYB_related

Protein Properties

Length: 298aa MW: 32801.1 Da PI: 9.7919

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G09600.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	44.7	3.2e-14	43	87	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r +WT+eE++++++a +++ + Wk+I +g +t q++s+ qky AT3G09600.1 43 RESWTEEEHDKFLEALQLFDRD-WKKIEDFVG-SKTVIQIRSHAQKY 87 789***************77.*****.***********9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	1.27E-17	37	93	IPR009057	Homeodomain-like
PROSITE profile	PS51294	16.291	38	92	IPR017930	Myb domain
Gene3D	G3DSA:1.10.10.60	2.7E-7	41	93	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	8.9E-19	41	90	IPR006447	Myb domain, plants
SMART	SM00717	1.1E-11	42	90	IPR001005	SANT/Myb domain
Pfam	PF00249	7.1E-12	43	87	IPR001005	SANT/Myb domain
CDD	cd00167	2.29E-9	45	88	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009651	Biological Process	response to salt stress
GO:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0009737	Biological Process	response to abscisic acid
GO:0009739	Biological Process	response to gibberellin
GO:0009751	Biological Process	response to salicylic acid
GO:0009753	Biological Process	response to jasmonic acid
GO:0032922	Biological Process	circadian regulation of gene expression
GO:0043966	Biological Process	histone H3 acetylation
GO:0046686	Biological Process	response to cadmium ion
GO:0048573	Biological Process	photoperiodism, flowering
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 298 aa Download sequence Send to blast
MSSSPSRNPT NAEAPPPPPT STDAVAEGSS KKVRKPYTIT KSRESWTEEE HDKFLEALQL 60 FDRDWKKIED FVGSKTVIQI RSHAQKYFLK VQKNGTLAHV PPPRPKRKAA HPYPQKASKN 120 AQMPLQVSTS FTTTRNGDMP GYASWDDASM LLNRVISPQH ELATLRGAEA DIGSKGLLNV 180 SSPSTSGMGS SSRTVSGSEI VRKAKQPPVL HGVPDFAEVY NFIGSVFDPE TRGHVEKLKE 240 MDPINFETVL LLMRNLTVNL SNPDLESTRK VLLSYDNVTT ELPSVVSLVK NSTSDKSA

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	20268704	0.0
Genevisible	258723_at	1e-176
Expression Atlas	AT3G09600	-
AtGenExpress	AT3G09600	-
ATTED-II	AT3G09600	-

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator of evening element (EE)-containing clock-controlled genes. Forms a negative feedback loop with APRR5. Regulates the pattern of histone H3 acetylation of the TOC1 promoter. {ECO:0000269\|PubMed:21205033, ECO:0000269\|PubMed:21474993, ECO:0000269\|PubMed:21483796, ECO:0000269\|PubMed:23638299}.

Function -- GeneRIF ? help Back to Top
RVE8/LCL5 expression shows a rhythmic oscillation that is controlled by the circadian clock. Alteration of RVE8/LCL5 expression affects the photoperiodic regulation of flowering time. [PMID: 21205033] RVE8/LCL5 binds to the promoter of key clock component TOC1 (Timing of CAB expression 1) and regulates its circadian expression. [PMID: 21474993] RVE8 is a new component of the plant circadian oscillator that takes part in a novel transcriptional feedback loop. [REVEILLE 8] [RVE8]. [PMID: 21483796] RVE8 affects Global Circadian-regulated transcription. Long-period mutant in Arabidopsis, rve8-1, has a global alteration in phase of all clock-controlled genes. [RVE8] [PMID: 23185460] This study defines a switch in the regulatory activity of RVE8-LNK interaction, from a synergic coactivating role of evening-expressed clock genes to a repressive antagonistic function modulating anthocyanin biosynthesis around midday. [PMID: 25848001] REVEILLE clock genes rve3 4 5 6 8 mutants are much larger than wild-type plants, with both increased leaf area and biomass. [PMID: 28254761]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00338	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G09600.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian-regulation. Peak of expression in the afternoon. Down-regulated by cold. {ECO:0000269\|PubMed:21205033, ECO:0000269\|PubMed:22902701, ECO:0000269\|PubMed:23638299}.

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

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	abscisic acid, auxin, ethylene, gibberellin, jasmonic acid, salicylic acid

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Delay and reduction in levels of evening-phased clock gene transcripts and long circadian period. {ECO:0000269\|PubMed:21483796, ECO:0000269\|PubMed:23638299}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G09600

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY091106	0.0	AY091106.1 Arabidopsis thaliana unknown protein (At3g09600) mRNA, complete cds.
GenBank	AY122969	0.0	AY122969.1 Arabidopsis thaliana unknown protein (At3g09600) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001327348.1	0.0	Homeodomain-like superfamily protein
Refseq	NP_187571.2	0.0	Homeodomain-like superfamily protein
Swissprot	Q8RWU3	0.0	RVE8_ARATH; Protein REVEILLE 8
TrEMBL	D7L8A7	0.0	D7L8A7_ARALL; Myb family transcription factor
STRING	AT3G09600.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9303	26	33
Representative plant	OGRP928	15	58

Link Out ? help Back to Top
Phytozome	AT3G09600.1
Entrez Gene	820117
iHOP	AT3G09600
wikigenes	AT3G09600

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Dal Bosco C, et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem., 2004. 279(2): p. 1060-9 [PMID:14576160] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Rizhsky L,Davletova S,Liang H,Mittler R The zinc finger protein Zat12 is required for cytosolic ascorbate peroxidase 1 expression during oxidative stress in Arabidopsis. J. Biol. Chem., 2004. 279(12): p. 11736-43 [PMID:14722088] S ABA activates ADPR cyclase and cADPR induces a subset of ABA-responsive genes in Arabidopsis. Plant J., 2004. 38(3): p. 381-95 [PMID:15086800] Yanhui C, et al. The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol. Biol., 2006. 60(1): p. 107-24 [PMID:16463103] Gutierrez L, et al. Identification of new gene expression regulators specifically expressed during plant seed maturation. J. Exp. Bot., 2006. 57(9): p. 1919-32 [PMID:16606634] Manfield IW, et al. Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res., 2006. 34(Web Server issue): p. W504-9 [PMID:16845059] Lee DJ, et al. Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response. Mol. Genet. Genomics, 2007. 277(2): p. 115-37 [PMID:17061125] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Agudelo-Romero P, et al. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol. J., 2008. 5: p. 92 [PMID:18684336] Rawat R, et al. REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(39): p. 16883-8 [PMID:19805390] Farinas B,Mas P Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. Plant J., 2011. 66(2): p. 318-29 [PMID:21205033] Farinas B,Mas P Histone acetylation and the circadian clock: a role for the MYB transcription factor RVE8/LCL5. Plant Signal Behav, 2011. 6(4): p. 541-3 [PMID:21474993] Rawat R, et al. REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genet., 2011. 7(3): p. e1001350 [PMID:21483796] James AB,Syed NH,Brown JW,Nimmo HG Thermoplasticity in the plant circadian clock: how plants tell the time-perature. Plant Signal Behav, 2012. 7(10): p. 1219-23 [PMID:22902701] Hsu PY,Harmer SL Circadian phase has profound effects on differential expression analysis. PLoS ONE, 2012. 7(11): p. e49853 [PMID:23185460] Hsu PY,Devisetty UK,Harmer SL Accurate timekeeping is controlled by a cycling activator in Arabidopsis. Elife, 2013. 2: p. e00473 [PMID:23638299] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Xie Q, et al. LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator. Plant Cell, 2014. 26(7): p. 2843-57 [PMID:25012192] Fogelmark K,Troein C Rethinking transcriptional activation in the Arabidopsis circadian clock. PLoS Comput. Biol., 2014. 10(7): p. e1003705 [PMID:25033214] P Time-dependent sequestration of RVE8 by LNK proteins shapes the diurnal oscillation of anthocyanin biosynthesis. Proc. Natl. Acad. Sci. U.S.A., 2015. 112(16): p. 5249-53 [PMID:25848001] Xing H, et al. LNK1 and LNK2 recruitment to the evening element require morning expressed circadian related MYB-like transcription factors. Plant Signal Behav, 2015. 10(3): p. e1010888 [PMID:25848708] 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]