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

AT5G02840.1

Common Name

F9G14.150, LCL1, RVE4

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: 293aa MW: 32207.1 Da PI: 5.0924

Description

LHY/CCA1-like 1

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G02840.1	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	39.1	1.7e-12	48	92	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r +WT+ E++++++a +++ + Wk+I +g +t q++s+ qky AT5G02840.1 48 RESWTEGEHDKFLEALQLFDRD-WKKIEDFVG-SKTVIQIRSHAQKY 92 789***************77.*****.***********9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	2.02E-16	42	98	IPR009057	Homeodomain-like
PROSITE profile	PS51294	14.942	43	97	IPR017930	Myb domain
Gene3D	G3DSA:1.10.10.60	2.8E-6	46	98	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	2.3E-18	46	95	IPR006447	Myb domain, plants
SMART	SM00717	7.6E-10	47	95	IPR001005	SANT/Myb domain
Pfam	PF00249	3.1E-10	48	92	IPR001005	SANT/Myb domain
CDD	cd00167	1.34E-7	50	93	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:0007623	Biological Process	circadian rhythm
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:0046686	Biological Process	response to cadmium ion
GO:0005634	Cellular Component	nucleus
GO:0005737	Cellular Component	cytoplasm
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:0000003	anatomy	whole plant
PO:0000013	anatomy	cauline leaf
PO:0000014	anatomy	rosette leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009001	anatomy	fruit
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:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001017	developmental stage	M germinated pollen stage
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:0007131	developmental stage	seedling development stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 293 aa Download sequence Send to blast
MTSTNPVVAE VIPAETSTDA TETTIATTEA GEAPEKKVRK AYTITKSRES WTEGEHDKFL 60 EALQLFDRDW KKIEDFVGSK TVIQIRSHAQ KYFLKVQKNG TLAHVPPPRP KRKAAHPYPQ 120 KASKNAQMSL HVSMSFPTQI NNLPGYTPWD DDTSALLNIA VSGVIPPEDE LDTLCGAEVD 180 VGSNDMISET SPSASGIGSS SRTLSDSKGL RLAKQAPSMH GLPDFAEVYN FIGSVFDPDS 240 KGRMKKLKEM DPINFETVLL LMRNLTVNLS NPDFEPTSEY VDAAEEGHEH LSS

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.20108	0.0	flower\| leaf\| root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145357565	0.0
Genevisible	250972_at	0.0
Expression Atlas	AT5G02840	-
AtGenExpress	AT5G02840	-
ATTED-II	AT5G02840	-

Functional Description ? help Back to Top
Source	Description
TAIR	CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.
UniProt	Probable transcription factor. {ECO:0000250, ECO:0000269\|PubMed:17363273}.

Function -- GeneRIF ? help Back to Top
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
MP00484	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G02840.1

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 -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G02840

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ937209	0.0	AJ937209.1 Arabidopsis thaliana mRNA for myb transcription factor LHY-CCA1-like1 (lcl1 gene).
GenBank	AY519514	0.0	AY519514.1 Arabidopsis thaliana MYB transcription factor (At5g02840) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_568108.1	0.0	LHY/CCA1-like 1
Refseq	NP_850756.1	0.0	LHY/CCA1-like 1
Swissprot	Q6R0G4	0.0	RVE4_ARATH; Protein REVEILLE 4
TrEMBL	A0A178U8Z5	0.0	A0A178U8Z5_ARATH; LCL1
STRING	AT5G02840.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM15213	11	18
Representative plant	OGRP928	15	58

Link Out ? help Back to Top
Phytozome	AT5G02840.1
Entrez Gene	831766
iHOP	AT5G02840
wikigenes	AT5G02840

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] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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] Sharma N,Cram D,Huebert T,Zhou N,Parkin IA Exploiting the wild crucifer Thlaspi arvense to identify conserved and novel genes expressed during a plant's response to cold stress. Plant Mol. Biol., 2007. 63(2): p. 171-84 [PMID:16972165] Osuna D, et al. Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J., 2007. 49(3): p. 463-91 [PMID:17217462] Martini J, et al. Multifocal two-photon laser scanning microscopy combined with photo-activatable GFP for in vivo monitoring of intracellular protein dynamics in real time. J. Struct. Biol., 2007. 158(3): p. 401-9 [PMID:17363273] Soitamo AJ,Piippo M,Allahverdiyeva Y,Battchikova N,Aro EM Light has a specific role in modulating Arabidopsis gene expression at low temperature. BMC Plant Biol., 2008. 8: p. 13 [PMID:18230142] 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] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Lu SX,Knowles SM,Andronis C,Ong MS,Tobin EM CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis. Plant Physiol., 2009. 150(2): p. 834-43 [PMID:19218364] 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] 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] 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]