PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G02840.2
Common NameF9G14.150, LCL1, RVE4
Organism
Taxonomic ID
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
AT5G02840.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding39.11.7e-124892147
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                     r +WT+ E++++++a +++  + Wk+I   +g  +t  q++s+ qky
      AT5G02840.2 48 RESWTEGEHDKFLEALQLFDRD-WKKIEDFVG-SKTVIQIRSHAQKY 92
                     789*****************77.*********.*************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.02E-164298IPR009057Homeodomain-like
PROSITE profilePS5129414.9424397IPR017930Myb domain
Gene3DG3DSA:1.10.10.602.8E-64698IPR009057Homeodomain-like
TIGRFAMsTIGR015572.3E-184695IPR006447Myb domain, plants
SMARTSM007177.6E-104795IPR001005SANT/Myb domain
PfamPF002493.1E-104892IPR001005SANT/Myb domain
CDDcd001671.34E-75093No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0009651Biological Processresponse to salt stress
GO:0009723Biological Processresponse to ethylene
GO:0009733Biological Processresponse to auxin
GO:0009737Biological Processresponse to abscisic acid
GO:0009739Biological Processresponse to gibberellin
GO:0009751Biological Processresponse to salicylic acid
GO:0009753Biological Processresponse to jasmonic acid
GO:0046686Biological Processresponse to cadmium ion
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000003anatomywhole plant
PO:0000013anatomycauline leaf
PO:0000014anatomyrosette leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009001anatomyfruit
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering 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.201080.0flower| leaf| root| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453575650.0
Genevisible250972_at0.0
Expression AtlasAT5G02840-
AtGenExpressAT5G02840-
ATTED-IIAT5G02840-
Functional Description ? help Back to Top
Source Description
TAIRCCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.
UniProtProbable transcription factor. {ECO:0000250, ECO:0000269|PubMed:17363273}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00484DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G02840.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid, auxin, ethylene, gibberellin, jasmonic acid, salicylic acid
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G02840
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ9372090.0AJ937209.1 Arabidopsis thaliana mRNA for myb transcription factor LHY-CCA1-like1 (lcl1 gene).
GenBankAY5195140.0AY519514.1 Arabidopsis thaliana MYB transcription factor (At5g02840) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_568108.10.0protein LHY/CCA1-like 1
RefseqNP_850756.10.0protein LHY/CCA1-like 1
SwissprotQ6R0G40.0RVE4_ARATH; Protein REVEILLE 4
TrEMBLQ9LZ010.0Q9LZ01_ARATH; Putative uncharacterized protein F9G14_150
STRINGAT5G02840.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]