PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G25560.1
Common NameAtMYB18, LAF1, M7J2.70, MYB18
Organism
Arabidopsis thaliana
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
Protein Properties Length: 283aa    MW: 32433 Da    PI: 7.9027
Description myb domain protein 18
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G25560.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding42.21.9e-131259148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     +g W++eEde+l   +  +G  +W+t++ + g+ R +k+c++rw +yl
      AT4G25560.1 12 KGLWSPEEDEKLRSFILSYGHSCWTTVPIKAGLQRNGKSCRLRWINYL 59
                     678*******************************************97 PP
2Myb_DNA-binding43.85.8e-1469110548
                      -HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   5 TteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      ++eE+e ++  +  lG++ W+ Ia+ ++ gRt++++k++w+++l
      AT4G25560.1  69 SAEEEETILTFHSSLGNK-WSQIAKFLP-GRTDNEIKNYWHSHL 110
                      89****************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129414.995759IPR017930Myb domain
SuperFamilySSF466893.29E-279106IPR009057Homeodomain-like
SMARTSM007171.3E-91161IPR001005SANT/Myb domain
PfamPF002491.3E-111259IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.606.3E-201366IPR009057Homeodomain-like
CDDcd001671.52E-71559No hitNo description
PROSITE profilePS5129421.50660114IPR017930Myb domain
SMARTSM007172.1E-1264112IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.602.6E-2367114IPR009057Homeodomain-like
CDDcd001672.65E-969110No hitNo description
PfamPF002492.6E-1269110IPR001005SANT/Myb domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0009585Biological Processred, far-red light phototransduction
GO:0009751Biological Processresponse to salicylic acid
GO:0010018Biological Processfar-red light signaling pathway
GO:0030154Biological Processcell differentiation
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0016607Cellular Componentnuclear speck
GO:0000981Molecular FunctionRNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001135Molecular Functiontranscription factor activity, RNA polymerase II transcription factor recruiting
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009005anatomyroot
Sequence ? help Back to Top
Protein Sequence    Length: 283 aa     Download sequence    Send to blast
MAKTKYGERH RKGLWSPEED EKLRSFILSY GHSCWTTVPI KAGLQRNGKS CRLRWINYLR  60
PGLKRDMISA EEEETILTFH SSLGNKWSQI AKFLPGRTDN EIKNYWHSHL KKKWLKSQSL  120
QDAKSISPPS SSSSSLVACG KRNPETLISN HVFSFQRLLE NKSSSPSQES NGNNSHQCSS  180
APEIPRLFFS EWLSSSYPHT DYSSEFTDSK HSQAPNVEET LSAYEEMGDV DQFHYNEMMI  240
NNSNWTLNDI VFGSKCKKQE HHIYREASDC NSSAEFFSPS TTT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A3e-24121137107B-MYB
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO306869280.0
Genevisible245234_at0.0
Expression AtlasAT4G25560-
AtGenExpressAT4G25560-
ATTED-IIAT4G25560-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed at very low level. Expressed in cauline leaves. {ECO:0000269|PubMed:11581165}.
Functional Description ? help Back to Top
Source Description
TAIRMember of the R2R3 factor gene family.
UniProtTranscription factor that promotes photomorphogenesis in the light by participating in the transmission of phytochrome A (phyA) signals to downstream responses (PubMed:11581165, PubMed:19482971). Probably acts by activating expression of light-induced genes. In darkness, its degradation prevents the activation of light-induced genes (PubMed:11581165). {ECO:0000269|PubMed:11581165, ECO:0000269|PubMed:19482971}.
Function -- GeneRIF ? help Back to Top
  1. in addition to their independent functions in phyA signaling, LAF1 and HFR1 also cooperate post-translationally to stabilize each other through inhibition of ubiquitination by COP1, thereby enhancing phyA photoresponses
    [PMID: 17699755]
  2. HY5 transmits phyA signals through an FHY1/FHL-independent pathway but it may also modulate FHY1/FHL signal through its interaction with HFR1 and LAF1.[LAF1]
    [PMID: 23503597]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G25560.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By hormones or elicitors treatment. By exposure to abiotic stress. {ECO:0000269|PubMed:9839469}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDsalicylic acid
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G11260, AT1G02340
IntActSearch Q9M0K4
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Partially blind to far-red (FR). Impaired inhibition of hypocotyl elongation and cotyledons expansion under continuous FR light conditions. {ECO:0000269|PubMed:19482971}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G25560
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5196090.0AY519609.1 Arabidopsis thaliana MYB transcription factor (At4g25560) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_194286.10.0myb domain protein 18
SwissprotQ9M0K40.0LAF1_ARATH; Transcription factor LAF1
TrEMBLA0A178V3M00.0A0A178V3M0_ARATH; MYB18
STRINGAT4G25560.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM4282646
Representative plantOGRP5171784
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. Ballesteros ML, et al.
    LAF1, a MYB transcription activator for phytochrome A signaling.
    Genes Dev., 2001. 15(19): p. 2613-25
    [PMID:11581165]
  3. Stracke R,Werber M,Weisshaar B
    The R2R3-MYB gene family in Arabidopsis thaliana.
    Curr. Opin. Plant Biol., 2001. 4(5): p. 447-56
    [PMID:11597504]
  4. Seo HS, et al.
    LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1.
    Nature, 2003. 423(6943): p. 995-9
    [PMID:12827204]
  5. Gong W, et al.
    Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
    Plant Physiol., 2004. 135(2): p. 773-82
    [PMID:15208423]
  6. Jang IC,Yang JY,Seo HS,Chua NH
    HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling.
    Genes Dev., 2005. 19(5): p. 593-602
    [PMID:15741320]
  7. Yang J, et al.
    Repression of light signaling by Arabidopsis SPA1 involves post-translational regulation of HFR1 protein accumulation.
    Plant J., 2005. 43(1): p. 131-41
    [PMID:15960622]
  8. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  9. 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]
  10. Jang IC,Yang SW,Yang JY,Chua NH
    Independent and interdependent functions of LAF1 and HFR1 in phytochrome A signaling.
    Genes Dev., 2007. 21(16): p. 2100-11
    [PMID:17699755]
  11. Yang SW,Jang IC,Henriques R,Chua NH
    FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE associate with the Arabidopsis transcription factors LAF1 and HFR1 to transmit phytochrome A signals for inhibition of hypocotyl elongation.
    Plant Cell, 2009. 21(5): p. 1341-59
    [PMID:19482971]
  12. Gong W, et al.
    The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors.
    Mol Plant, 2008. 1(1): p. 27-41
    [PMID:19802365]
  13. Jang IC,Henriques R,Chua NH
    Three transcription factors, HFR1, LAF1 and HY5, regulate largely independent signaling pathways downstream of phytochrome A.
    Plant Cell Physiol., 2013. 54(6): p. 907-16
    [PMID:23503597]
  14. Kranz HD, et al.
    Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana.
    Plant J., 1998. 16(2): p. 263-76
    [PMID:9839469]