Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G12870.1
Common NameATMYB46, MYB46, T24H18.40
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: 280aa    MW: 31541.3 Da    PI: 6.0373
Description myb domain protein 46
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G12870.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     +g W++eEd +l ++    G g+W+ +a+  g+ R++k+c++rw +yl
                     678*******************************************97 PP

  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                      rg+++++E++l+++ +  lG++ W+ Ia++++ gRt++++k++w++
                      89********************.*********.***********97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129414.8421567IPR017930Myb domain
SMARTSM007172.0E-101969IPR001005SANT/Myb domain
PfamPF002492.1E-132067IPR001005SANT/Myb domain
CDDcd001671.75E-82367No hitNo description
PROSITE profilePS5129424.44968122IPR017930Myb domain
SMARTSM007172.3E-1572120IPR001005SANT/Myb domain
PfamPF002491.7E-1473116IPR001005SANT/Myb domain
CDDcd001671.11E-1075115No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0009751Biological Processresponse to salicylic acid
GO:0030154Biological Processcell differentiation
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0050832Biological Processdefense response to fungus
GO:1901348Biological Processpositive regulation of secondary cell wall biogenesis
GO:0005634Cellular Componentnucleus
GO:0000981Molecular FunctionRNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001135Molecular Functiontranscription factor activity, RNA polymerase II transcription factor recruiting
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA 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:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0003015anatomyprimary root differentiation zone
PO:0006202anatomyinterfascicular region
PO:0025022anatomycollective leaf structure
PO:0025257anatomyprimary root elongation zone
PO:0007611developmental stagepetal differentiation and expansion stage
Sequence ? help Back to Top
Protein Sequence    Length: 280 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT5G12870-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed at low levels in stems and siliques, specifically in xylem. {ECO:0000269|PubMed:16581911, ECO:0000269|PubMed:17890373, ECO:0000269|PubMed:9839469}.
Functional Description ? help Back to Top
Source Description
TAIRMember of the R2R3 factor gene family.
UniProtTranscription activator. Involved in the regulation of secondary wall biosynthesis in fibers and vessels (PubMed:17890373). Transcription activator of the mannan synthase CSLA9 that recognizes and binds to the DNA consensus sequence 5'-[AG][GT]T[AT]GGT[GA]-3' cis-regulatory element of CSLA9 promoter (PubMed:24243147). {ECO:0000269|PubMed:17890373, ECO:0000269|PubMed:24243147}.
Function -- GeneRIF ? help Back to Top
  1. These results demonstrate that MYB46 is a direct target of SND1 and is another key player in the transcriptional network involved in the regulation of secondary wall biosynthesis in Arabidopsis.
    [PMID: 17890373]
  2. MYB46 activates the expression of selected transcription factors and genes involved in the biosynthesis of secondary wall components.
    [PMID: 19674407]
  3. MYB83 and MYB46, both of which are SND1 direct targets, function redundantly in the transcriptional regulatory cascade leading to secondary wall formation in fibers and vessels.
    [PMID: 19808805]
  4. MYB46 gene expression does not change following interaction with pathogens. myb46 mutants have enhanced disease resistance to B. cinerea.
    [PMID: 21282403]
  5. The observed coordinated down-regulation of CesA genes is more pronounced, and occurs earlier, in myb46 mutant plants.
    [PMID: 21617373]
  6. MYB46 activates the secondary wall MYB-responsive element sites in the promoters of MYB46 direct targets. MYB46 and MYB83 directly activate a set of downstream transcription factors.
    [PMID: 22197883]
  7. MYB46 recognizes a cis-acting regulatory motif M46RE
    [PMID: 22271306]
  8. MYB46 mediated the transcriptional regulation of secondary wall biosynthesis.
    [PMID: 22914575]
  9. Data conclude that MYB46 is an obligate component of the transcriptional regulatory complex toward the commitment of secondary wall cellulose synthesis in Arabidopsis.
    [PMID: 23726771]
  10. Data indicate that transcription factors ANAC041, bZIP1 and MYB46 directly regulate the expression of CSLA9.
    [PMID: 24243147]
  11. MYB46 functions as a central and direct regulator of the genes involved in the biosynthesis of all three major secondary wall components.
    [PMID: 24879533]
  12. MYB46 is a unique transcription factor in that it directly regulates the biosynthesis genes for all of the three major components of the secondary wall as well as the transcription factors in the biosynthesis pathway.
    [PMID: 24984711]
  13. directly regulates all three secondary wall-associated cellulose synthase genes
    [PMID: 26011122]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Slightly induced by salicylic acid (SA). Positively regulated by SND1 and homolog proteins. {ECO:0000269|PubMed:16463103, ECO:0000269|PubMed:17890373}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G32770 (A), AT1G71930 (A), AT2G46770 (A), AT3G61910 (A), AT5G62380 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G16490(A), AT1G62990(A), AT1G79180(A), AT4G22680(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDsalicylic acid
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G12870
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5196210.0AY519621.1 Arabidopsis thaliana MYB transcription factor (At5g12870) mRNA, complete cds.
GenBankBT0004550.0BT000455.1 Arabidopsis thaliana putative transcription factor (MYB46) (At5g12870) mRNA, complete cds.
GenBankBT0025490.0BT002549.1 Arabidopsis thaliana putative transcription factor (MYB46) (At5g12870) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_196791.10.0transcription factor MYB46
SwissprotQ9LXV20.0MYB46_ARATH; Transcription factor MYB46
TrEMBLD7M5380.0D7M538_ARALL; AtMYB46
STRINGAT5G12870.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
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
  2. Stracke R,Werber M,Weisshaar B
    The R2R3-MYB gene family in Arabidopsis thaliana.
    Curr. Opin. Plant Biol., 2001. 4(5): p. 447-56
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  4. Zhao C,Craig JC,Petzold HE,Dickerman AW,Beers EP
    The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl.
    Plant Physiol., 2005. 138(2): p. 803-18
  5. 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
  6. Lee JY, et al.
    Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.
    Proc. Natl. Acad. Sci. U.S.A., 2006. 103(15): p. 6055-60
  7. Mace DL, et al.
    Quantification of transcription factor expression from Arabidopsis images.
    Bioinformatics, 2006. 22(14): p. e323-31
  8. Zhong R,Richardson EA,Ye ZH
    The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis.
    Plant Cell, 2007. 19(9): p. 2776-92
  9. Zhong R,Lee C,Zhou J,McCarthy RL,Ye ZH
    A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.
    Plant Cell, 2008. 20(10): p. 2763-82
  10. Zhou J,Lee C,Zhong R,Ye ZH
    MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis.
    Plant Cell, 2009. 21(1): p. 248-66
  11. Cheng H, et al.
    Gibberellin acts through jasmonate to control the expression of MYB21, MYB24, and MYB57 to promote stamen filament growth in Arabidopsis.
    PLoS Genet., 2009. 5(3): p. e1000440
  12. Ko JH,Kim WC,Han KH
    Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis.
    Plant J., 2009. 60(4): p. 649-65
  13. McCarthy RL,Zhong R,Ye ZH
    MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis.
    Plant Cell Physiol., 2009. 50(11): p. 1950-64
  14. Zhong R,Ye ZH
    Transcriptional regulation of lignin biosynthesis.
    Plant Signal Behav, 2009. 4(11): p. 1028-34
  15. Winzell A,Aspeborg H,Wang Y,Ezcurra I
    Conserved CA-rich motifs in gene promoters of Pt x tMYB021-responsive secondary cell wall carbohydrate-active enzymes in Populus.
    Biochem. Biophys. Res. Commun., 2010. 394(3): p. 848-53
  16. McCarthy RL, et al.
    The poplar MYB transcription factors, PtrMYB3 and PtrMYB20, are involved in the regulation of secondary wall biosynthesis.
    Plant Cell Physiol., 2010. 51(6): p. 1084-90
  17. Ram
    MYB46 modulates disease susceptibility to Botrytis cinerea in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1920-35
  18. Ram
    Enhanced disease resistance to Botrytis cinerea in myb46 Arabidopsis plants is associated to an early down-regulation of CesA genes.
    Plant Signal Behav, 2011. 6(6): p. 911-3
  19. Zhong R, et al.
    Transcriptional activation of secondary wall biosynthesis by rice and maize NAC and MYB transcription factors.
    Plant Cell Physiol., 2011. 52(10): p. 1856-71
  20. Zhong R,Ye ZH
    MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes.
    Plant Cell Physiol., 2012. 53(2): p. 368-80
  21. Kim WC,Ko JH,Han KH
    Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis.
    Plant Mol. Biol., 2012. 78(4-5): p. 489-501
  22. Ko JH,Kim WC,Kim JY,Ahn SJ,Han KH
    MYB46-mediated transcriptional regulation of secondary wall biosynthesis.
    Mol Plant, 2012. 5(5): p. 961-3
  23. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  24. Yan L, et al.
    The heterologous expression in Arabidopsis thaliana of sorghum transcription factor SbbHLH1 downregulates lignin synthesis.
    J. Exp. Bot., 2013. 64(10): p. 3021-32
  25. Kim WC,Kim JY,Ko JH,Kim J,Han KH
    Transcription factor MYB46 is an obligate component of the transcriptional regulatory complex for functional expression of secondary wall-associated cellulose synthases in Arabidopsis thaliana.
    J. Plant Physiol., 2013. 170(15): p. 1374-8
  26. Kim WC, et al.
    Transcription factors that directly regulate the expression of CSLA9 encoding mannan synthase in Arabidopsis thaliana.
    Plant Mol. Biol., 2014. 84(4-5): p. 577-87
  27. Kim WC,Kim JY,Ko JH,Kang H,Han KH
    Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis.
    Plant Mol. Biol., 2014. 85(6): p. 589-99
  28. Ko JH,Jeon HW,Kim WC,Kim JY,Han KH
    The MYB46/MYB83-mediated transcriptional regulatory programme is a gatekeeper of secondary wall biosynthesis.
    Ann. Bot., 2014. 114(6): p. 1099-107
  29. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  30. Kim WC, et al.
    MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis.
    Plant J., 2013. 73(1): p. 26-36
  31. 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