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 AT1G16490.1
Common NameATMYB58, F3O9.29, MYB58
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: 274aa    MW: 31460.7 Da    PI: 4.8766
Description myb domain protein 58
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G16490.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding48.32.4e-151663148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     rg+W+ +Ed++l+  +++ G ++W++ ++  g+ R++k+c++rw +yl
      AT1G16490.1 16 RGPWSHDEDLKLISFIHKNGHENWRSLPKQAGLLRCGKSCRLRWINYL 63
                     89******************************99************97 PP
2Myb_DNA-binding513.2e-1669114148
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      rg++++eE++ ++++++ +G++ W++Ia++++ gRt++++k+ w+++l
      AT1G16490.1  69 RGNFSAEEEDTIIKLHQSFGNK-WSKIASKLP-GRTDNEIKNVWHTHL 114
                      89********************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.3E-22766IPR009057Homeodomain-like
PROSITE profilePS5129414.4691163IPR017930Myb domain
SuperFamilySSF466893.63E-2814110IPR009057Homeodomain-like
SMARTSM007171.5E-111565IPR001005SANT/Myb domain
PfamPF002491.5E-141663IPR001005SANT/Myb domain
CDDcd001672.67E-81863No hitNo description
PROSITE profilePS5129424.99464118IPR017930Myb domain
Gene3DG3DSA:1.10.10.605.4E-2767118IPR009057Homeodomain-like
SMARTSM007171.2E-1468116IPR001005SANT/Myb domain
PfamPF002496.5E-1569114IPR001005SANT/Myb domain
CDDcd001679.91E-1071114No 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:0009809Biological Processlignin biosynthetic process
GO:0030154Biological Processcell differentiation
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:2000652Biological Processregulation 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: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:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000272anatomyprotoxylem
PO:0005352anatomyxylem
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight 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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 274 aa     Download sequence    Send to blast
MGKGRAPCCD KTKVKRGPWS HDEDLKLISF IHKNGHENWR SLPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFSAEEEDTI IKLHQSFGNK WSKIASKLPG RTDNEIKNVW HTHLKKRLSS  120
ETNLNADEAG SKGSLNEEEN SQESSPNASM SFAGSNISSK DDDAQISQMF EHILTYSEFT  180
GMLQEVDKPE LLEMPFDLDP DIWSFIDGSD SFQQPENRAL QESEEDEVDK WFKHLESELG  240
LEENDNQQQQ QQHKQGTEDE HSSSLLESYE LLIH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A8e-24161207110B-MYB
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible262715_at0.0
Expression AtlasAT1G16490-
AtGenExpressAT1G16490-
ATTED-IIAT1G16490-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In nonelongating internodes, highly expressed in interfascicular fibers and xylem cells but not in parenchymatous pith cells. In elongating internodes, predominantly expressed in protoxylem vessels. {ECO:0000269|PubMed:19122102}.
UniprotTISSUE SPECIFICITY: Expressed in leaves (PubMed:9839469). Specifically expressed in fibers and vessels undergoing secondary wall thickening, especially in inflorescence stems (PubMed:19122102). {ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:9839469}.
Functional Description ? help Back to Top
Source Description
TAIRMember of the R2R3 factor gene family.
UniProtTranscriptional activator that binds DNA to the AC cis-elements 5'-ACCTACC-3', 5'-ACCAACC-3' and 5'-ACCTAAC-3' of promoters and specifically activates lignin biosynthetic genes during secondary wall formation mediated by SND1. {ECO:0000269|PubMed:19122102}.
Function -- GeneRIF ? help Back to Top
  1. MYB58 and MYB63 are specifically expressed in fibers and vessels undergoing secondary wall thickening, and are transcriptional activators of lignin biosynthesis.
    [PMID: 19122102]
  2. The UGT72E3/2 was combined with the sinapyl alcohol synthesis pathway gene F5H encoding ferulate 5-hydroxylase and the lignin biosynthesis transcriptional activator MYB58.
    [PMID: 24667164]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00144DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G16490.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Slightly induced by light (PubMed:9839469). Regulated by the SND1 close homologs NST1, NST2, VND6, and VND7 and their downstream targets MYB46 and MYB83 (PubMed:19122102, PubMed:22197883). {ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:22197883, ECO:0000269|PubMed:9839469}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
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), AT5G12870 (A), AT5G62380 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G15950(A), AT1G51680(A), AT2G30490(A), AT2G37040(A), AT2G38080(A), AT2G40890(A), AT4G34050(A), AT4G37970(A), AT5G48930(A), AT5G54160(A)
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G16490
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4934590.0AB493459.1 Arabidopsis thaliana At1g16490 mRNA for hypothetical protein, partial cds, clone: RAAt1g16490.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_173098.10.0myb domain protein 58
SwissprotQ9SA470.0MYB58_ARATH; Transcription factor MYB58
TrEMBLD7KEF90.0D7KEF9_ARALL; AtMYB58
STRINGAT1G16490.10.0(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. 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]
  3. 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
    [PMID:19122102]
  4. Zhong R,Ye ZH
    Transcriptional regulation of lignin biosynthesis.
    Plant Signal Behav, 2009. 4(11): p. 1028-34
    [PMID:19838072]
  5. Zhao Q, et al.
    Syringyl lignin biosynthesis is directly regulated by a secondary cell wall master switch.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(32): p. 14496-501
    [PMID:20660755]
  6. 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
    [PMID:22197883]
  7. Chu Y,Kwon T,Nam J
    Enzymatic and metabolic engineering for efficient production of syringin, sinapyl alcohol 4-O-glucoside, in Arabidopsis thaliana.
    Phytochemistry, 2014. 102: p. 55-63
    [PMID:24667164]
  8. Fernández-Pérez F,Vivar T,Pomar F,Pedreño MA,Novo-Uzal E
    Peroxidase 4 is involved in syringyl lignin formation in Arabidopsis thaliana.
    J. Plant Physiol., 2015. 175: p. 86-94
    [PMID:25506770]
  9. 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
    [PMID:25750178]
  10. Noda S, et al.
    The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63.
    Planta, 2015. 242(3): p. 589-600
    [PMID:26070439]
  11. Takeuchi M,Kegasa T,Watanabe A,Tamura M,Tsutsumi Y
    Expression analysis of transporter genes for screening candidate monolignol transporters using Arabidopsis thaliana cell suspensions during tracheary element differentiation.
    J. Plant Res., 2018. 131(2): p. 297-305
    [PMID:28921082]