PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G17800.1
Common NameAtMYB56, MYB56
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
Protein Properties Length: 323aa    MW: 36892.1 Da    PI: 9.7415
Description myb domain protein 56
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G17800.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding50.74e-1693138147
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 
                      rg W + Ed +l+++v+q+G+ +W++I++++  gR++k+c++rw++ 
      AT5G17800.1  93 RGHWRPTEDAKLKELVAQFGPQNWNLISNHLL-GRSGKSCRLRWFNQ 138
                      899****************************9.***********996 PP

2Myb_DNA-binding52.41.3e-16146188246
                      SSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   2 grWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                       ++T+eE+ +l+ a++ +G++ W++I+r ++ gRt++ +k++w+ 
      AT5G17800.1 146 RAFTEEEEFRLLAAHRAYGNK-WALISRLFP-GRTDNAVKNHWHV 188
                      689******************.*********.***********96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129417.04188139IPR017930Myb domain
SMARTSM007171.5E-1392141IPR001005SANT/Myb domain
PfamPF002491.6E-1593138IPR001005SANT/Myb domain
SuperFamilySSF466898.99E-2893186IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.609.8E-2594146IPR009057Homeodomain-like
CDDcd001675.79E-1296137No hitNo description
PROSITE profilePS5129424.347140194IPR017930Myb domain
SMARTSM007173.0E-14144192IPR001005SANT/Myb domain
PfamPF002497.1E-14146187IPR001005SANT/Myb domain
CDDcd001671.73E-10147187No hitNo description
Gene3DG3DSA:1.10.10.601.7E-19147193IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0030154Biological Processcell differentiation
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051782Biological Processnegative regulation of cell division
GO:0071367Biological Processcellular response to brassinosteroid stimulus
GO:0005634Cellular Componentnucleus
GO:0000981Molecular FunctionRNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001046Molecular Functioncore promoter sequence-specific DNA binding
GO:0001135Molecular Functiontranscription factor activity, RNA polymerase II transcription factor recruiting
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0006081anatomyprimary root apical meristem
PO:0009005anatomyroot
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009052anatomyflower pedicel
PO:0020149anatomyquiescent center
PO:0025022anatomycollective leaf structure
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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 323 aa     Download sequence    Send to blast
MNPNLLEKDL RGKETTNGSI RYKEANNFRS LPNSHTAACK TSLNNPSISR NHPHNKSASV  60
LESEDEHGNE RGENEKSLRM RGKSGINTKV CSRGHWRPTE DAKLKELVAQ FGPQNWNLIS  120
NHLLGRSGKS CRLRWFNQLD PRINKRAFTE EEEFRLLAAH RAYGNKWALI SRLFPGRTDN  180
AVKNHWHVIM ARRTRESQRQ RQQPPPTLSR DAEMTVSSSC RYNQGKFINE EDDDDDVSAV  240
STCTTELSLT PPSSAYQPRF FNYDSTLASG KDGQCVQRAE VNGIYGKKMD HQNHHTISVS  300
ERKVEMKMRS GYYYFDFLGV GAS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A7e-32931947108B-MYB
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.73310.0root| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453581500.0
Genevisible250051_at0.0
Expression AtlasAT5G17800-
AtGenExpressAT5G17800-
ATTED-IIAT5G17800-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in developing seeds. {ECO:0000269|PubMed:23911125}.
UniprotTISSUE SPECIFICITY: Mostly expressed in flowers (at protein level) and siliques, and, to a lower extent, in roots, stems and leaves (PubMed:25343985). Expressed in embryos (e.g. heart and torpedo stages) and cotyledons, and, at low levels, in roots and inflorescence (PubMed:23911125). Accumulates specifically in root apical meristem quiescent center (QC) and vascular initial cells (PubMed:16581911, PubMed:24981610). {ECO:0000269|PubMed:16581911, ECO:0000269|PubMed:23911125, ECO:0000269|PubMed:24981610, ECO:0000269|PubMed:25343985}.
Functional Description ? help Back to Top
Source Description
TAIRMember of the R2R3 factor gene family.
UniProtActs as a cell-specific local repressor of quiescent center (QC) self-renewal by cell divisions in the primary root. Counteracts brassinosteroid (BR)-mediated cell division in the QC cells (PubMed:24981610). Regulates maternally seed size, especially before the heart stage, promoting both endothelial cells expansion and cell number in the outer integument layer of the seed coat (PubMed:23911125). Modulates the expression of genes involved in cell wall metabolism such as cell division and expansion (PubMed:23911125, PubMed:24981610). Negative regulator of flowering via the repression of FT transcription (PubMed:25343985). {ECO:0000269|PubMed:23911125, ECO:0000269|PubMed:24981610, ECO:0000269|PubMed:25343985}.
Function -- GeneRIF ? help Back to Top
  1. MYB56 represents an unknown pathway for positively controlling the seed size.
    [PMID: 23911125]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00516DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G17800.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Levels follow a circadian cycle with a progressive decrease during the day time (at protein level) (PubMed:25343985). Down-regulated by brassinosteroids (BRs) in a dose- and time-dependent manner. Repressed by BES1. Auto-activation of expression (PubMed:24981610). Targeted to 26S proteasomal degradation by the CULLIN3 (CUL3)-based E3 ligases CRL3(BPMs) (PubMed:25343985). {ECO:0000269|PubMed:24981610, ECO:0000269|PubMed:25343985}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G17800, AT1G19350
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G17800
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1761930.0AK176193.1 Arabidopsis thaliana mRNA for MYB56 R2R3-MYB factor family member, complete cds, clone: RAFL23-05-P12.
GenBankAK1762770.0AK176277.1 Arabidopsis thaliana mRNA for MYB56 R2R3-MYB factor family member, complete cds, clone: RAFL23-20-A13.
GenBankAY5196270.0AY519627.1 Arabidopsis thaliana MYB transcription factor (At5g17800) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_197282.10.0myb domain protein 56
SwissprotQ6R0530.0MYB56_ARATH; Transcription factor MYB56
TrEMBLA0A178UDD20.0A0A178UDD2_ARATH; MYB56
STRINGAT5G17800.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM99771836
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. Nawy T, et al.
    Transcriptional profile of the Arabidopsis root quiescent center.
    Plant Cell, 2005. 17(7): p. 1908-25
    [PMID:15937229]
  4. Nakayama N, et al.
    Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens.
    Plant Cell, 2005. 17(9): p. 2486-506
    [PMID:16055634]
  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
    [PMID:16463103]
  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
    [PMID:16581911]
  7. Mace DL, et al.
    Quantification of transcription factor expression from Arabidopsis images.
    Bioinformatics, 2006. 22(14): p. e323-31
    [PMID:16873489]
  8. Day RC,Herridge RP,Ambrose BA,Macknight RC
    Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation.
    Plant Physiol., 2008. 148(4): p. 1964-84
    [PMID:18923020]
  9. Zhang Y,Liang W,Shi J,Xu J,Zhang D
    MYB56 encoding a R2R3 MYB transcription factor regulates seed size in Arabidopsis thaliana.
    J Integr Plant Biol, 2013. 55(11): p. 1166-78
    [PMID:23911125]
  10. Vilarrasa-Blasi J, et al.
    Regulation of plant stem cell quiescence by a brassinosteroid signaling module.
    Dev. Cell, 2014. 30(1): p. 36-47
    [PMID:24981610]
  11. Chen L,Bernhardt A,Lee J,Hellmann H
    Identification of Arabidopsis MYB56 as a novel substrate for CRL3BPM E3 ligases.
    Mol Plant, 2015.
    [PMID:25343985]
  12. Chen L,Bernhardt A,Lee J,Hellmann H
    Identification of Arabidopsis MYB56 as a novel substrate for CRL3(BPM) E3 ligases.
    Mol Plant, 2015. 8(2): p. 242-50
    [PMID:25618823]
  13. Frigola D,Caño-Delgado AI,Ibañes M
    Methods for Modeling Brassinosteroid-Mediated Signaling in Plant Development.
    Methods Mol. Biol., 2017. 1564: p. 103-120
    [PMID:28124249]
  14. Espinosa-Ruiz A, et al.
    TOPLESS mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana.
    Development, 2017. 144(9): p. 1619-1628
    [PMID:28320734]
  15. Jeong CY, et al.
    AtMyb56 Regulates Anthocyanin Levels via the Modulation of AtGPT2 Expression in Response to Sucrose in Arabidopsis.
    Mol. Cells, 2018. 41(4): p. 351-361
    [PMID:29487277]