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 XP_009131611.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MYB
Protein Properties Length: 313aa    MW: 35447.7 Da    PI: 10.0735
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009131611.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding51.22.9e-1677122147
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 
                      rg W + Ed +l+++v+q+G+ +W++Ia+++  gR++k+c++rw + 
   XP_009131611.1  77 RGHWRPTEDAKLKELVAQFGPQNWNLIAHHLL-GRSGKSCRLRWCNQ 122
                      899****************************9.***********985 PP
2Myb_DNA-binding537.8e-17129173147
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 
                      ++++T+eE+ +l+ a++ +G++ W++I+r ++ gRt++ +k++w+ +
   XP_009131611.1 129 KKAFTEEEESRLLTAHRAYGNK-WSLISRFFP-GRTDNAVKNHWHVV 173
                      679*******************.*********.***********976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129417.2472123IPR017930Myb domain
SMARTSM007172.9E-1476125IPR001005SANT/Myb domain
SuperFamilySSF466891.72E-2877170IPR009057Homeodomain-like
PfamPF002491.1E-1577122IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.608.8E-2678130IPR009057Homeodomain-like
CDDcd001679.19E-1380121No hitNo description
PROSITE profilePS5129424.363124178IPR017930Myb domain
SMARTSM007175.9E-15128176IPR001005SANT/Myb domain
PfamPF002493.2E-14129172IPR001005SANT/Myb domain
CDDcd001674.20E-11131174No hitNo description
Gene3DG3DSA:1.10.10.603.3E-20131176IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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:0001046Molecular Functioncore promoter sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 313 aa     Download sequence    Send to blast
MDPKLIEKVL TGNKTIKLSR RFEEANNFGS PPNSHTNLSL ARNHLHNKSY SVLERGENEN  60
SLKRRGNNGM NKKLCSRGHW RPTEDAKLKE LVAQFGPQNW NLIAHHLLGR SGKSCRLRWC  120
NQLDPRINKK AFTEEEESRL LTAHRAYGNK WSLISRFFPG RTDNAVKNHW HVVMARRTRA  180
SERQQALHAP SGNAEMTVLS VYRYNRGGFF GRVAEGTLVN EADDDDGSAV STCTTELSLT  240
PPSSTHQPRF LHDDNTLASG KDGQCVQRAE VNGIYSKKMD HQNHHTTTVS EREVEMKTKS  300
GFYFFDFLGV GAS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A2e-31771787108B-MYB
Search in ModeBase
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
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00516DAPTransfer from AT5G17800Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009131611.1
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
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1761931e-133AK176193.1 Arabidopsis thaliana mRNA for MYB56 R2R3-MYB factor family member, complete cds, clone: RAFL23-05-P12.
GenBankAK1762771e-133AK176277.1 Arabidopsis thaliana mRNA for MYB56 R2R3-MYB factor family member, complete cds, clone: RAFL23-20-A13.
GenBankAY5196271e-133AY519627.1 Arabidopsis thaliana MYB transcription factor (At5g17800) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009131611.10.0PREDICTED: transcription factor MYB23-like
SwissprotQ6R0531e-161MYB56_ARATH; Transcription factor MYB56
TrEMBLM4CQD30.0M4CQD3_BRARP; Uncharacterized protein
STRINGBra006422.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM99771836
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G17800.11e-150myb domain protein 56
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]