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_009146724.1
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: 502aa    MW: 55545.2 Da    PI: 5.7212
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009146724.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding47.25e-153582148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     +g+WT  Ed +l+++v+++G g+W+++ ++  + R++k+c++rw ++l
   XP_009146724.1 35 KGPWTSTEDGILINYVRKHGEGNWNAVQKYTSLARCGKSCRLRWANHL 82
                     79******************************************9986 PP
2Myb_DNA-binding49.68.9e-1688131146
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                      +g++++eE+ l+v+ ++++G++ W+  a++++ gRt++++k++w++
   XP_009146724.1  88 KGAFSQEEERLIVQMHAKMGNK-WAQMAEHLP-GRTDNEIKNYWNT 131
                      799*******************.*********.***********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129414.7983082IPR017930Myb domain
SMARTSM007176.8E-113484IPR001005SANT/Myb domain
SuperFamilySSF466895.03E-2934129IPR009057Homeodomain-like
PfamPF002491.2E-133582IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.603.0E-223689IPR009057Homeodomain-like
CDDcd001672.25E-93782No hitNo description
PROSITE profilePS5129425.21583137IPR017930Myb domain
SMARTSM007171.0E-1687135IPR001005SANT/Myb domain
PfamPF002491.4E-1488131IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.608.9E-2590136IPR009057Homeodomain-like
CDDcd001673.21E-1290131No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009723Biological Processresponse to ethylene
GO:0009751Biological Processresponse to salicylic acid
GO:0043068Biological Processpositive regulation of programmed cell death
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0045926Biological Processnegative regulation of growth
GO:0048235Biological Processpollen sperm cell differentiation
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 502 aa     Download sequence    Send to blast
MSYTAESDDD GMHSPAGDSI GYGCKSRGKG SVLKKGPWTS TEDGILINYV RKHGEGNWNA  60
VQKYTSLARC GKSCRLRWAN HLRPNLKKGA FSQEEERLIV QMHAKMGNKW AQMAEHLPGR  120
TDNEIKNYWN TRIKRRHRAG LPLYPPELHV EDLQWSEEYI TSNVTRVNRR RHHQDILQLG  180
NSKADVLFDD LNFATSLLPG ASDVLDMFTC NMLGTGASSS PYESYMPPIL PSPKQLRESG  240
SLFPMCSSNI KQEFHSPEPF QNPRSCSISP CDVGHHSPYG NQHPSDVMIS DSHAFTDGML  300
PTSKPLFGAV KLELPSFQYS ETSGFDQWKT TPSPPHSDPL DSVDAYIQSP PPLEIEKDES  360
NCFSSCDTGL LDMLLPNAKI KTSAKRSLAL PEIPIPTQLS AGENSPDSAG NVVKTEELDQ  420
VWEPKRVDIT RPDVLLASSW LDQQGCFGIV RDSSNMSDAL ALLLGGEDIE NSYVTVGSSS  480
SGQAQQGVES CTWTNMPPVW SL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1mse_C1e-31321361104C-Myb DNA-Binding Domain
1msf_C1e-31321361104C-Myb DNA-Binding Domain
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In germinating seeds, present in the root tip and in a linear array of up to 20 to 30 cells above the root tip. Strongly expressed in the inflorescence apex, and, to some extent, in the inflorescence stem, the vascular tissue, and the vascular tissue in leaf primordia (PubMed:11743113). In flowers, expressed in sepals, style, receptacle, anther filaments, and connective but not in anthers themselves (PubMed:15722475). {ECO:0000269|PubMed:11743113, ECO:0000269|PubMed:15722475}.
UniprotTISSUE SPECIFICITY: Mostly expressed in roots (e.g. root tips), stems, pollen, shoot apices, flowers and floral shoot tips, and, to a lower extent, in leaves and siliques. {ECO:0000269|PubMed:11743113, ECO:0000269|PubMed:15722475, ECO:0000269|PubMed:24278028}.
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator of alpha-amylase expression that binds to 5'-CAACTGTC-3' motif in target gene promoter (PubMed:11743113). In vegetative tissues, inhibits growth by reducing cell proliferation. Promotes the expression of aleurone-related genes (e.g. CP1, CP, GASA1, BXL1 and BXL2) in seeds. Together with MYB33 and MYB101, promotes the programmed cell death (PCD) the vacuolation of protein storage vacuoles (PSVs) in the aleurone layers during seed germination (PubMed:20699403). Together with MYB33, facilitates anther and tapetum development (PubMed:15722475). {ECO:0000269|PubMed:11743113, ECO:0000269|PubMed:15722475, ECO:0000269|PubMed:20699403}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00348DAPTransfer from AT3G11440Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009146724.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by microRNA159 (miR159a and miR159b) in vegetative tissues (PubMed:20699403, PubMed:17916625, PubMed:15226253). Specific expression in floral organs and in the shoot apices is regulated via miR159-mediated degradation (PubMed:15722475). Slightly induced by ethylene and salicylic acid (PubMed:16463103). {ECO:0000269|PubMed:15226253, ECO:0000269|PubMed:15722475, ECO:0000269|PubMed:16463103, ECO:0000269|PubMed:17916625, ECO:0000269|PubMed:20699403}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1895470.0AC189547.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH004P05, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009146724.10.0PREDICTED: transcription factor GAMYB isoform X1
RefseqXP_018514760.10.0PREDICTED: transcription factor GAMYB isoform X1
SwissprotQ9FR970.0MYB65_ARATH; Transcription factor MYB65
TrEMBLA0A078F5800.0A0A078F580_BRANA; BnaA05g27620D protein
TrEMBLA0A397ZI040.0A0A397ZI04_BRACM; Uncharacterized protein
STRINGBra034842.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM38022859
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G11440.10.0myb domain protein 65
Publications ? help Back to Top
  1. 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]
  2. Allen RS, et al.
    Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(41): p. 16371-6
    [PMID:17916625]
  3. Li J,Reichel M,Millar AA
    Determinants beyond both complementarity and cleavage govern microR159 efficacy in Arabidopsis.
    PLoS Genet., 2014. 10(3): p. e1004232
    [PMID:24626050]
  4. Li Y,Alonso-Peral M,Wong G,Wang MB,Millar AA
    Ubiquitous miR159 repression of MYB33/65 in Arabidopsis rosettes is robust and is not perturbed by a wide range of stresses.
    BMC Plant Biol., 2016. 16(1): p. 179
    [PMID:27542984]
  5. Liu B,De Storme N,Geelen D
    Gibberellin Induces Diploid Pollen Formation by Interfering with Meiotic Cytokinesis.
    Plant Physiol., 2017. 173(1): p. 338-353
    [PMID:27621423]
  6. Zheng Z, et al.
    Target RNA Secondary Structure Is a Major Determinant of miR159 Efficacy.
    Plant Physiol., 2017. 174(3): p. 1764-1778
    [PMID:28515145]
  7. Xue T,Liu Z,Dai X,Xiang F
    Primary root growth in Arabidopsis thaliana is inhibited by the miR159 mediated repression of MYB33, MYB65 and MYB101.
    Plant Sci., 2017. 262: p. 182-189
    [PMID:28716415]
  8. Kim MH, et al.
    Poplar MYB transcription factor PtrMYB012 and its Arabidopsis AtGAMYB orthologs are differentially repressed by the Arabidopsis miR159 family.
    Tree Physiol., 2018. 38(6): p. 801-812
    [PMID:29301041]