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 RrC3926_p3
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family MYB_related
Protein Properties Length: 535aa    MW: 59315.3 Da    PI: 5.8674
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3926_p3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding45.81.4e-144996148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     +g+WT  Ed  l+d+vk++G g+W+ + ++  + R++k+c++rw ++l
       RrC3926_p3 49 KGPWTSTEDGVLIDYVKRHGEGNWNNVQKHTSLARCGKSCRLRWANHL 96
                     79******************************************9986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129419.92146100IPR017930Myb domain
SMARTSM007174.6E-104898IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.604.4E-2250103IPR009057Homeodomain-like
SuperFamilySSF466895.47E-2350126IPR009057Homeodomain-like
CDDcd001671.09E-85196No hitNo description
PfamPF139213.8E-1452111No hitNo description
SMARTSM007172.3E-8101172IPR001005SANT/Myb domain
PROSITE profilePS5129410.593101174IPR017930Myb domain
CDDcd001679.12E-6104168No hitNo description
Gene3DG3DSA:1.10.10.604.4E-21104173IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 535 aa     Download sequence    Send to blast
MSYTMDESDD AMYSSIYNYE SPSTASDNIG NNGCTSSRGG RGSVLNLKKG PWTSTEDGVL  60
IDYVKRHGEG NWNNVQKHTS LARCGKSCRL RWANHLRPNL KKGAFSKEEE QVIVEMHARM  120
GNKWAQMAEL VSSIEKSIHK LILSLVLIFC VYQLPGRTDN EIKNYWNTRI KRRQRAGLPL  180
YPPGTHVVED LHWSQEYQST GVVDRRRHQE FSQLGNSKAN VLFEDLNFAN VLFEDLNFAT  240
SLLPGASDML ACNMLGAGAS SYTPPILPSH SNNIRQEFQS PERFQYAAPQ KNPRSFSISD  300
HHPMYGGNQN PSDVMMIQDS HTFTDGMLPA SKPSFGAVKL ELPSFQYSET GGFDQWKTTT  360
TPSPPQSDLL DSVDTYIQSP PPLEMDEPDC FSSCDTGLLD MLLHEAKIKA SAKHGLLLSS  420
SEKSINSTTC ATQNVPRVGE SEAFQNIWTR SEIPIPTQLS GGGNSSDSHS VIFEALAGYV  480
VKTEELDQVW EPKRGVDVTR PDALLASSWQ DQQGRFGIVR DSSSMSDALA LLLGG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A1e-28461734107B-MYB
1h8a_C2e-284417320127MYB TRANSFORMING PROTEIN
Search in ModeBase
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}.
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018441909.10.0PREDICTED: LOW QUALITY PROTEIN: transcription factor GAMYB-like
SwissprotQ9FR970.0MYB65_ARATH; Transcription factor MYB65
TrEMBLM4CCW10.0M4CCW1_BRARP; Uncharacterized protein
STRINGBra002042.1-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]