PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10013393m
Common NameCARUB_v10013393mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family MYB
Protein Properties Length: 547aa    MW: 60281.4 Da    PI: 6.5991
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10013393mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding49.97.1e-164289148
                     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
  Carubv10013393m 42 KGPWTSTEDGILIDYVKKHGEGNWNAVQKHTSLARCGKSCRLRWANHL 89
                     79******************************************9986 PP
2Myb_DNA-binding51.22.8e-1695138146
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                      +g++++eE++l+v+ ++++G++ W+  a++++ gRt++++k++w++
  Carubv10013393m  95 KGAFSQEEEQLIVEMHAKMGNK-WAQMAEHLP-GRTDNEIKNYWNT 138
                      799*******************.*********.***********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0016932.9E-2821546IPR016310Transcription factor, GAMYB
PROSITE profilePS5129414.523789IPR017930Myb domain
SuperFamilySSF466894.12E-2941136IPR009057Homeodomain-like
SMARTSM007171.4E-114191IPR001005SANT/Myb domain
PfamPF002495.4E-144289IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.605.8E-234396IPR009057Homeodomain-like
CDDcd001677.47E-104489No hitNo description
PROSITE profilePS5129425.7890144IPR017930Myb domain
SMARTSM007177.3E-1794142IPR001005SANT/Myb domain
PfamPF002494.8E-1595138IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.603.9E-2597143IPR009057Homeodomain-like
CDDcd001673.67E-1297138No 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:0009908Biological Processflower development
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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 547 aa     Download sequence    Send to blast
MSYKTTVESD DGMHSSIHNE SPAADRIANG YRSRGRGGVL KKGPWTSTED GILIDYVKKH  60
GEGNWNAVQK HTSLARCGKS CRLRWANHLR PNLKKGAFSQ EEEQLIVEMH AKMGNKWAQM  120
AEHLPGRTDN EIKNYWNTRI KRRQRAGLPL YPPEIHVEDL QWSEEYTKSK IIGVDRRRHH  180
DFLQLGNAKA NALFDDLNFA ASLLPAASDL SDLVACNLLG TGASSSWYES YMSPILPSPK  240
QFWESGSRFP MCSSNIKHEF QSPEHFQNTA SQKNPRSCSI SPCGVHHPPY GNQPSSDMMM  300
ILDSHTFTDG MLPTSKPSFG AVKLELPSFQ YSETSAFDQW KATPSPPQSD LLDSVDAYIQ  360
SPPPSEIEES DCFSSCDTGL LDMLLHEAKI KTSAKHSLPL SSPEKSLSST TSTTNAIQNV  420
PRPQIKSGEL EDSQKNLARS EISIPRQLSA GGISSGNFVK TEESDHVWEP KRVDMTRPDV  480
LLASSWFDQG CYGIVRDTSS MSDALALLLG GDDIGNSYVT VGSSSGQAPR GVGSCGWTNM  540
PPVWSL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A9e-32401435107B-MYB
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00348DAPTransfer from AT3G11440Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10013393m
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
GenBankAY5195850.0AY519585.1 Arabidopsis thaliana MYB transcription factor (At3g11440) mRNA, complete cds.
GenBankBT0039400.0BT003940.1 Arabidopsis thaliana clone RAFL15-06-P04 (R20731) putative Myb DNA-binding protein (At3g11440) mRNA, complete cds.
GenBankBT0051200.0BT005120.1 Arabidopsis thaliana clone U20731 putative Myb DNA-binding protein (At3g11440) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006297374.10.0transcription factor MYB65
RefseqXP_023642784.10.0transcription factor MYB65
SwissprotQ9FR970.0MYB65_ARATH; Transcription factor MYB65
TrEMBLR0G4540.0R0G454_9BRAS; Transcription factor
STRINGXP_006297374.10.0(Capsella rubella)
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]