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 AT3G49690.1
Common NameATMYB84, MYB84, RAX3, T16K5.40
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: 310aa    MW: 35578.1 Da    PI: 7.311
Description myb domain protein 84
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G49690.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding46.11.1e-141462148
                     TSSS-HHHHHHHHHHHHHTTTT.-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGgg.tWktIartmgkgRtlkqcksrwqkyl 48
                     +g+W++eEd +l+ +++  G+g +W + ++++g++R++k+c++rw++yl
      AT3G49690.1 14 KGPWSPEEDAKLKSYIENSGTGgNWIALPQKIGLKRCGKSCRLRWLNYL 62
                     79*********************************************97 PP

2Myb_DNA-binding36.89.3e-1269111246
                      SSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   2 grWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                      g +++eE+ ++  +    G++ W+ Ia+ ++ gRt++++k++w++
      AT3G49690.1  69 GGFSEEEENIICSLYLTIGSR-WSIIAAQLP-GRTDNDIKNYWNT 111
                      569******************.*********.***********97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129412.058962IPR017930Myb domain
SuperFamilySSF466892.65E-2511109IPR009057Homeodomain-like
SMARTSM007171.1E-101364IPR001005SANT/Myb domain
PfamPF002495.6E-141462IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.601.0E-231569IPR009057Homeodomain-like
CDDcd001673.17E-71662No hitNo description
PROSITE profilePS5129420.44263117IPR017930Myb domain
SMARTSM007171.5E-1067115IPR001005SANT/Myb domain
PfamPF002491.2E-1069111IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.602.0E-2370118IPR009057Homeodomain-like
CDDcd001675.21E-771113No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0007275Biological Processmulticellular organism development
GO:0009751Biological Processresponse to salicylic acid
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0000981Molecular FunctionRNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001135Molecular Functiontranscription factor activity, RNA polymerase II transcription factor recruiting
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0009005anatomyroot
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0020100anatomyhypocotyl
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 310 aa     Download sequence    Send to blast
MGRAPCCDKA NVKKGPWSPE EDAKLKSYIE NSGTGGNWIA LPQKIGLKRC GKSCRLRWLN  60
YLRPNIKHGG FSEEEENIIC SLYLTIGSRW SIIAAQLPGR TDNDIKNYWN TRLKKKLINK  120
QRKELQEACM EQQEMMVMMK RQHQQQQIQT SFMMRQDQTM FTWPLHHHNV QVPALFMNQT  180
NSFCDQEDVK PVLIKNMVKI EDQELEKTNP HHHQDSMTNA FDHLSFSQLL LDPNHNHLGS  240
GEGFSMNSIL SANTNSPLLN TSNDNQWFGN FQAETVNLFS GASTSTSADQ STISWEDISS  300
LVYSDSKQFF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A4e-23141177108B-MYB
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453392990.0
Genevisible252233_at0.0
Expression AtlasAT3G49690-
AtGenExpressAT3G49690-
ATTED-IIAT3G49690-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Accumulates in an adaxial ball-shaped set of cells in three to five cell layers around the L3 layer of the shoot apical meristem (SAM) in youg plantlets. In the inflorescence meristem, confined to the axils of flower primordia. {ECO:0000269|PubMed:16461581}.
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:16461581}.
Functional Description ? help Back to Top
Source Description
TAIR"Putative homolog of the Blind gene in tomato. Together with RAX1 and RAX3 belong to the class R2R3 MYB genes; encoded by the Myb-like transcription factor MYB84, regulates axillary meristem formation. "
UniProtTranscription activator (By similarity). Positively regulates axillary meristems (AMs) formation and development, especially during inflorescence. {ECO:0000250, ECO:0000269|PubMed:16461581}.
Function -- GeneRIF ? help Back to Top
  1. rax mutants show new phenotypes that are characterized by defects in lateral bud formation in overlapping zones along the shoot axis. RAX genes are partially redundant in function and allow a fine-tuning of secondary axis formation [RAX3]
    [PMID: 16461581]
  2. SKI2, SKI3 and SKI8 are required for degradation of 5′-fragments generated by miRNA-guided RISC cleavage in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. [SKI2]
    [PMID: 26464441]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00089SELEX26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G49690.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDsalicylic acid
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9M2Y9
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G49690
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5195970.0AY519597.1 Arabidopsis thaliana MYB transcription factor (At3g49690) mRNA, complete cds.
GenBankBT0292240.0BT029224.1 Arabidopsis thaliana At3g49690 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_190538.10.0myb domain protein 84
SwissprotQ9M2Y90.0RAX3_ARATH; Transcription factor RAX3
TrEMBLA0A178VK290.0A0A178VK29_ARATH; RAX3
STRINGAT3G49690.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM29412568
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. Kersten B, et al.
    Generation of Arabidopsis protein chips for antibody and serum screening.
    Plant Mol. Biol., 2003. 52(5): p. 999-1010
    [PMID:14558660]
  4. Rogers LA, et al.
    Comparison of lignin deposition in three ectopic lignification mutants.
    New Phytol., 2005. 168(1): p. 123-40
    [PMID:16159327]
  5. 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]
  6. Müller D,Schmitz G,Theres K
    Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis.
    Plant Cell, 2006. 18(3): p. 586-97
    [PMID:16461581]
  7. 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]
  8. Ehrenreich IM,Stafford PA,Purugganan MD
    The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping.
    Genetics, 2007. 176(2): p. 1223-36
    [PMID:17435248]
  9. Jeifetz D,David-Schwartz R,Borovsky Y,Paran I
    CaBLIND regulates axillary meristem initiation and transition to flowering in pepper.
    Planta, 2011. 234(6): p. 1227-36
    [PMID:21773792]
  10. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  11. Branscheid A, et al.
    SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis.
    Nucleic Acids Res., 2015. 43(22): p. 10975-88
    [PMID:26464441]
  12. Guo D, et al.
    The WRKY Transcription Factor WRKY71/EXB1 Controls Shoot Branching by Transcriptionally Regulating RAX Genes in Arabidopsis.
    Plant Cell, 2015. 27(11): p. 3112-27
    [PMID:26578700]
  13. Pal S, et al.
    TransDetect Identifies a New Regulatory Module Controlling Phosphate Accumulation.
    Plant Physiol., 2017. 175(2): p. 916-926
    [PMID:28827455]
  14. Kranz HD, et al.
    Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana.
    Plant J., 1998. 16(2): p. 263-76
    [PMID:9839469]