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 AT2G33880.1
Common NameHB-3, STIP, T1B8.31, WOX9, WOX9A
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 WOX
Protein Properties Length: 378aa    MW: 42089.2 Da    PI: 9.0578
Description homeobox-3
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G33880.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
     Homeobox   2 rkRttftkeqleeLeelFek.nrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57 
                  ++R+++++eq+++Le+ F++   +p +ee++++ ++l    ++ +++V++WFqNr+ + k+
                  89*****************99*************************************995 PP

  Wus_type_Homeobox   2 artRWtPtpeQikiLeelyksGlrtPnkeeiqritaeLeeyGkiedkNVfyWFQNrkaRerqk 64 
                        689**********************************************************99 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007110.68949114IPR001356Homeobox domain
SMARTSM003891.2E-851118IPR001356Homeobox domain
CDDcd000862.13E-852114No hitNo description
PfamPF000468.7E-1653113IPR001356Homeobox domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008284Biological Processpositive regulation of cell proliferation
GO:0009735Biological Processresponse to cytokinin
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0010075Biological Processregulation of meristem growth
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0000229anatomyflower meristem
PO:0002002anatomyembryo basal cell
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020003anatomyplant ovule
PO:0020109anatomyembryo hypophysis
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular 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: 378 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.146990.0bud| root
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT2G33880-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in the basal daughter cell of the zygote (PubMed:14711878). Unlike WOX2 and WOX8, it is not expressed in the egg cell or the zygote (PubMed:14711878). During two subsequent rounds of transverse cell divisions, it is restricted to the hypophysis (PubMed:14711878). At the 8-cell stage, it expands into the central domain of the embryo, in addition to weakening in the hypophysis (PubMed:14711878). After protoderm formation, expression in the central embryo domain is restricted to the protodermal cells and also disappears from the hypophyseal cell (PubMed:14711878). In subsequent stages, a ring of expression remains at the presumptive boundary between root and hypocotyl, at about the same position as WOX2 expression in heart stage embryos (PubMed:14711878). In addition to its embryonic expression, it is expressed postembryonically in the epidermal cells of the placenta during gynoecium development, but not in the developing ovules (PubMed:14711878). The placental expression disappears soon after fertilization (PubMed:14711878). Expression dynamics require MP and BDL, but not GN activity (PubMed:14711878). Detected as early as the first zygotic division in both the apical and the basal daughter cells (PubMed:17706632). By late globular to early transition stage, the protein is evenly distributed through out the embryo and the suspensor (PubMed:17706632). The basal half of the embryo, especially cells in the protoderm layer, starts to show slightly higher levels of expression by early heart stage (PubMed:17706632). {ECO:0000269|PubMed:14711878, ECO:0000269|PubMed:17706632}.
UniprotTISSUE SPECIFICITY: Expressed in the basal cell and later at the boundary between suspensor and proembryo (PubMed:14711878). Expressed at low levels in proliferating tissues post embryonically (PubMed:15753038). Detected in vegetative shoot apical meristem, leaf primordia, floral meristems, emerging floral organs, epidermal layer of the placenta and in the upper portion of the root meristematic zone (PubMed:15753038, PubMed:20110319). {ECO:0000269|PubMed:14711878, ECO:0000269|PubMed:15753038, ECO:0000269|PubMed:20110319}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a protein with similarity to WUS type homeodomain protein. Required for meristem growth and development and acts through positive regulation of WUS. Loss of function phenotypes include embryo lethality, hyponastic cotyledons, reduced root development and smaller meristems. Phenotypes can be rescued by addition of sucrose in the growth media. Overexpression can partially rescue the triple mutant cytokinin receptor phenotype suggesting HB-3 is a downstream effector of cytokinin signaling.
UniProtHomeodomain transcription factor required for meristem growth and early development (PubMed:15753038). Promotes cell proliferation and prevents premature differentiation in meristematic tissues during postembryonic development (PubMed:15753038). Essential for maintaining tissue growth during embryogenesis (PubMed:17706632). May act by repressing TSS to promote meristematic proliferation (PubMed:21185286). Involved in the transcriptional activation of a subset of cytokinin response factors (PubMed:20110319). May act as a negative regulator of cytokinin signaling in the dark (PubMed:21057190). {ECO:0000269|PubMed:15753038, ECO:0000269|PubMed:17706632, ECO:0000269|PubMed:20110319, ECO:0000269|PubMed:21057190, ECO:0000303|PubMed:21185286}.
Function -- GeneRIF ? help Back to Top
  1. STIMPY (STIP; also called WOX9) is a homeobox gene required for the growth of the vegetative shoot apical meristem, in part by positively regulating WUSCHEL protein expression. [STIMPY] [STIP] [WOX9]
    [PMID: 15753038]
  2. Complete loss of STIP activity results in early embryonic arrest, most likely due to a failure in cell division.
    [PMID: 17706632]
  3. cytokinin signaling is involved in activation of the homeobox gene STIMPY (STIP or WOX9) expression in meristematic tissues, which is essential for maintaining the meristematic fate
    [PMID: 20110319]
  4. Stip mutants show enhanced de-etiolation phenotype in response to cytokinin treatment in the dark, suggesting that STIP may be a negative regulator of cytokinin signaling under this condition.
    [PMID: 21057190]
  5. Expression of WOX8 is independent of the axis patterning signal auxin, but, together with the redundant gene WOX9, is activated in the zygote, its basal daughter cell, and the hypophysis by the zinc-finger transcription factor WRKY2.
    [PMID: 21316593]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated in the zygote after fertilization by the transcription factor WRKY2. {ECO:0000269|PubMed:21316593}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G17950(A), AT3G11260(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G18380, AT5G08330, AT5G16560, AT5G60120, AT1G14920
IntActSearch Q6X7J4
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Embryonic lethality when homozygous (PubMed:17706632). Reduction in embryonic growth, failure in axillary shoot apical meristem and leaf-primordia initiation and growth, and failure in primary root growth and lateral root initiation when heterozygous (PubMed:15753038, PubMed:17706632). Wox8 and wox9 double mutants are embryo lethal, with embryos disrupted as early as the first cell division in the embryo proper (PubMed:17706632). {ECO:0000269|PubMed:15753038, ECO:0000269|PubMed:17706632}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G33880
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY2514010.0AY251401.1 Arabidopsis thaliana WOX9 protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
SwissprotQ6X7J40.0WOX9_ARATH; WUSCHEL-related homeobox 9
TrEMBLA0A178VQA80.0A0A178VQA8_ARATH; Homeobox-3
STRINGAT2G33880.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP61031220
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
  2. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
  3. R
    Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes.
    Plant J., 2002. 32(2): p. 243-53
  4. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Haecker A, et al.
    Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana.
    Development, 2004. 131(3): p. 657-68
  7. Son O, et al.
    Induction of a homeodomain-leucine zipper gene by auxin is inhibited by cytokinin in Arabidopsis roots.
    Biochem. Biophys. Res. Commun., 2005. 326(1): p. 203-9
  8. Wu X,Dabi T,Weigel D
    Requirement of homeobox gene STIMPY/WOX9 for Arabidopsis meristem growth and maintenance.
    Curr. Biol., 2005. 15(5): p. 436-40
  9. Tan QK,Irish VF
    The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development.
    Plant Physiol., 2006. 140(3): p. 1095-108
  10. Wu X,Chory J,Weigel D
    Combinations of WOX activities regulate tissue proliferation during Arabidopsis embryonic development.
    Dev. Biol., 2007. 309(2): p. 306-16
  11. Rebocho AB, et al.
    Role of EVERGREEN in the development of the cymose petunia inflorescence.
    Dev. Cell, 2008. 15(3): p. 437-47
  12. Skylar A,Hong F,Chory J,Weigel D,Wu X
    STIMPY mediates cytokinin signaling during shoot meristem establishment in Arabidopsis seedlings.
    Development, 2010. 137(4): p. 541-9
  13. Hirakawa Y,Kondo Y,Fukuda H
    TDIF peptide signaling regulates vascular stem cell proliferation via the WOX4 homeobox gene in Arabidopsis.
    Plant Cell, 2010. 22(8): p. 2618-29
  14. Zhang X,Zong J,Liu J,Yin J,Zhang D
    Genome-wide analysis of WOX gene family in rice, sorghum, maize, Arabidopsis and poplar.
    J Integr Plant Biol, 2010. 52(11): p. 1016-26
  15. Skylar A,Wu X
    STIMPY mutants have increased cytokinin sensitivity during dark germination.
    Plant Signal Behav, 2010. 5(11): p. 1437-9
  16. Skylar A,Sung F,Hong F,Chory J,Wu X
    Metabolic sugar signal promotes Arabidopsis meristematic proliferation via G2.
    Dev. Biol., 2011. 351(1): p. 82-9
  17. Ueda M,Zhang Z,Laux T
    Transcriptional activation of Arabidopsis axis patterning genes WOX8/9 links zygote polarity to embryo development.
    Dev. Cell, 2011. 20(2): p. 264-70
  18. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
  19. Jeong S,Palmer TM,Lukowitz W
    The RWP-RK factor GROUNDED promotes embryonic polarity by facilitating YODA MAP kinase signaling.
    Curr. Biol., 2011. 21(15): p. 1268-76
  20. Gaudinier A, et al.
    Enhanced Y1H assays for Arabidopsis.
    Nat. Methods, 2011. 8(12): p. 1053-5
  21. Wang W, et al.
    Dwarf Tiller1, a Wuschel-related homeobox transcription factor, is required for tiller growth in rice.
    PLoS Genet., 2014. 10(3): p. e1004154
  22. Mar
    Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners.
    Plant Physiol., 2014. 166(2): p. 1022-32
  23. Zhu T,Moschou PN,Alvarez JM,Sohlberg JJ,von Arnold S
    Wuschel-related homeobox 8/9 is important for proper embryo patterning in the gymnosperm Norway spruce.
    J. Exp. Bot., 2014. 65(22): p. 6543-52
  24. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  25. Raines T, et al.
    The cytokinin response factors modulate root and shoot growth and promote leaf senescence in Arabidopsis.
    Plant J., 2016. 85(1): p. 134-47
  26. Dolzblasz A, et al.
    Stem Cell Regulation by Arabidopsis WOX Genes.
    Mol Plant, 2016. 9(7): p. 1028-39
  27. Blein T,Pautot V,Laufs P
    Combinations of Mutations Sufficient to Alter Arabidopsis Leaf Dissection.
    Plants (Basel), 2013. 2(2): p. 230-47