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 AT1G23380.2
Common NameF26F24.25, F28C11.2, KNAT6, KNAT6L, KNAT6S
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 TALE
Protein Properties Length: 329aa    MW: 37189.9 Da    PI: 4.6703
Description KNOTTED1-like homeobox gene 6
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G23380.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
     Homeobox  21 knrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                  k +yp++ ++  LA+ +gL+++q+ +WF N+R ++
                  669*****************************885 PP

          ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                  +LK++LlrK+++++++Lk EFs
                  69*******************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM011889.7E-5226247IPR005539ELK domain
PROSITE profilePS512139.69226246IPR005539ELK domain
PfamPF037893.6E-7226247IPR005539ELK domain
PROSITE profilePS5007112.341246309IPR001356Homeobox domain
SMARTSM003891.9E-12248313IPR001356Homeobox domain
CDDcd000868.68E-12255310No hitNo description
PfamPF059204.8E-17266305IPR008422Homeobox KN domain
PROSITE patternPS000270284307IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010073Biological Processmeristem maintenance
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0009009anatomyplant embryo
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 329 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G23380-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in torpedo stage embryos at the boundaries between the presumptive SAM and the cotyledons. Later expressed between the cotyledons and the meristem, and between the cotyledons. In seedlings, localised in stipules and at the boundaries between the SAM and the emerging primordia. Expressed at the site of lateral roots. {ECO:0000269|PubMed:16798887}.
UniprotTISSUE SPECIFICITY: Expressed predominantly in shoot apices of seedlings, and, to a lower extent, in rosette leaves. {ECO:0000269|PubMed:11311158}.
Functional Description ? help Back to Top
Source Description
TAIRhomeodomain transcription factor KNAT6, belonging to class I of KN transcription factor family (which also includes KNAT1 and KNAT2). Expression is increased in as and bop1 leaf mutants.
UniProtPlays a role in meristem function. Contributes to the shoot apical meristem (SAM) maintenance and organ separation by controlling boundary establishment in embryo in a CUC1, CUC2 and STM-dependent manner. Involved in maintaining cells in an undifferentiated, meristematic state. Probably binds to the DNA sequence 5'-TGAC-3'. {ECO:0000269|PubMed:16798887}.
Function -- GeneRIF ? help Back to Top
  1. KNAT6 contributes to SAM maintenance and boundary establishment in the embryo via the SHOOT MERISTEMLESS(STM)/CUP-SHAPED COTYLEDON (CUC) pathway.
    [PMID: 16798887]
  2. KNAT6 and KNAT2 expression is restricted by BP and PNY to promote correct inflorescence development
    [PMID: 18390591]
  3. Results suggested that the late-flowering phenotype of the as1-1 and as2-1 mutants might have been caused by the ectopic expression of KNAT126 triple mutation.
    [PMID: 19891706]
  4. The data indicate that the ATH1-KNAT2 complex acts redundantly with KNAT6, both of which are negatively regulated by BP during pedicel development.
    [PMID: 22140242]
  5. BOP1/2 gain-of-function in stems promotes expression of the boundary gene KNOTTED1-LIKE FROM ARABIDOPSIS THALIANA6 (KNAT6) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1).
    [PMID: 22751300]
  6. our results indicate that BP interacts with the chromatin remodeling factor BRM to regulate the expression of KNAT2 and KNAT6 in control of inflorescence architecture.
    [PMID: 25822547]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Seems to be repressed by AS2 and AS1 but induced by STM, CUC1 and CUC2. {ECO:0000269|PubMed:11311158, ECO:0000269|PubMed:16798887}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G62360 (A), AT1G65620 (R), AT2G37630 (R), AT3G15170 (A), AT5G53950 (A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G62990, AT1G75410
IntActSearch Q84JS6
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G23380
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0723620.0AB072362.1 Arabidopsis thaliana KNAT6L mRNA for homeodomain transcription factor KNAT6, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_173752.30.0homeobox protein knotted-1-like 6
SwissprotQ84JS60.0KNAT6_ARATH; Homeobox protein knotted-1-like 6
TrEMBLD7KNF20.0D7KNF2_ARALL; Uncharacterized protein
STRINGAT1G23380.20.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP16717148
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. Semiarti E, et al.
    The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana regulates formation of a symmetric lamina, establishment of venation and repression of meristem-related homeobox genes in leaves.
    Development, 2001. 128(10): p. 1771-83
  3. Ha CM, et al.
    The BLADE-ON-PETIOLE 1 gene controls leaf pattern formation through the modulation of meristematic activity in Arabidopsis.
    Development, 2003. 130(1): p. 161-72
  4. Harrar Y,Bellec Y,Bellini C,Faure JD
    Hormonal control of cell proliferation requires PASTICCINO genes.
    Plant Physiol., 2003. 132(3): p. 1217-27
  5. Lin WC,Shuai B,Springer PS
    The Arabidopsis LATERAL ORGAN BOUNDARIES-domain gene ASYMMETRIC LEAVES2 functions in the repression of KNOX gene expression and in adaxial-abaxial patterning.
    Plant Cell, 2003. 15(10): p. 2241-52
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  7. Hibara K,Takada S,Tasaka M
    CUC1 gene activates the expression of SAM-related genes to induce adventitious shoot formation.
    Plant J., 2003. 36(5): p. 687-96
  8. Bhatt AM,Etchells JP,Canales C,Lagodienko A,Dickinson H
    VAAMANA--a BEL1-like homeodomain protein, interacts with KNOX proteins BP and STM and regulates inflorescence stem growth in Arabidopsis.
    Gene, 2004. 328: p. 103-11
  9. Dean G,Casson S,Lindsey K
    KNAT6 gene of Arabidopsis is expressed in roots and is required for correct lateral root formation.
    Plant Mol. Biol., 2004. 54(1): p. 71-84
  10. Tattersall AD, et al.
    The mutant crispa reveals multiple roles for PHANTASTICA in pea compound leaf development.
    Plant Cell, 2005. 17(4): p. 1046-60
  11. Hackbusch J,Richter K,Müller J,Salamini F,Uhrig JF
    A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(13): p. 4908-12
  12. Ledbedeva OV,Ezhova TA,Melzer S
    [Gene TAENIATA is a novel negative regulator of the Arabidopsis thaliana homeobox genes KNAT1, KNAT2, KNAT6, and STM].
    Genetika, 2005. 41(8): p. 1068-74
  13. 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
  14. Belles-Boix E, et al.
    KNAT6: an Arabidopsis homeobox gene involved in meristem activity and organ separation.
    Plant Cell, 2006. 18(8): p. 1900-7
  15. Alonso-Cantabrana H, et al.
    Common regulatory networks in leaf and fruit patterning revealed by mutations in the Arabidopsis ASYMMETRIC LEAVES1 gene.
    Development, 2007. 134(14): p. 2663-71
  16. Ha CM,Jun JH,Nam HG,Fletcher JC
    BLADE-ON-PETIOLE 1 and 2 control Arabidopsis lateral organ fate through regulation of LOB domain and adaxial-abaxial polarity genes.
    Plant Cell, 2007. 19(6): p. 1809-25
  17. Ragni L,Belles-Boix E,Günl M,Pautot V
    Interaction of KNAT6 and KNAT2 with BREVIPEDICELLUS and PENNYWISE in Arabidopsis inflorescences.
    Plant Cell, 2008. 20(4): p. 888-900
  18. Takahashi H, et al.
    Knowledge-based fuzzy adaptive resonance theory and its application to the analysis of gene expression in plants.
    J. Biosci. Bioeng., 2008. 106(6): p. 587-93
  19. Scofield S,Dewitte W,Murray JA
    A model for Arabidopsis class-1 KNOX gene function.
    Plant Signal Behav, 2008. 3(4): p. 257-9
  20. Ikezaki M, et al.
    Genetic networks regulated by ASYMMETRIC LEAVES1 (AS1) and AS2 in leaf development in Arabidopsis thaliana: KNOX genes control five morphological events.
    Plant J., 2010. 61(1): p. 70-82
  21. Tabata R, et al.
    Arabidopsis auxin response factor6 and 8 regulate jasmonic acid biosynthesis and floral organ development via repression of class 1 KNOX genes.
    Plant Cell Physiol., 2010. 51(1): p. 164-75
  22. Abraham-Ju
    Class I KNOX genes are associated with organogenesis during bulbil formation in Agave tequilana.
    J. Exp. Bot., 2010. 61(14): p. 4055-67
  23. Khan M, et al.
    Antagonistic interaction of BLADE-ON-PETIOLE1 and 2 with BREVIPEDICELLUS and PENNYWISE regulates Arabidopsis inflorescence architecture.
    Plant Physiol., 2012. 158(2): p. 946-60
  24. Li Y,Pi L,Huang H,Xu L
    ATH1 and KNAT2 proteins act together in regulation of plant inflorescence architecture.
    J. Exp. Bot., 2012. 63(3): p. 1423-33
  25. Butenko MA,Shi CL,Aalen RB
    KNAT1, KNAT2 and KNAT6 act downstream in the IDA-HAE/HSL2 signaling pathway to regulate floral organ abscission.
    Plant Signal Behav, 2012. 7(1): p. 135-8
  26. Khan M,Tabb P,Hepworth SR
    BLADE-ON-PETIOLE1 and 2 regulate Arabidopsis inflorescence architecture in conjunction with homeobox genes KNAT6 and ATH1.
    Plant Signal Behav, 2012. 7(7): p. 788-92
  27. We
    Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life.
    Cell Host Microbe, 2014. 16(3): p. 364-75
  28. 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
  29. Zhao M, et al.
    Arabidopsis BREVIPEDICELLUS interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA to regulate KNAT2 and KNAT6 expression in control of inflorescence architecture.
    PLoS Genet., 2015. 11(3): p. e1005125
  30. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86