PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G09960.1
Common NameAGL11, STK, T5L19.90
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
Protein Properties Length: 230aa    MW: 26183.6 Da    PI: 9.7159
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G09960.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                 79***********************************************8 PP

        K-box   4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                  ++++ ++e +a+++qqe+akL+++i+++q+++R+l+G++L+sLs+keL+q+e++Lek++++iRskK+elll +ie+ qk+e el++en +Lr+k++e
                  34445999**************************************************************************************986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004327.0E-42160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006634.034161IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.89E-33282IPR002100Transcription factor, MADS-box
CDDcd002658.60E-43276No hitNo description
PRINTSPR004045.9E-33323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.4E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004045.9E-332338IPR002100Transcription factor, MADS-box
PRINTSPR004045.9E-333859IPR002100Transcription factor, MADS-box
PfamPF014864.6E-2585171IPR002487Transcription factor, K-box
PROSITE profilePS5129714.50687177IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0080155Biological Processregulation of double fertilization forming a zygote and endosperm
GO:0090376Biological Processseed trichome differentiation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0009052anatomyflower pedicel
PO:0020003anatomyplant ovule
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001185developmental stageplant embryo globular stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 230 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P2e-21169169Myocyte-specific enhancer factor 2B
1tqe_Q2e-21169169Myocyte-specific enhancer factor 2B
1tqe_R2e-21169169Myocyte-specific enhancer factor 2B
1tqe_S2e-21169169Myocyte-specific enhancer factor 2B
6c9l_A2e-21169169Myocyte-specific enhancer factor 2B
6c9l_B2e-21169169Myocyte-specific enhancer factor 2B
6c9l_C2e-21169169Myocyte-specific enhancer factor 2B
6c9l_D2e-21169169Myocyte-specific enhancer factor 2B
6c9l_E2e-21169169Myocyte-specific enhancer factor 2B
6c9l_F2e-21169169Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.29180.0bud| flower| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT4G09960-
Functional Description ? help Back to Top
Source Description
TAIRa MADS box transcription factor expressed in the carpel and ovules
UniProtProbable transcription factor (Probable). Is required, together with TT16/AGL32 for the maternal control of endothelium formation, which is essential for female gametophyte development and fertilization, and seed formation (PubMed:22176531). {ECO:0000269|PubMed:22176531, ECO:0000305}.
Function -- GeneRIF ? help Back to Top
  1. These experiments indicate that the ectopic co-expression of SEPALLATA3 and SHATTERPROOF1 and/or SEEDSTICK is probably not sufficient to homeotically transform vegetative tissues into carpels with ovules.
    [PMID: 16515858]
  2. The stk shp1 shp2 ant quadruple mutant ovule lacks integument development as in ant single mutant.
    [PMID: 20041269]
  3. STK and ABS played a role in the maternal control of endothelium formation, as the abs stk double mutant completely lacks endothelium.
    [PMID: 22176531]
  4. Data indicate that SEEDSTICK (STK) and SEPALLATA3 (SEP3) dimers can induce loop formation in the VERDANDI (VDD) promoter by binding to two nearby CC(A/T)6GG (CArG) boxes essential for promoter activity.
    [PMID: 23847151]
  5. STK might recruit or regulate histone modifying factors to control their activity in Arabidopsis.
    [PMID: 25521508]
  6. studies reveal a molecular network controlled by STK that regulates cell wall properties of the seed coat, demonstrating that developmental regulators controlling organ identity also coordinate specific aspects of cell wall characteristics.
    [PMID: 27624758]
Cis-element ? help Back to Top
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 AT2G01930 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G24260(A), AT2G42830(A), AT3G58780(A), AT4G18960(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G37940, AT5G13790, AT5G15800, AT1G24260, AT1G48150
IntActSearch Q38836
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G09960
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankATU201820.0U20182.1 Arabidopsis thaliana MADS-box protein AGL11 (AGL11) mRNA, complete cds.
GenBankAY0872010.0AY087201.1 Arabidopsis thaliana clone 32791 mRNA, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001329611.11e-168K-box region and MADS-box transcription factor family protein
SwissprotQ388361e-169AGL11_ARATH; Agamous-like MADS-box protein AGL11
TrEMBLA0A1P8B8891e-167A0A1P8B889_ARATH; K-box region and MADS-box transcription factor family protein
STRINGAT4G09960.31e-167(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Yung MH,Schaffer R,Putterill J
    Identification of genes expressed during early Arabidopsis carpel development by mRNA differential display: characterisation of ATCEL2, a novel endo-1,4-beta-D-glucanase gene.
    Plant J., 1999. 17(2): p. 203-8
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  3. Tzeng TY,Chen HY,Yang CH
    Ectopic expression of carpel-specific MADS box genes from lily and lisianthus causes similar homeotic conversion of sepal and petal in Arabidopsis.
    Plant Physiol., 2002. 130(4): p. 1827-36
  4. Parenicov√° L, et al.
    Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world.
    Plant Cell, 2003. 15(7): p. 1538-51
  5. Favaro R, et al.
    MADS-box protein complexes control carpel and ovule development in Arabidopsis.
    Plant Cell, 2003. 15(11): p. 2603-11
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  7. Kooiker M, et al.
    BASIC PENTACYSTEINE1, a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK.
    Plant Cell, 2005. 17(3): p. 722-9
  8. de Folter S, et al.
    Comprehensive interaction map of the Arabidopsis MADS Box transcription factors.
    Plant Cell, 2005. 17(5): p. 1424-33
  9. Kaufmann K,Anfang N,Saedler H,Theissen G
    Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein.
    Mol. Genet. Genomics, 2005. 274(2): p. 103-18
  10. Skipper M,Johansen LB,Pedersen KB,Frederiksen S,Johansen BB
    Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.).
    Gene, 2006. 366(2): p. 266-74
  11. Battaglia R,Brambilla V,Colombo L,Stuitje AR,Kater MM
    Functional analysis of MADS-box genes controlling ovule development in Arabidopsis using the ethanol-inducible alc gene-expression system.
    Mech. Dev., 2006. 123(4): p. 267-76
  12. de Folter S, et al.
    A Bsister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis.
    Plant J., 2006. 47(6): p. 934-46
  13. Gray-Mitsumune M, et al.
    Loss of ovule identity induced by overexpression of the fertilization-related kinase 2 (ScFRK2), a MAPKKK from Solanum chacoense.
    J. Exp. Bot., 2006. 57(15): p. 4171-87
  14. Brambilla V, et al.
    Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis.
    Plant Cell, 2007. 19(8): p. 2544-56
  15. Nain V, et al.
    Cloning of an ovule specific promoter from Arabidopsis thaliana and expression of beta-glucuronidase.
    Indian J. Exp. Biol., 2008. 46(4): p. 207-11
  16. Tani E, et al.
    Characterization and expression analysis of AGAMOUS-like, SEEDSTICK-like, and SEPALLATA-like MADS-box genes in peach (Prunus persica) fruit.
    Plant Physiol. Biochem., 2009. 47(8): p. 690-700
  17. Brambilla V,Kater M,Colombo L
    Ovule integument identity determination in Arabidopsis.
    Plant Signal Behav, 2008. 3(4): p. 246-7
  18. Losa A,Colombo M,Brambilla V,Colombo L
    Genetic interaction between AINTEGUMENTA (ANT) and the ovule identity genes SEEDSTICK (STK), SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2).
    Sex. Plant Reprod., 2010. 23(2): p. 115-21
  19. Matias-Hernandez L, et al.
    VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis.
    Plant Cell, 2010. 22(6): p. 1702-15
  20. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
  21. Dreni L, et al.
    Functional analysis of all AGAMOUS subfamily members in rice reveals their roles in reproductive organ identity determination and meristem determinacy.
    Plant Cell, 2011. 23(8): p. 2850-63
  22. Mizzotti C, et al.
    The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development.
    Plant J., 2012. 70(3): p. 409-20
  23. Severing EI, et al.
    Predicting the impact of alternative splicing on plant MADS domain protein function.
    PLoS ONE, 2012. 7(1): p. e30524
  24. Simonini S, et al.
    Basic pentacysteine proteins mediate MADS domain complex binding to the DNA for tissue-specific expression of target genes in Arabidopsis.
    Plant Cell, 2012. 24(10): p. 4163-72
  25. Mendes MA, et al.
    MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis.
    Plant Cell, 2013. 25(7): p. 2560-72
  26. Mizzotti C, et al.
    SEEDSTICK is a master regulator of development and metabolism in the Arabidopsis seed coat.
    PLoS Genet., 2014. 10(12): p. e1004856
  27. 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
  28. Ezquer I, et al.
    The Developmental Regulator SEEDSTICK Controls Structural and Mechanical Properties of the Arabidopsis Seed Coat.
    Plant Cell, 2016. 28(10): p. 2478-2492
  29. Rounsley SD,Ditta GS,Yanofsky MF
    Diverse roles for MADS box genes in Arabidopsis development.
    Plant Cell, 1995. 7(8): p. 1259-69