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 AT4G09960.1
Common NameAGL11, STK, T5L19.90
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 MIKC_MADS
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
1SRF-TF99.21.7e-31958150
                 S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                 krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva+i+fs++g+lyey+
  AT4G09960.1  9 KRIENSTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSTRGRLYEYA 58
                 79***********************************************8 PP

2K-box103.33.1e-34771734100
        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
  AT4G09960.1  77 TNTSTVQEINAAYYQQESAKLRQQIQTIQNSNRNLMGDSLSSLSVKELKQVENRLEKAISRIRSKKHELLLVEIENAQKREIELDNENIYLRTKVAE 173
                  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:0009010anatomyseed
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020003anatomyplant ovule
PO:0020024anatomyendothelium
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
MGRGKIEIKR IENSTNRQVT FCKRRNGLLK KAYELSVLCD AEVALIVFST RGRLYEYANN  60
NIRSTIERYK KACSDSTNTS TVQEINAAYY QQESAKLRQQ IQTIQNSNRN LMGDSLSSLS  120
VKELKQVENR LEKAISRIRS KKHELLLVEI ENAQKREIEL DNENIYLRTK VAEVERYQQH  180
HHQMVSGSEI NAIEALASRN YFAHSIMTAG SGSGNGGSYS DPDKKILHLG
3D Structure ? help Back to Top
Structure
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
Genevisible255014_at0.0
Expression AtlasAT4G09960-
AtGenExpressAT4G09960-
ATTED-IIAT4G09960-
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
SourceLink
PlantRegMapAT4G09960.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
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
    [PMID:10074717]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  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
    [PMID:12481066]
  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
    [PMID:12837945]
  5. Favaro R, et al.
    MADS-box protein complexes control carpel and ovule development in Arabidopsis.
    Plant Cell, 2003. 15(11): p. 2603-11
    [PMID:14555696]
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  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
    [PMID:15722463]
  8. de Folter S, et al.
    Comprehensive interaction map of the Arabidopsis MADS Box transcription factors.
    Plant Cell, 2005. 17(5): p. 1424-33
    [PMID:15805477]
  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
    [PMID:16080001]
  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
    [PMID:16236468]
  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
    [PMID:16515858]
  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
    [PMID:16925602]
  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
    [PMID:17110585]
  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
    [PMID:17693535]
  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
    [PMID:18512328]
  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
    [PMID:19409800]
  17. Brambilla V,Kater M,Colombo L
    Ovule integument identity determination in Arabidopsis.
    Plant Signal Behav, 2008. 3(4): p. 246-7
    [PMID:19704643]
  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
    [PMID:20041269]
  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
    [PMID:20581305]
  20. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  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
    [PMID:21810995]
  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
    [PMID:22176531]
  23. Severing EI, et al.
    Predicting the impact of alternative splicing on plant MADS domain protein function.
    PLoS ONE, 2012. 7(1): p. e30524
    [PMID:22295091]
  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
    [PMID:23054472]
  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
    [PMID:23847151]
  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
    [PMID:25521508]
  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
    [PMID:25750178]
  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
    [PMID:27624758]
  29. Rounsley SD,Ditta GS,Yanofsky MF
    Diverse roles for MADS box genes in Arabidopsis development.
    Plant Cell, 1995. 7(8): p. 1259-69
    [PMID:7549482]