PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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 Name

AGL11, STK, T5L19.90

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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
AT4G09960.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	99.2	1.7e-31	9	58	1	50
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
2	K-box	103.3	3.1e-34	77	173	4	100
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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	7.0E-42	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	34.034	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	5.89E-33	2	82	IPR002100	Transcription factor, MADS-box
CDD	cd00265	8.60E-43	2	76	No hit	No description
PRINTS	PR00404	5.9E-33	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.4E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	5.9E-33	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	5.9E-33	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	4.6E-25	85	171	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	14.506	87	177	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0048316	Biological Process	seed development
GO:0048481	Biological Process	plant ovule development
GO:0080155	Biological Process	regulation of double fertilization forming a zygote and endosperm
GO:0090376	Biological Process	seed trichome differentiation
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020003	anatomy	plant ovule
PO:0020024	anatomy	endothelium
PO:0025022	anatomy	collective leaf structure
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering 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

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_Q	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_R	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_S	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_A	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_B	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_C	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_D	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_E	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_F	2e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.2918	0.0	bud\| flower\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	255014_at	0.0
Expression Atlas	AT4G09960	-
AtGenExpress	AT4G09960	-
ATTED-II	AT4G09960	-

Functional Description ? help Back to Top
Source	Description
TAIR	a MADS box transcription factor expressed in the carpel and ovules
UniProt	Probable 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
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] The stk shp1 shp2 ant quadruple mutant ovule lacks integument development as in ant single mutant. [PMID: 20041269] STK and ABS played a role in the maternal control of endothelium formation, as the abs stk double mutant completely lacks endothelium. [PMID: 22176531] 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] STK might recruit or regulate histone modifying factors to control their activity in Arabidopsis. [PMID: 25521508] 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
Source	Link
PlantRegMap	AT4G09960.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

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
BioGRID	AT4G37940, AT5G13790, AT5G15800, AT1G24260, AT1G48150
IntAct	Search Q38836

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G09960

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	ATU20182	0.0	U20182.1 Arabidopsis thaliana MADS-box protein AGL11 (AGL11) mRNA, complete cds.
GenBank	AY087201	0.0	AY087201.1 Arabidopsis thaliana clone 32791 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001329611.1	1e-168	K-box region and MADS-box transcription factor family protein
Swissprot	Q38836	1e-169	AGL11_ARATH; Agamous-like MADS-box protein AGL11
TrEMBL	A0A1P8B889	1e-167	A0A1P8B889_ARATH; K-box region and MADS-box transcription factor family protein
STRING	AT4G09960.3	1e-167	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT4G09960.1
Entrez Gene	826586
iHOP	AT4G09960
wikigenes	AT4G09960

Publications ? help Back to Top
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] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] 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] Parenicová 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] 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] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] Brambilla V,Kater M,Colombo L Ovule integument identity determination in Arabidopsis. Plant Signal Behav, 2008. 3(4): p. 246-7 [PMID:19704643] 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] 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] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] 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] 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] 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] 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] 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] 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] 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] 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] 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]