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

AT3G02310.1

Common Name

AGL4, F14P3.4, SEP2

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: 250aa MW: 28577.5 Da PI: 8.5487

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G02310.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	98.8	2.2e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtf+kRrng+lKKA+ELSvLCdaev++i+fs++gklye++s AT3G02310.1 9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVSLIVFSNRGKLYEFCS 59 79***********************************************96 PP
2	K-box	93.4	3.9e-31	78	173	4	99
K-box 4 ssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 + +++ +++ e++++e+ kLk ++enLqr+qR+llGedL++L+ keL+qLe+qL+ slk++R K++++l+q+++lq ke+ l ++n+aL++kle AT3G02310.1 78 IEVNNKPAKELENSYREYLKLKGRYENLQRQQRNLLGEDLGPLNSKELEQLERQLDGSLKQVRCIKTQYMLDQLSDLQGKEHILLDANRALSMKLE 173 56667788999**********************************************************************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.319	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	4.2E-41	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	7.93E-45	2	77	No hit	No description
SuperFamily	SSF55455	1.11E-33	2	80	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.8E-32	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	9.9E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.8E-32	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.8E-32	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	9.0E-25	85	172	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	14.39	88	178	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:0009611	Biological Process	response to wounding
GO:0030154	Biological Process	cell differentiation
GO:0048481	Biological Process	plant ovule development
GO:0071486	Biological Process	cellular response to high light intensity
GO:0071492	Biological Process	cellular response to UV-A
GO:0005634	Cellular Component	nucleus
GO:0009523	Cellular Component	photosystem II
GO:0016021	Cellular Component	integral component of membrane
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:0000037	anatomy	shoot apex
PO:0009001	anatomy	fruit
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:0009052	anatomy	flower pedicel
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007602	developmental stage	floral organ primordium development stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 250 aa Download sequence Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVSLIVFSN RGKLYEFCST 60 SNMLKTLERY QKCSYGSIEV NNKPAKELEN SYREYLKLKG RYENLQRQQR NLLGEDLGPL 120 NSKELEQLER QLDGSLKQVR CIKTQYMLDQ LSDLQGKEHI LLDANRALSM KLEDMIGVRH 180 HHIGGGWEGG DQQNIAYGHP QAHSQGLYQS LECDPTLQIG YSHPVCSEQM AVTVQGQSQQ 240 GNGYIPGWML

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ox0_A	6e-33	75	174	1	103	Developmental protein SEPALLATA 3
4ox0_B	6e-33	75	174	1	103	Developmental protein SEPALLATA 3
4ox0_C	6e-33	75	174	1	103	Developmental protein SEPALLATA 3
4ox0_D	6e-33	75	174	1	103	Developmental protein SEPALLATA 3
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.41155	0.0	flower\| inflorescence\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	42563430	0.0
Genevisible	259124_at	0.0
Expression Atlas	AT3G02310	-
AtGenExpress	AT3G02310	-
ATTED-II	AT3G02310	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed early during flower development.

Functional Description ? help Back to Top
Source	Description
TAIR	MADS-box protein, binds K domain of AG in vivo
UniProt	Probable transcription factor. Functions with SEPALLATA1/AGL2 and SEPALLATA3/AGL9 to ensure proper development of petals, stamens and carpels and to prevent the indeterminate growth of the flower meristem. Forms a heterodimer via the K-box domain with AG, that could be involved in genes regulation during floral meristem development.

Function -- GeneRIF ? help Back to Top
CLV3, SEPALLATA1 (SEP1), and SEP2 are FHY3 target genes. [PMID: 27469166]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G02310.1

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

Interaction -- BIND ? help Back to Top
Source	Intact With	Description
BIND	AT4G18960	AG interacts with AGL4.

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT3G02310, AT3G57230, AT4G18960, AT4G37940, AT5G23260
IntAct	Search P29384

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Triple mutations in the SEP1, SEP2 and SEP3 genes result in the replacement of the stamens and petals by sepals and of the carpels by a new mutant flower with sepaloid organs. {ECO:0000269\|PubMed:9418042}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G02310

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	ATHAGL4A	0.0	M55552.1 Arabidopsis thaliana transcription factor (AGL4) mRNA, complete cds.
GenBank	BT020478	0.0	BT020478.1 Arabidopsis thaliana At3g02310 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_186880.1	0.0	K-box region and MADS-box transcription factor family protein
Swissprot	P29384	0.0	SEP2_ARATH; Developmental protein SEPALLATA 2
TrEMBL	A0A384L9U7	0.0	A0A384L9U7_ARATH; SEP2
TrEMBL	Q5XXL4	0.0	Q5XXL4_ARATH; At3g02310
STRING	AT3G02310.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3289	27	65
Representative plant	OGRP16	17	761

Link Out ? help Back to Top
Phytozome	AT3G02310.1
Entrez Gene	821151
iHOP	AT3G02310
wikigenes	AT3G02310

Publications ? help Back to Top
Sung SK,Yu GH,Nam J,Jeong DH,An G Developmentally regulated expression of two MADS-box genes, MdMADS3 and MdMADS4, in the morphogenesis of flower buds and fruits in apple. Planta, 2000. 210(4): p. 519-28 [PMID:10787044] Pelaz S,Ditta GS,Baumann E,Wisman E,Yanofsky MF B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature, 2000. 405(6783): p. 200-3 [PMID:10821278] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Pelaz S,Gustafson-Brown C,Kohalmi SE,Crosby WL,Yanofsky MF APETALA1 and SEPALLATA3 interact to promote flower development. Plant J., 2001. 26(4): p. 385-94 [PMID:11439126] Li J,Jia D,Chen X HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear RNA binding protein. Plant Cell, 2001. 13(10): p. 2269-81 [PMID:11595801] 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] Moore RC,Grant SR,Purugganan MD Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana. Mol. Biol. Evol., 2005. 22(1): p. 91-103 [PMID:15371526] Ditta G,Pinyopich A,Robles P,Pelaz S,Yanofsky MF The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr. Biol., 2004. 14(21): p. 1935-40 [PMID:15530395] Yang Y,Jack T Defining subdomains of the K domain important for protein-protein interactions of plant MADS proteins. Plant Mol. Biol., 2004. 55(1): p. 45-59 [PMID:15604664] 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] Malcomber ST,Kellogg EA SEPALLATA gene diversification: brave new whorls. Trends Plant Sci., 2005. 10(9): p. 427-35 [PMID:16099195] 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 [PMID:16280546] Ma H,Yanofsky MF,Meyerowitz EM AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes. Genes Dev., 1991. 5(3): p. 484-95 [PMID:1672119] 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] Jetha K,Thei Arabidopsis SEPALLATA proteins differ in cooperative DNA-binding during the formation of floral quartet-like complexes. Nucleic Acids Res., 2014. 42(17): p. 10927-42 [PMID:25183521] Maejima K, et al. Degradation of class E MADS-domain transcription factors in Arabidopsis by a phytoplasmal effector, phyllogen. Plant Signal Behav, 2015. 10(8): p. e1042635 [PMID:26179462] Wang X, et al. An exon skipping in a SEPALLATA-Like gene is associated with perturbed floral and fruits development in cucumber. J Integr Plant Biol, 2016. 58(9): p. 766-71 [PMID:26936301] Li D, et al. FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9375-80 [PMID:27469166] Savidge B,Rounsley SD,Yanofsky MF Temporal relationship between the transcription of two Arabidopsis MADS box genes and the floral organ identity genes. Plant Cell, 1995. 7(6): p. 721-33 [PMID:7647563] Tandre K,Albert VA,Sund Conifer homologues to genes that control floral development in angiosperms. Plant Mol. Biol., 1995. 27(1): p. 69-78 [PMID:7865797] Greco R, et al. MADS box genes expressed in developing inflorescences of rice and sorghum. Mol. Gen. Genet., 1997. 253(5): p. 615-23 [PMID:9065695] Fan HY,Hu Y,Tudor M,Ma H Specific interactions between the K domains of AG and AGLs, members of the MADS domain family of DNA binding proteins. Plant J., 1997. 12(5): p. 999-1010 [PMID:9418042]