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

AT5G65060.1

Common Name

AGL70, FCL3, MAF3

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: 196aa MW: 22129.5 Da PI: 8.4455

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G65060.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	62.9	3.5e-20	9	56	1	48
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48 krienks rqvtfskRr+g++ KA LS+LC+ +av+ +s +gkly+ AT5G65060.1 9 KRIENKSSRQVTFSKRRKGLIEKARQLSILCESSIAVVAVSGSGKLYD 56 79********************************************96 PP
2	K-box	40.1	1.5e-14	95	164	29	98
K-box 29 enLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 e L+ q +l ++++ s+ L ++e+qLe++l+ iR+kK+el++e ++ lq++ek l een+ L +++ AT5G65060.1 95 ELLEIVQSKLEESNVDNVSVDSLISMEEQLETALSVIRAKKTELMMEDMKSLQEREKLLIEENQILASQV 164 66777777888888999*************************************************9987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	3.9E-29	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	27.067	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	5.36E-25	1	74	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.2E-22	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.6E-20	10	55	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.2E-22	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.2E-22	38	59	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	11.732	80	170	IPR002487	Transcription factor, K-box
Pfam	PF01486	5.6E-11	95	164	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:0009910	Biological Process	negative regulation of flower development
GO:0010048	Biological Process	vernalization response
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000293	anatomy	guard cell

Sequence ? help Back to Top
Protein Sequence Length: 196 aa Download sequence Send to blast
MGRRKVEIKR IENKSSRQVT FSKRRKGLIE KARQLSILCE SSIAVVAVSG SGKLYDSASG 60 DNMSKIIDRY EIHHADELKA LDLAEKIRNY LPHKELLEIV QSKLEESNVD NVSVDSLISM 120 EEQLETALSV IRAKKTELMM EDMKSLQERE KLLIEENQIL ASQVGKKTFL VIEGDRGMSR 180 ENGSGNKVPE TLSLLK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6byy_A	9e-16	1	70	1	69	MEF2 CHIMERA
6byy_B	9e-16	1	70	1	69	MEF2 CHIMERA
6byy_C	9e-16	1	70	1	69	MEF2 CHIMERA
6byy_D	9e-16	1	70	1	69	MEF2 CHIMERA
6bz1_A	9e-16	1	70	1	69	MEF2 CHIMERA
6bz1_B	9e-16	1	70	1	69	MEF2 CHIMERA
6bz1_C	9e-16	1	70	1	69	MEF2 CHIMERA
6bz1_D	9e-16	1	70	1	69	MEF2 CHIMERA
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.49225	0.0	bud\| flower\| inflorescence\| leaf\| root

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	247217_s_at	1e-118
Expression Atlas	AT5G65060	-
AtGenExpress	AT5G65060	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Mostly expressed in roots, leaves and flowers, and, to a lower extent, in inflorescence, siliques, pollen and shoots. {ECO:0000269\|PubMed:12837945, ECO:0000269\|PubMed:12949148}.

Functional Description ? help Back to Top
Source	Description
TAIR	MADS domain protein - flowering regulator that is closely related to FLC
UniProt	Probable transcription factor involved in the negative regulation of flowering time, probably through the photoperiodic and vernalization pathways; more efficient in cv. Landsberg erecta than in cv. Columbia background. Prevents premature flowering (PubMed:12724541, PubMed:25339407). Involved in the modulation of vernalization impact on flowering according to genotype acclimation to altitude (PubMed:25339407). {ECO:0000269\|PubMed:12724541, ECO:0000269\|PubMed:25339407}.

Function -- GeneRIF ? help Back to Top
Association studies support a correlation between the described MAF2-MAF3 gene rearrangements and flowering time variation in the species [PMID: 19139056]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G65060.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed during vernalization (PubMed:12724541). Regulated by HAM1 and HAM2 via epigenetic modification of chromatins at H4K5 acetylation during flowering (PubMed:23273925). {ECO:0000269\|PubMed:12724541, ECO:0000269\|PubMed:23273925}.

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

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G65060

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY231445	0.0	AY231445.1 Arabidopsis thaliana MADS affecting flowering 3 variant I (MAF3) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_201311.1	1e-137	K-box region and MADS-box transcription factor family protein
Swissprot	Q9LSR7	1e-139	AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBL	C0J8J7	1e-135	C0J8J7_ARATH; MAF3
STRING	AT5G65060.1	1e-137	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM986	19	87
Representative plant	OGRP16	17	761

Link Out ? help Back to Top
Phytozome	AT5G65060.1
Entrez Gene	836630
iHOP	AT5G65060
wikigenes	AT5G65060

Publications ? help Back to Top
Alvarez-Buylla ER, et al. MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J., 2000. 24(4): p. 457-66 [PMID:11115127] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Ratcliffe OJ,Kumimoto RW,Wong BJ,Riechmann JL Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold. Plant Cell, 2003. 15(5): p. 1159-69 [PMID:12724541] 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] Kofuji R, et al. Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses. Mol. Biol. Evol., 2003. 20(12): p. 1963-77 [PMID:12949148] Scheible WR, et al. Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol., 2004. 136(1): p. 2483-99 [PMID:15375205] Albert VA, et al. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol., 2005. 5: p. 5 [PMID:15799777] 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] Wang J,Tian L,Lee HS,Chen ZJ Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids. Genetics, 2006. 173(2): p. 965-74 [PMID:16547097] Timms L, et al. Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics, 2006. 173(4): p. 2227-35 [PMID:16783026] Conte MG,Gaillard S,Droc G,Perin C Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. BMC Genomics, 2008. 9: p. 183 [PMID:18426584] Cao Y,Dai Y,Cui S,Ma L Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis. Plant Cell, 2008. 20(10): p. 2586-602 [PMID:18849490] Caicedo AL,Richards C,Ehrenreich IM,Purugganan MD Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis thaliana MAF2-5 flowering time gene cluster. Mol. Biol. Evol., 2009. 26(3): p. 699-711 [PMID:19139056] 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] Rosloski SM, et al. Functional analysis of splice variant expression of MADS AFFECTING FLOWERING 2 of Arabidopsis thaliana. Plant Mol. Biol., 2013. 81(1-2): p. 57-69 [PMID:23111501] Xiao J, et al. Requirement of histone acetyltransferases HAM1 and HAM2 for epigenetic modification of FLC in regulating flowering in Arabidopsis. J. Plant Physiol., 2013. 170(4): p. 444-51 [PMID:23273925] Suter L,Rüegg M,Zemp N,Hennig L,Widmer A Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. Plant Physiol., 2014. 166(4): p. 1928-42 [PMID:25339407] Nasim Z,Fahim M,Ahn JH Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay. Front Plant Sci, 2017. 8: p. 191 [PMID:28261246]