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 AT5G65070.2
Common NameAGL69, FCL4, MAF4
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: 231aa    MW: 26405.6 Da    PI: 9.2265
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G65070.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF74.21.1e-23959151
                 S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                 krienks rqvtf+kRrng++ KA  LS+LC+  va+ii+s tg+ly +ss
  AT5G65070.2  9 KRIENKSSRQVTFCKRRNGLMEKARQLSILCESSVALIIISATGRLYSFSS 59
                 79***********************************************96 PP

2K-box33.91.3e-121431954698
        K-box  46 LslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                   s+  L++Le+qL+++l+  R++K+el++e +++ q+kek l+een++L+++l
  AT5G65070.2 143 VSIDCLKSLEEQLKTALSVTRARKTELMMELVKTHQEKEKLLREENQSLTNQL 195
                  57778********************************************9986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.1E-32160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006629.254161IPR002100Transcription factor, MADS-box
CDDcd002651.53E-33278No hitNo description
SuperFamilySSF554551.83E-26277IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-24323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003193.0E-221057IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-242338IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-243859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.13111204IPR002487Transcription factor, K-box
PfamPF014861.0E-8140195IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009910Biological Processnegative regulation of flower development
GO:0005634Cellular Componentnucleus
GO:0016021Cellular Componentintegral component of membrane
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
PO:0020030anatomycotyledon
PO:0020100anatomyhypocotyl
Sequence ? help Back to Top
Protein Sequence    Length: 231 aa     Download sequence    Send to blast
MGRRKVEIKR IENKSSRQVT FCKRRNGLME KARQLSILCE SSVALIIISA TGRLYSFSSG  60
DSMAKILSRY ELEQADDLKT LCLNIVERDQ HRITLFFTVG IALESPRRGS KLDLEEKTLN  120
YLSHKELLET IQCKIEEAKS DNVSIDCLKS LEEQLKTALS VTRARKTELM MELVKTHQEK  180
EKLLREENQS LTNQLIKMGK MKKSVEAEDA RAMSPESSSD NKPPETLLLL K
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-17170169MEF2C
5f28_B1e-17170169MEF2C
5f28_C1e-17170169MEF2C
5f28_D1e-17170169MEF2C
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible247223_at0.0
Expression AtlasAT5G65070-
AtGenExpressAT5G65070-
Functional Description ? help Back to Top
Source Description
TAIREncodes MADS-box containing FLC paralog. Five splice variants have been identified but not characterized with respect to expression patterns and/or differing function. Overexpression of the gene in the Landsberg ecotype leads to a delay in flowering, transcript levels of MAF4 are reduced after a 6 week vernalization.
UniProtTranscription factor involved in the negative regulation of flowering time in short days, probably through the photoperiodic and vernalization pathways. Prevents premature flowering, particularly in the cv. Landsberg erecta background. In non-inductive photoperiods (e.g. short days), required for flowering through VIL2-mediated maintenance of the epigenetically repressed state of MAF5 via H3K9me2 and plant homeodomain / polycomb repressive complex 2 (PHD-PRC2)-dependent H3K27me3. {ECO:0000269|PubMed:12724541, ECO:0000269|PubMed:18798874, ECO:0000269|PubMed:18852898, ECO:0000269|PubMed:20837520, ECO:0000269|PubMed:21150261, ECO:0000269|PubMed:21175890, ECO:0000269|PubMed:21398257, ECO:0000269|PubMed:22378382}.
Function -- GeneRIF ? help Back to Top
  1. MADS AFFECTING FLOWERING 4 (MAF4) and MAF5 are also upregulated in TEK knockdown plants.
    [PMID: 23733063]
  2. RING1A suppresses the expression of MAF4 and MAF5 through affecting H3K27me3 levels at these loci to regulate the floral transition
    [PMID: 24553292]
  3. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3
    [PMID: 30498193]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G65070.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by vernalization. Repressed by VIL2, AGL6, CLF, EMF2 and FIE via epigenetic chromatin H3K27me3 and H3K9me2 regulation during the vegetative development. {ECO:0000269|PubMed:12724541}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G65070
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF2144860.0AF214486.1 Arabidopsis thaliana MADS box protein FCL2 (FCL2) mRNA, partial cds.
GenBankAY2314500.0AY231450.1 Arabidopsis thaliana MADS affecting flowering 4 variant I (MAF4) mRNA, complete cds.
GenBankAY2314530.0AY231453.1 Arabidopsis thaliana MADS affecting flowering 4 variant IV (MAF4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001119499.11e-166K-box region and MADS-box transcription factor family protein
SwissprotQ683D71e-82MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBLQ9LSR61e-165Q9LSR6_ARATH; K-box region and MADS-box transcription factor family protein
STRINGAl_scaffold_0008_30551e-141(Arabidopsis lyrata)
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Rossel JB,Wilson IW,Pogson BJ
    Global changes in gene expression in response to high light in Arabidopsis.
    Plant Physiol., 2002. 130(3): p. 1109-20
    [PMID:12427978]
  3. 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]
  4. 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]
  5. 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]
  6. N
    Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry.
    Mol. Cell Proteomics, 2003. 2(11): p. 1234-43
    [PMID:14506206]
  7. Albert VA, et al.
    Floral gene resources from basal angiosperms for comparative genomics research.
    BMC Plant Biol., 2005. 5: p. 5
    [PMID:15799777]
  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. Pina C,Pinto F,Feij
    Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation.
    Plant Physiol., 2005. 138(2): p. 744-56
    [PMID:15908605]
  10. Deal RB,Kandasamy MK,McKinney EC,Meagher RB
    The nuclear actin-related protein ARP6 is a pleiotropic developmental regulator required for the maintenance of FLOWERING LOCUS C expression and repression of flowering in Arabidopsis.
    Plant Cell, 2005. 17(10): p. 2633-46
    [PMID:16141450]
  11. 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]
  12. 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]
  13. Deal RB,Topp CN,McKinney EC,Meagher RB
    Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z.
    Plant Cell, 2007. 19(1): p. 74-83
    [PMID:17220196]
  14. 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]
  15. Xu L, et al.
    The E2 ubiquitin-conjugating enzymes, AtUBC1 and AtUBC2, play redundant roles and are involved in activation of FLC expression and repression of flowering in Arabidopsis thaliana.
    Plant J., 2009. 57(2): p. 279-88
    [PMID:18798874]
  16. 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]
  17. Day RC,Herridge RP,Ambrose BA,Macknight RC
    Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation.
    Plant Physiol., 2008. 148(4): p. 1964-84
    [PMID:18923020]
  18. 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]
  19. Yu CW, et al.
    HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis.
    Plant Physiol., 2011. 156(1): p. 173-84
    [PMID:21398257]
  20. 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]
  21. Xu Y,Gan ES,Ito T
    The AT-hook/PPC domain protein TEK negatively regulates floral repressors including MAF4 and MAF5.
    Plant Signal Behav, 2014.
    [PMID:23733063]
  22. Shen L, et al.
    The putative PRC1 RING-finger protein AtRING1A regulates flowering through repressing MADS AFFECTING FLOWERING genes in Arabidopsis.
    Development, 2014. 141(6): p. 1303-12
    [PMID:24553292]
  23. Liu B, et al.
    Interplay of the histone methyltransferases SDG8 and SDG26 in the regulation of transcription and plant flowering and development.
    Biochim. Biophys. Acta, 2016. 1859(4): p. 581-90
    [PMID:26854085]
  24. Gong X,Shen L,Peng YZ,Gan Y,Yu H
    DNA Topoisomerase Iα Affects the Floral Transition.
    Plant Physiol., 2017. 173(1): p. 642-654
    [PMID:27837087]
  25. Cui Z, et al.
    SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis.
    BMC Biol., 2017. 15(1): p. 80
    [PMID:28893254]
  26. Zhao X, et al.
    Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA.
    Nat Commun, 2018. 9(1): p. 5056
    [PMID:30498193]