PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID 886791
Common NameARALYDRAFT_686235
Organism
Arabidopsis lyrata
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: 233aa    MW: 26541.8 Da    PI: 9.4407
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
886791genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF74.11.1e-23959151
            S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
  SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
            krienks rqvtf+kRrng++ KA  LS+LC+  va+ii+s tg+ly +ss
  886791  9 KRIENKSSRQVTFCKRRNGLMEKARQLSILCESSVALIIISATGRLYSFSS 59
            79***********************************************96 PP
2K-box28.65.8e-111451974799
   K-box  47 slkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
             s+  L++Le+q++++l+  R++K el +e +++lq+kek l een+ L+++l+
  886791 145 SIDCLKSLEEQIKTALSITRARKAELTMEFVKTLQEKEKLLIEENQVLTSQLK 197
             6777*********************************************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
CDDcd002652.48E-33278No hitNo description
SuperFamilySSF554551.57E-26278IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-24323IPR002100Transcription factor, MADS-box
PfamPF003193.1E-221057IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-242338IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-243859IPR002100Transcription factor, MADS-box
PROSITE profilePS512979.219112202IPR002487Transcription factor, K-box
PfamPF014861.1E-7141196IPR002487Transcription 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
Sequence ? help Back to Top
Protein Sequence    Length: 233 aa     Download sequence    Send to blast
MGRRKVEIKR IENKSSRQVT FCKRRNGLME KARQLSILCE SSVALIIISA TGRLYSFSSG  60
DSMAKILSRY ELQQADDLKT LCLNIVDKDQ DRDTLFFTAG IALESLRHGS KLVDLEEKNL  120
NYLSHKELLE IIQCKIEETK SDNVSIDCLK SLEEQIKTAL SITRARKAEL TMEFVKTLQE  180
KEKLLIEENQ VLTSQLKKMG KMKKSRETED ARAMSPENSS RNKPPETLLL LK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-17170169MEF2C
5f28_B2e-17170169MEF2C
5f28_C2e-17170169MEF2C
5f28_D2e-17170169MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap886791
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-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF2144861e-136AF214486.1 Arabidopsis thaliana MADS box protein FCL2 (FCL2) mRNA, partial cds.
GenBankAY2314501e-136AY231450.1 Arabidopsis thaliana MADS affecting flowering 4 variant I (MAF4) mRNA, complete cds.
GenBankAY2314531e-136AY231453.1 Arabidopsis thaliana MADS affecting flowering 4 variant IV (MAF4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020889324.11e-164protein MADS AFFECTING FLOWERING 5 isoform X2
SwissprotQ683D71e-83MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBLD7MT761e-165D7MT76_ARALL; Predicted protein
STRINGAl_scaffold_0008_30551e-166(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM9861987
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G65070.21e-145MIKC_MADS family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]