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 496727
Common NameARALYDRAFT_496727
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: 178aa    MW: 20169.2 Da    PI: 8.4355
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
496727genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF65.55.6e-21956148
            S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
  SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
            krienks rqvtfskRr+g++ KA  LSvLC+  +av+++s +gkly 
  496727  9 KRIENKSSRQVTFSKRRKGLIEKARQLSVLCESSIAVLVVSGSGKLYN 56
            79********************************************96 PP
2K-box39.22.9e-14951622996
   K-box  29 enLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 
             e L+  q +l   ++++ s+  L ++e+qLe++l+ iR+kK+el++e+++ lq+ e  l+een+ L +
  496727  95 ELLEIVQSKLEEPNVDTVSVDSLISMEEQLETALSVIRAKKTELMMEEVKSLQETEMLLREENQILAS 162
             556666666666778899**********************************************9976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006627.614161IPR002100Transcription factor, MADS-box
SMARTSM004321.2E-30160IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.62E-25171IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-23323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.2E-201055IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-232338IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-233859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129711.23580172IPR002487Transcription factor, K-box
PfamPF014861.1E-1097162IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
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: 178 aa     Download sequence    Send to blast
MGRRKVEIKR IENKSSRQVT FSKRRKGLIE KARQLSVLCE SSIAVLVVSG SGKLYNSASG  60
DNMSKIIDRY EIQRADELKA LDLAEKIRNY LPHKELLEIV QSKLEEPNVD TVSVDSLISM  120
EEQLETALSV IRAKKTELMM EEVKSLQETE MLLREENQIL ASHSQVTKTS LIYDSRS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6bz1_A1e-16170169MEF2 CHIMERA
6bz1_B1e-16170169MEF2 CHIMERA
6bz1_C1e-16170169MEF2 CHIMERA
6bz1_D1e-16170169MEF2 CHIMERA
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap496727
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY2314450.0AY231445.1 Arabidopsis thaliana MADS affecting flowering 3 variant I (MAF3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020889301.11e-123agamous-like MADS-box protein AGL31 isoform X3
SwissprotQ9LSR71e-101AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLD7MT751e-122D7MT75_ARALL; MADS-box protein AGL27-I
STRINGfgenesh2_kg.8__2543__AT5G65050.21e-122(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
AT5G65060.11e-103MIKC_MADS family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]