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 XP_009150584.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MIKC_MADS
Protein Properties Length: 199aa    MW: 22761.2 Da    PI: 9.065
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009150584.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF68.27.6e-22956148
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                    krienks rqvtf+kRrng++ KA  LSvLC+  vav+++s tgkly 
  XP_009150584.1  9 KRIENKSSRQVTFCKRRNGLIEKARQLSVLCESSVAVLVVSATGKLYN 56
                    79********************************************97 PP
2K-box32.34.3e-1210316637100
           K-box  37 hllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                     +l   +++  s+  L++Le+qLe++l+  R++K++l++e +++ ++kek l een  L +k+ e
  XP_009150584.1 103 NLEEANVDGVSVDSLNSLEEQLETALSVTRATKTKLMMEFLKTRREKEKLLIEENLVLASKVTE 166
                     455667888999**********************************************999865 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006627.824161IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.4E-25172IPR002100Transcription factor, MADS-box
SMARTSM004322.5E-31160IPR002100Transcription factor, MADS-box
CDDcd002655.71E-32279No hitNo description
PRINTSPR004043.5E-23323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003197.5E-211055IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-232338IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-233859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.48580170IPR002487Transcription factor, K-box
PfamPF014864.0E-9107164IPR002487Transcription 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:0010048Biological Processvernalization response
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: 199 aa     Download sequence    Send to blast
MGRKKVEIKR IENKSSRQVT FCKRRNGLIE KARQLSVLCE SSVAVLVVSA TGKLYNSSSG  60
DNLSKIIDRY KIQQADDLQT LDLEEITRNY LPHKKLLELV QSNLEEANVD GVSVDSLNSL  120
EEQLETALSV TRATKTKLMM EFLKTRREKE KLLIEENLVL ASKVTEIWKQ TFLVTRDETS  180
MLPEYRFGNN PPETLSLLK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-15170169MEF2C
5f28_B4e-15170169MEF2C
5f28_C4e-15170169MEF2C
5f28_D4e-15170169MEF2C
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE 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
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
PlantRegMapXP_009150584.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009150584.11e-142PREDICTED: agamous-like MADS-box protein AGL27 isoform X1
SwissprotQ9LSR79e-94AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLM4E6E61e-136M4E6E6_BRARP; Uncharacterized protein
STRINGBra024350.1-P1e-137(Brassica rapa)
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
AT5G65060.14e-96MIKC_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]