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_009130486.1
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: 192aa    MW: 21496.4 Da    PI: 6.5594
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130486.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF64.61e-20956148
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                    k ienks rqvtfskRr+g++ KA  LSvLC+  vav+++s +gkly 
  XP_009130486.1  9 KLIENKSSRQVTFSKRRTGLIEKARQLSVLCESSVAVLVVSASGKLYN 56
                    569*******************************************97 PP
2K-box37.69.7e-141021643698
           K-box  36 RhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                      +l   +++s s+  L +Le+qLe++l+  R++K+el +e ++ lq+ke+ l+een  L +++
  XP_009130486.1 102 SNLEEPNVDSVSVDSLISLEDQLETALSATRARKTELTMEFVKMLQEKEELLREENLVLVSQI 164
                     55555678999*********************************************9999887 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006627.081161IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.92E-25173IPR002100Transcription factor, MADS-box
SMARTSM004321.8E-30160IPR002100Transcription factor, MADS-box
PRINTSPR004048.9E-22323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.0E-201155IPR002100Transcription factor, MADS-box
PRINTSPR004048.9E-222338IPR002100Transcription factor, MADS-box
PRINTSPR004048.9E-223859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.2380170IPR002487Transcription factor, K-box
PfamPF014861.3E-10104163IPR002487Transcription 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: 192 aa     Download sequence    Send to blast
MGRRKVEIKL IENKSSRQVT FSKRRTGLIE KARQLSVLCE SSVAVLVVSA SGKLYNSSSG  60
DNMTNIVDRY EIQHAGELRS LDLAEKTRNY LPHKELLESV KSNLEEPNVD SVSVDSLISL  120
EDQLETALSA TRARKTELTM EFVKMLQEKE ELLREENLVL VSQIGTTNGR RENNSPVNSS  180
GINPPETLPL LK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.130760.0flower| root
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_009130486.1
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_009130486.11e-135PREDICTED: agamous-like MADS-box protein AGL27 isoform X1
SwissprotQ9LSR72e-90AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLA0A078GXS51e-134A0A078GXS5_BRANA; BnaA02g34510D protein
TrEMBLA0A3G5BC841e-134A0A3G5BC84_BRARC; Maf-like protein
STRINGBo2g166500.11e-124(Brassica oleracea)
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
AT1G77080.41e-65MIKC_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]