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_009130487.1
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: 183aa    MW: 20498.4 Da    PI: 9.0553
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130487.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF64.89.4e-21956148
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                    k ienks rqvtfskRr+g++ KA  LSvLC+  vav+++s +gkly 
  XP_009130487.1  9 KLIENKSSRQVTFSKRRTGLIEKARQLSVLCESSVAVLVVSASGKLYN 56
                    569*******************************************97 PP
2K-box37.31.1e-13981554198
           K-box  41 edLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                     e+++s s+  L +Le+qLe++l+  R++K+el +e ++ lq+ke+ l+een  L +++
  XP_009130487.1  98 ESVKSVSVDSLISLEDQLETALSATRARKTELTMEFVKMLQEKEELLREENLVLVSQI 155
                     78999**********************************************9999887 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF554553.4E-25173IPR002100Transcription factor, MADS-box
PROSITE profilePS5006627.081161IPR002100Transcription factor, MADS-box
SMARTSM004321.8E-30160IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004048.0E-22323IPR002100Transcription factor, MADS-box
PfamPF003191.9E-201155IPR002100Transcription factor, MADS-box
PRINTSPR004048.0E-222338IPR002100Transcription factor, MADS-box
PRINTSPR004048.0E-223859IPR002100Transcription factor, MADS-box
PROSITE profilePS512979.72470161IPR002487Transcription factor, K-box
PfamPF014861.0E-1096154IPR002487Transcription 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: 183 aa     Download sequence    Send to blast
MGRRKVEIKL IENKSSRQVT FSKRRTGLIE KARQLSVLCE SSVAVLVVSA SGKLYNSSSG  60
DNMTNIVDRY EIQHAGELRS LDLAEKTRNY LPHKELLESV KSVSVDSLIS LEDQLETALS  120
ATRARKTELT MEFVKMLQEK EELLREENLV LVSQIGTTNG RRENNSPVNS SGINPPETLP  180
LLK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.130761e-173flower| 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_009130487.1
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1667412e-98AC166741.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH080C09, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009130487.11e-128PREDICTED: agamous-like MADS-box protein AGL27 isoform X2
SwissprotQ9LSR73e-83AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLA0A398AGN21e-127A0A398AGN2_BRACM; Uncharacterized protein
STRINGBo2g166500.11e-115(Brassica oleracea)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G65060.11e-63MIKC_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]