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_009130489.1
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: 22796.5 Da    PI: 10.1552
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130489.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF75.25.2e-24956148
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                    krienks rqvtf+kRrng++KKA  LS+LC+  va++i+sstgkly 
  XP_009130489.1  9 KRIENKSSRQVTFCKRRNGLMKKARQLSILCESSVALLIVSSTGKLYS 56
                    79********************************************96 PP
2K-box32.63.4e-121101644498
           K-box  44 esLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                     +++s++ L +Le+q +++l+  R++K el++e +++lq+kek l+eenk L ++l
  XP_009130489.1 110 DNMSIESLISLEEQFKSALSLTRARKAELMMEFLKTLQEKEKLLREENKVLASQL 164
                     68*************************************************9987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004325.6E-34160IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.14E-27175IPR002100Transcription factor, MADS-box
PROSITE profilePS5006628.889161IPR002100Transcription factor, MADS-box
CDDcd002651.69E-32278No hitNo description
PRINTSPR004041.3E-24323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003197.8E-231056IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-242338IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-243859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.61780170IPR002487Transcription factor, K-box
PfamPF014865.6E-9108164IPR002487Transcription 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: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
MGRRKVEIKR IENKSSRQVT FCKRRNGLMK KARQLSILCE SSVALLIVSS TGKLYSSSSG  60
DSMAKILTRY KTQHADELKT VDLAEKTRNY LSHEELLEIV QCKLEEAKND NMSIESLISL  120
EEQFKSALSL TRARKAELMM EFLKTLQEKE KLLREENKVL ASQLTKMKKS RFLEAEDERA  180
MSLAKSFGNN TPETLSLLK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-18170169MEF2C
5f28_B2e-18170169MEF2C
5f28_C2e-18170169MEF2C
5f28_D2e-18170169MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.225220.0leaf
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
PlantRegMapXP_009130489.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009130489.11e-139PREDICTED: protein MADS AFFECTING FLOWERING 5-like
SwissprotQ683D71e-90MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBLM4ESV41e-138M4ESV4_BRARP; Uncharacterized protein
STRINGBra031884.1-P1e-139(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
AT5G65070.13e-90MIKC_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]