PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC25_p9
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family MIKC_MADS
Protein Properties Length: 234aa    MW: 26343.6 Da    PI: 8.4637
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC25_p9genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF70.21.8e-22956148
              S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
    SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
              krienks rqvtf+kRrng++ KA  LS+LC+  vav+i+sstgk+y 
  RrC25_p9  9 KRIENKSSRQVTFCKRRNGLMEKARQLSILCGSSVAVLIVSSTGKVYS 56
              79********************************************96 PP
2K-box35.83.4e-131202001699
     K-box  16 slqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
               + ++++  Lk+ +e+ q +   l   +++++sl+ L +Le+q +++l+  R+kK+el++e +++ q+kek l++en+ L ++l+
  RrC25_p9 120 EKTRNYLSLKELLESVQGK---LEEANIDNISLESLISLEEQFKTALSLARAKKTELMMELVKTFQEKEKLLRDENTVLASQLA 200
               5556666777777776665...77789****************************************************99986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006627.698161IPR002100Transcription factor, MADS-box
SMARTSM004321.0E-32160IPR002100Transcription factor, MADS-box
SuperFamilySSF554558.11E-24161IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-22323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.8E-221056IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-222338IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-223859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129711.201115205IPR002487Transcription factor, K-box
PfamPF014866.0E-8130199IPR002487Transcription 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: 234 aa     Download sequence    Send to blast
MGRRKMEIKR IENKSSRQVT FCKRRNGLME KARQLSILCG SSVAVLIVSS TGKVYSSSSG  60
DSFNGLFIMR FCFCLDLSTA WPRSSSIMKY DMLMSLKPCL TPLNFVSTSA TGPLIEDLKE  120
KTRNYLSLKE LLESVQGKLE EANIDNISLE SLISLEEQFK TALSLARAKK TELMMELVKT  180
FQEKEKLLRD ENTVLASQLA KTGKENEFLE TEGERAMLLE YSSGNNPPET LPLL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1mnm_A7e-153591874PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR)
1mnm_B7e-153591874PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR)
Search in ModeBase
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}.
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1667412e-55AC166741.1 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_018493416.11e-111PREDICTED: protein MADS AFFECTING FLOWERING 5-like
SwissprotQ683D71e-71MAF5_ARATH; Protein MADS AFFECTING FLOWERING 5
TrEMBLA0A3P6AQW01e-102A0A3P6AQW0_BRAOL; Uncharacterized protein
STRINGBra024351.1-P4e-99(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
AT5G65070.36e-69MIKC_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]