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 RrC2764_p2
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: 163aa    MW: 18231.9 Da    PI: 7.4153
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC2764_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF65.17.5e-21956148
                S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
      SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                k ienks rqvtfskRr+g++ KA  LSvLC+  vav+++s +gkly 
  RrC2764_p2  9 KLIENKSSRQVTFSKRRTGLIEKARQLSVLCESSVAVLVVSASGKLYN 56
                569*******************************************97 PP
2K-box25.74.7e-10941502884
       K-box  28 ienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkke 84 
                 +e L++ + +l   ++++ s+  L +Le+qLe++l   R++K+el +e ++ lq+k 
  RrC2764_p2  94 NELLESVKSNLEESNVDNVSVDSLISLEDQLETALCATRARKTELKMEFVKMLQEKV 150
                 77888888889999999*************************************997 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
SuperFamilySSF554551.96E-25173IPR002100Transcription factor, MADS-box
SMARTSM004321.8E-30160IPR002100Transcription factor, MADS-box
PRINTSPR004046.3E-22323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.5E-201155IPR002100Transcription factor, MADS-box
PRINTSPR004046.3E-222338IPR002100Transcription factor, MADS-box
PRINTSPR004046.3E-223859IPR002100Transcription factor, MADS-box
PROSITE profilePS512978.01580163IPR002487Transcription factor, K-box
PfamPF014868.5E-794151IPR002487Transcription 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: 163 aa     Download sequence    Send to blast
MGRRKVEIKL IENKSSRQVT FSKRRTGLIE KARQLSVLCE SSVAVLVVSA SGKLYNSSSG  60
DNMTNIIDRY EIQHAGELRS LDLAEKTRIY LPHNELLESV KSNLEESNVD NVSVDSLISL  120
EDQLETALCA TRARKTELKM EFVKMLQEKV SATIPVIIGY ADS
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}.
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_018439874.11e-100PREDICTED: agamous-like MADS-box protein AGL27
SwissprotQ9LSR72e-78AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLM4ESV81e-96M4ESV8_BRARP; Uncharacterized protein
STRINGBra031888.1-P2e-97(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
AT5G65060.17e-68MIKC_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]