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 RrC1523_p4
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: 141aa    MW: 16207.7 Da    PI: 10.4723
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1523_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF94.35.7e-30959151
                S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
      SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++ klye+ss
  RrC1523_p4  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPSSKLYEFSS 59
                79***********************************************96 PP
2K-box55.72.1e-1981141969
       K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskK 69 
                 + + ++++++ e   L k+ie+L+ ++R+llGe+++ +s++eLqqLe+qLe++l++iR+kK
  RrC1523_p4  81 KRDDNSQQSRGETYGLTKKIEQLEISKRKLLGEGIDACSIEELQQLENQLERGLTRIRAKK 141
                 6788899999**************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.413161IPR002100Transcription factor, MADS-box
SMARTSM004324.4E-40160IPR002100Transcription factor, MADS-box
CDDcd002651.80E-40370No hitNo description
SuperFamilySSF554556.41E-33374IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004042.1E-30323IPR002100Transcription factor, MADS-box
PfamPF003197.8E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004042.1E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004042.1E-303859IPR002100Transcription factor, MADS-box
PfamPF014864.1E-1783141IPR002487Transcription factor, K-box
PROSITE profilePS512971186141IPR002487Transcription 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: 141 aa     Download sequence    Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP SSKLYEFSSS  60
GMAKTIERYQ RRVKEIGINH KRDDNSQQSR GETYGLTKKI EQLEISKRKL LGEGIDACSI  120
EELQQLENQL ERGLTRIRAK K
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3mu6_A3e-20369268Myocyte-specific enhancer factor 2A
3mu6_B3e-20369268Myocyte-specific enhancer factor 2A
3mu6_C3e-20369268Myocyte-specific enhancer factor 2A
3mu6_D3e-20369268Myocyte-specific enhancer factor 2A
6byy_A3e-20169169MEF2 CHIMERA
6byy_B3e-20169169MEF2 CHIMERA
6byy_C3e-20169169MEF2 CHIMERA
6byy_D3e-20169169MEF2 CHIMERA
6bz1_A3e-20169169MEF2 CHIMERA
6bz1_B3e-20169169MEF2 CHIMERA
6bz1_C3e-20169169MEF2 CHIMERA
6bz1_D3e-20169169MEF2 CHIMERA
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. {ECO:0000269|PubMed:16778081}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Maintained at very low levels by the polycomb-group (PcG) proteins MSI1, CLF, and EMF2 via histone methylation (H3K27me3). Derepressed upon cold treatment (vernalization). {ECO:0000269|PubMed:16778081}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3126641e-135AF312664.1 Arabidopsis thaliana MADS-box protein AGL19 (AGL19) mRNA, complete cds.
GenBankAY1425231e-135AY142523.1 Arabidopsis thaliana putative MADS box AGL protein (At4g22950) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018444499.11e-97PREDICTED: agamous-like MADS-box protein AGL19
SwissprotO827431e-87AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A398ALC21e-93A0A398ALC2_BRACM; Uncharacterized protein
STRINGBo1g031900.12e-91(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM7828413
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.11e-80AGAMOUS-like 19
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. 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]