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 Rsa1.0_00297.1_g00012.1
Organism
Raphanus sativus
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: 221aa    MW: 24924.5 Da    PI: 9.1612
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00297.1_g00012.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF93.97.2e-30959151
                             S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                   SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                             krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs+t klye+ss
  Rsa1.0_00297.1_g00012.1  9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPTSKLYEFSS 59
                             79***********************************************96 PP
2K-box72.41.3e-2481170998
                    K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 
                               ++ ++++ + e   L k+ie+L  ++R+llGe+++ +s++eL+qLe+qLe++l++iR+kK++ll+e+ie+l++ e +l +enk+L
  Rsa1.0_00297.1_g00012.1  81 RDADHSQQARGETYGLTKKIEQLGISKRKLLGEGIDVCSIEELHQLENQLERGLTRIRAKKYQLLREEIEKLKEEEMNLIKENKEL 166
                              5667788899999************************************************************************* PP

                    K-box  95 rkkl 98 
                              ++kl
  Rsa1.0_00297.1_g00012.1 167 NEKL 170
                              *997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004324.4E-39160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.16161IPR002100Transcription factor, MADS-box
SuperFamilySSF554556.28E-32373IPR002100Transcription factor, MADS-box
CDDcd002657.48E-41371No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-30323IPR002100Transcription factor, MADS-box
PfamPF003191.5E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004045.6E-303859IPR002100Transcription factor, MADS-box
PfamPF014869.8E-2582170IPR002487Transcription factor, K-box
PROSITE profilePS5129713.88186176IPR002487Transcription 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: 221 aa     Download sequence    Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP TSKLYEFSSC  60
SIAKTIERYQ KRVKEIGTSK RDADHSQQAR GETYGLTKKI EQLGISKRKL LGEGIDVCSI  120
EELHQLENQL ERGLTRIRAK KYQLLREEIE KLKEEEMNLI KENKELNEKL SGTGAIVVAS  180
SSSTLTSSEV NTDGNDNMEV ETGLFIGPPE PRQSKKLCPQ S
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-18169169MEF2C
5f28_B1e-18169169MEF2C
5f28_C1e-18169169MEF2C
5f28_D1e-18169169MEF2C
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00297.1_g00012.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018448945.11e-160PREDICTED: agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_018448946.11e-160PREDICTED: agamous-like MADS-box protein AGL19 isoform X1
SwissprotO827431e-118AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A0D3BL251e-135A0A0D3BL25_BRAOL; Uncharacterized protein
TrEMBLA0A3P6B0L91e-135A0A3P6B0L9_BRAOL; Uncharacterized protein
STRINGBo3g165710.11e-136(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-101AGAMOUS-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]