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_02910.1_g00001.1
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: 254aa    MW: 29407.3 Da    PI: 7.9926
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02910.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF95.62.1e-30959151
                             S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                   SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                             krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifss+gk ye++s
  Rsa1.0_02910.1_g00001.1  9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSSRGKQYEFCS 59
                             79***********************************************96 PP
2K-box92.95.6e-31931751698
                    K-box  16 slqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                              ++q+e+ kLk++++ Lqr+qR+llGedL++Ls keL++Le+qL++slk+iR+ +++++l+q+++lq ke++l e+nk+Lr +l
  Rsa1.0_02910.1_g00001.1  93 NSQHEYLKLKERYDALQRTQRNLLGEDLGPLSTKELESLERQLDSSLKQIRALRTQFMLDQLNDLQSKERMLAETNKTLRLRL 175
                              789****************************************************************************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.828161IPR002100Transcription factor, MADS-box
SMARTSM004321.4E-40160IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.88E-33276IPR002100Transcription factor, MADS-box
CDDcd002651.39E-44276No hitNo description
PRINTSPR004046.5E-32323IPR002100Transcription factor, MADS-box
PfamPF003192.1E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004046.5E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004046.5E-323859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129715.28291181IPR002487Transcription factor, K-box
PfamPF014861.9E-2593175IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001708Biological Processcell fate specification
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010093Biological Processspecification of floral organ identity
GO:0048481Biological Processplant ovule development
GO:0048833Biological Processspecification of floral organ number
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: 254 aa     Download sequence    Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVALIIFSS RGKQYEFCSS  60
SSMLRTLDRY QKCNYGAPEP NVPSREALAV ELNSQHEYLK LKERYDALQR TQRNLLGEDL  120
GPLSTKELES LERQLDSSLK QIRALRTQFM LDQLNDLQSK ERMLAETNKT LRLRLADGYQ  180
MPLQLNPNPE DHHHVEYGRH QQVHEHSQQA FFQPLECEPI LQMGYQGQQD HGMGAGPSVN  240
NYMLGWLPYD TNSI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A6e-65751781104Developmental protein SEPALLATA 3
4ox0_B6e-65751781104Developmental protein SEPALLATA 3
4ox0_C6e-65751781104Developmental protein SEPALLATA 3
4ox0_D6e-65751781104Developmental protein SEPALLATA 3
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor active in inflorescence development and floral organogenesis.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00605ChIP-seqTransfer from AT1G24260Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02910.1_g00001.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKC9679600.0KC967960.1 Brassica oleracea var. viridis SEP3 (SEP3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018480830.10.0PREDICTED: developmental protein SEPALLATA 3 isoform X1
SwissprotO040671e-169AGL9_SINAL; Agamous-like MADS-box protein AGL9 homolog
TrEMBLA0A078GSN30.0A0A078GSN3_BRANA; BnaA09g28040D protein
TrEMBLA0A397Y0Q10.0A0A397Y0Q1_BRACM; Uncharacterized protein
STRINGBra032814.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM62202644
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G24260.21e-169MIKC_MADS family protein
Publications ? help Back to Top
  1. Bonhomme F,Sommer H,Bernier G,Jacqmard A
    Characterization of SaMADS D from Sinapis alba suggests a dual function of the gene: in inflorescence development and floral organogenesis.
    Plant Mol. Biol., 1997. 34(4): p. 573-82
    [PMID:9247539]