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 RrC338_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: 227aa    MW: 26410.4 Da    PI: 8.2119
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC338_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.34.3e-28959151
               S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
     SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
               krie+ + rqvtfskRr+g+lKKA+ELSvLCda+va i+fs+tg+ly+++s
  RrC338_p4  9 KRIEDMTSRQVTFSKRRKGLLKKAHELSVLCDAQVAAIVFSQTGRLYDFAS 59
               79***********************************************86 PP
2K-box50.31e-17841711094
      K-box  10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkk...ekelqeenkaL 94 
                +++   +l++e+a + ++ie Lq   R+l+G+dL+s+s++eL+++ +++eksl+ +Rs+K +l  ++ie+l+     e+e  +e  +L
  RrC338_p4  84 KQQYVRELKNEMAIMMDKIEILQLHCRKLMGQDLDSCSVEELKEITTKIEKSLTIVRSRKAKLNEDNIEKLKAEivaEREGLNERSRL 171
                55667899***************999*********************************************97522244444555555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.6E-40160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.511161IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.79E-30370IPR002100Transcription factor, MADS-box
PRINTSPR004046.9E-29323IPR002100Transcription factor, MADS-box
CDDcd002651.55E-39368No hitNo description
PfamPF003192.1E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004046.9E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004046.9E-293859IPR002100Transcription factor, MADS-box
PfamPF014865.6E-1786174IPR002487Transcription factor, K-box
PROSITE profilePS5129711.96788189IPR002487Transcription 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: 227 aa     Download sequence    Send to blast
MVRGKIEIKR IEDMTSRQVT FSKRRKGLLK KAHELSVLCD AQVAAIVFSQ TGRLYDFASS  60
DMQKMIDRCE IHRGEYFGAE RLQKQQYVRE LKNEMAIMMD KIEILQLHCR KLMGQDLDSC  120
SVEELKEITT KIEKSLTIVR SRKAKLNEDN IEKLKAEIVA EREGLNERSR LRQMENNMLS  180
FQFQEQPLWM QSRSLESEKN AHSCSSGNMD LSDVETDLSI GFPQNRV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-19166166MEF2C
5f28_B2e-19166166MEF2C
5f28_C2e-19166166MEF2C
5f28_D2e-19166166MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtMADS-box transcription factor that acts with AGL42 and AGL71 in the control of flowering time. Promotes flowering at the shoot apical and axillary meristems. Seems to act through a gibberellin-dependent pathway. Interacts genetically with SOC1 and its expression is directly regulated by SOC1. {ECO:0000269|PubMed:21609362}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1893095e-75AC189309.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB034C07, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009109211.11e-141PREDICTED: MADS-box protein AGL71-like
RefseqXP_009109212.11e-141PREDICTED: MADS-box protein AGL71-like
RefseqXP_013656515.11e-141MADS-box protein AGL71
RefseqXP_018509436.11e-141PREDICTED: MADS-box protein AGL71-like
SwissprotQ9FLH58e-77AGL72_ARATH; MADS-box protein AGL72
TrEMBLA0A078ISC41e-139A0A078ISC4_BRANA; BnaA08g30890D protein
STRINGBo8g050720.11e-137(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM88051235
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G51860.22e-72MIKC_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]