PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC2563_p1
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: 206aa    MW: 23589.1 Da    PI: 9.1307
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC2563_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.73.1e-28959151
                S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
      SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                kri+n++ rqvtfskRrng+lKKA+EL +LCdaev viifsstg+ly++ss
  RrC2563_p1  9 KRIDNSTSRQVTFSKRRNGLLKKAKELAILCDAEVGVIIFSSTGRLYDFSS 59
                79***********************************************96 PP
2K-box83.64.4e-2881170998
       K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                 + +++ + +q+e+a Lk++++nLq+++R+++Ge+L+ Ls+++Lq+Le+qLe sl+ +R kK+++l+e+i+el +  + +++en +L+kk+
  RrC2563_p1  81 NPASEIKFWQNEAAILKRQLHNLQENHRQMMGEELSGLSVEDLQKLENQLEMSLRDVRMKKEQMLIEEIKELNREGNLVHQENLDLQKKV 170
                 678899**********************************************************************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.071161IPR002100Transcription factor, MADS-box
SMARTSM004324.3E-40160IPR002100Transcription factor, MADS-box
CDDcd002651.39E-43273No hitNo description
SuperFamilySSF554554.19E-32273IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-28323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.2E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-283859IPR002100Transcription factor, MADS-box
PROSITE profilePS513539.01265206IPR006660Arsenate reductase-like
PfamPF014864.2E-2684170IPR002487Transcription factor, K-box
PROSITE profilePS5129715.61886176IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010440Biological Processstomatal lineage progression
GO:0048574Biological Processlong-day photoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008134Molecular Functiontranscription factor binding
GO:0042803Molecular Functionprotein homodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 206 aa     Download sequence    Send to blast
MGRGKIAIKR IDNSTSRQVT FSKRRNGLLK KAKELAILCD AEVGVIIFSS TGRLYDFSSS  60
SMKSVIERYR DAKCDTNSEM NPASEIKFWQ NEAAILKRQL HNLQENHRQM MGEELSGLSV  120
EDLQKLENQL EMSLRDVRMK KEQMLIEEIK ELNREGNLVH QENLDLQKKV SLMHQQNMEL  180
HKKVSEVEGV KSANKTSLLT NGLDIG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-19169169MEF2C
5f28_B1e-19169169MEF2C
5f28_C1e-19169169MEF2C
5f28_D1e-19169169MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of flowering time in long-day photoperiod. Participates in the repression of FT expression and floral transition, by interacting closely with the FLC-SVP pathways (PubMed:24876250). Functions in the satellite meristemoid lineage of stomatal development (PubMed:17704216). {ECO:0000269|PubMed:17704216, ECO:0000269|PubMed:24876250}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00410DAPTransfer from AT3G57230Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by the micro RNA miR824. {ECO:0000269|PubMed:18579782}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0300460.0BT030046.1 Arabidopsis thaliana At3g57230 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018484418.11e-148PREDICTED: agamous-like MADS-box protein AGL16
RefseqXP_018484419.11e-148PREDICTED: agamous-like MADS-box protein AGL16
SwissprotA2RVQ51e-129AGL16_ARATH; Agamous-like MADS-box protein AGL16
TrEMBLA0A078IH391e-140A0A078IH39_BRANA; BnaA03g51000D protein
TrEMBLA0A397L3M61e-140A0A397L3M6_BRACM; Uncharacterized protein
TrEMBLM4DMA61e-140M4DMA6_BRARP; Uncharacterized protein
STRINGBra017638.1-P1e-141(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53024105
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G57230.11e-132AGAMOUS-like 16
Publications ? help Back to Top
  1. Yang K,Jiang M,Le J
    A new loss-of-function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell.
    J Integr Plant Biol, 2014. 56(6): p. 539-49
    [PMID:24386951]