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 RrC18900_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: 157aa    MW: 17911.8 Da    PI: 10.1903
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC18900_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF92.12.8e-291058250
                 ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
       SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                 rienk++rqvtfskRr+g+ KKA+E+SvLCda+va+i+fs++gkl+eys
  RrC18900_p1 10 RIENKIRRQVTFSKRRTGLVKKAQEISVLCDADVALIVFSPKGKLFEYS 58
                 8***********************************************8 PP
2K-box70.74.4e-24861571283
        K-box  12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkk 83 
                  a + ++++e +kL + ++ +qr++Rhl Ge+++ Ls++eLq Le qL++slk+ Rs+Kn+l++e+i +l+kk
  RrC18900_p1  86 ASQGECSTECSKLLRMVDVMQRSLRHLNGEEVDALSIRELQDLEMQLDTSLKRTRSRKNQLMVESIAQLKKK 157
                  4567899***************************************************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004325.3E-37160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.6161IPR002100Transcription factor, MADS-box
CDDcd002651.32E-37279No hitNo description
SuperFamilySSF554553.4E-31284IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-28323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003195.5E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-283859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129712.90188157IPR002487Transcription factor, K-box
PfamPF014864.6E-2088157IPR002487Transcription 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: 157 aa     Download sequence    Send to blast
MGRGRVQLRR IENKIRRQVT FSKRRTGLVK KAQEISVLCD ADVALIVFSP KGKLFEYSAG  60
SSMESILERY ERCAYAGQDI TTPSLASQGE CSTECSKLLR MVDVMQRSLR HLNGEEVDAL  120
SIRELQDLEM QLDTSLKRTR SRKNQLMVES IAQLKKK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-19170169MEF2C
5f28_B3e-19170169MEF2C
5f28_C3e-19170169MEF2C
5f28_D3e-19170169MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in flower development. {ECO:0000250|UniProtKB:Q0HA25}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY1412381e-169AY141238.1 Arabidopsis thaliana MADS-box protein AGL79 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018454665.11e-108PREDICTED: truncated transcription factor CAULIFLOWER A-like
SwissprotQ6E6S71e-69AP1_VITVI; Agamous-like MADS-box protein AP1
TrEMBLA0A3N6S2J51e-104A0A3N6S2J5_BRACR; Uncharacterized protein
STRINGBra036201.1-P1e-103(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM130331525
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G30260.12e-98AGAMOUS-like 79
Publications ? help Back to Top
  1. Jaillon O, et al.
    The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Nature, 2007. 449(7161): p. 463-7
    [PMID:17721507]
  2. Díaz-Riquelme J,Lijavetzky D,Martínez-Zapater JM,Carmona MJ
    Genome-wide analysis of MIKCC-type MADS box genes in grapevine.
    Plant Physiol., 2009. 149(1): p. 354-69
    [PMID:18997115]
  3. Grimplet J,Martínez-Zapater JM,Carmona MJ
    Structural and functional annotation of the MADS-box transcription factor family in grapevine.
    BMC Genomics, 2016. 17: p. 80
    [PMID:26818751]