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 RrC422_p2
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: 230aa    MW: 26539.5 Da    PI: 7.1034
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC422_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF89.51.7e-28959151
               S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
     SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
               krien + rq+tfskRr+g+lKKA+ELSvLCda+va i+fs++gklye++s
  RrC422_p2  9 KRIENLTSRQITFSKRRKGLLKKAHELSVLCDAQVAAIVFSQKGKLYEFAS 59
               79***********************************************86 PP
2K-box51.15.8e-1883173996
      K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkk...ekelqeenkaLrk 96 
                +ee++ + l++e++ + ++ie Lq   R+l+G+dL+s+s++eL+++  q+e+sl+ iRs+K +l  +++ el+     ++el +e+++L++
  RrC422_p2  83 QEEKDVQDLKNEVTVMVNRIELLQLHCRKLMGQDLGSCSVEELNEITIQIERSLTLIRSRKAKLHEDEVGELKAEiagKRELVNEKTKLHE 173
                678999******************999*********************************************9763335666666666665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.427161IPR002100Transcription factor, MADS-box
SMARTSM004321.4E-40160IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-30323IPR002100Transcription factor, MADS-box
CDDcd002653.41E-38367No hitNo description
SuperFamilySSF554555.1E-30370IPR002100Transcription factor, MADS-box
PfamPF003194.4E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-303859IPR002100Transcription factor, MADS-box
PfamPF014863.2E-1783174IPR002487Transcription factor, K-box
PROSITE profilePS5129711.10488189IPR002487Transcription 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: 230 aa     Download sequence    Send to blast
MVRGKIEIKR IENLTSRQIT FSKRRKGLLK KAHELSVLCD AQVAAIVFSQ KGKLYEFASS  60
DMKKMMEQCE IYRSGYFHAE RLQEEKDVQD LKNEVTVMVN RIELLQLHCR KLMGQDLGSC  120
SVEELNEITI QIERSLTLIR SRKAKLHEDE VGELKAEIAG KRELVNEKTK LHEMENNLLS  180
FQFEEKPLWM QSRSLESEKN ASSSSSSACE NMNISDVETD LFIGLHRSQV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-18166166MEF2C
5f28_B2e-18166166MEF2C
5f28_C2e-18166166MEF2C
5f28_D2e-18166166MEF2C
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
GenBankAC2325421e-63AC232542.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH005L20, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018485063.11e-141PREDICTED: MADS-box protein AGL72-like
SwissprotQ9FLH53e-72AGL72_ARATH; MADS-box protein AGL72
TrEMBLA0A3P6ABR51e-128A0A3P6ABR5_BRACM; Uncharacterized protein
TrEMBLM4D8Z71e-128M4D8Z7_BRARP; Uncharacterized protein
STRINGBra012957.1-P1e-128(Brassica rapa)
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
AT5G51860.23e-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]