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 RrC302_p8
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: 201aa    MW: 22870.1 Da    PI: 8.192
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC302_p8genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.43.8e-28959151
               S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
     SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
               k+i+n + rqvtfskRr gi+KKA ELSvLCda+va+iifs tgkl+e+ss
  RrC302_p8  9 KKIDNITARQVTFSKRRRGIFKKADELSVLCDADVALIIFSATGKLFEFSS 59
               68***********************************************96 PP
2K-box54.45.2e-19901671794
      K-box  17 lqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 
                 + +l++L +e+e   +++R+l GedLe L+l+eLq+Le+ Le++l+++ +kK e+l++qi+ l k+   l+ ++++ 
  RrC302_p8  90 EDCNLSRLSQEVEDKTKQLRKLRGEDLEGLNLEELQRLEKLLESGLSRVSEKKGEFLMSQISSLEKRVVTLEMAKTMA 167
                5567899************************************************************99999876654 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006628.679161IPR002100Transcription factor, MADS-box
SMARTSM004323.6E-36160IPR002100Transcription factor, MADS-box
CDDcd002651.53E-36269No hitNo description
SuperFamilySSF554551.14E-29372IPR002100Transcription factor, MADS-box
PRINTSPR004047.0E-25323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003196.8E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004047.0E-252338IPR002100Transcription factor, MADS-box
PRINTSPR004047.0E-253859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129712.08787177IPR002487Transcription factor, K-box
PfamPF014861.6E-1591164IPR002487Transcription 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: 201 aa     Download sequence    Send to blast
MAREKRRIKK IDNITARQVT FSKRRRGIFK KADELSVLCD ADVALIIFSA TGKLFEFSSS  60
RMRDILERYN LHASNINKVM GQPSPYQQVE DCNLSRLSQE VEDKTKQLRK LRGEDLEGLN  120
LEELQRLEKL LESGLSRVSE KKGEFLMSQI SSLEKRVVTL EMAKTMALKE AVETESATTN  180
VSSYESGAPL EDDFSDTSLK L
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-17169169MEF2C
5f28_B2e-17169169MEF2C
5f28_C2e-17169169MEF2C
5f28_D2e-17169169MEF2C
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1425KRRIKKIDNITARQVTFSKRRR
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that mediates floral transition in response to vernalization. Promotes inflorescence fate in apical meristems. Acts in a dosage-dependent manner. Probably involved in the transduction of RLK-mediated signaling (e.g. IMK3 pathway). Together with AP1 and SVP, controls the identity of the floral meristem and regulates expression of class B, C and E genes. When associated with SOC1, mediates effect of gibberellins on flowering under short-day conditions, and regulates the expression of LEAFY (LFY), which links floral induction and floral development. Confers inflorescence characteristics to floral primordia and early flowering. {ECO:0000269|PubMed:12451184, ECO:0000269|PubMed:12609028, ECO:0000269|PubMed:12881501, ECO:0000269|PubMed:14716314, ECO:0000269|PubMed:16679456, ECO:0000269|PubMed:18339670, ECO:0000269|PubMed:18466303, ECO:0000269|PubMed:18694458, ECO:0000269|PubMed:19656343}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by vernalization in a FLC-independent manner. Repressed by the floral homeotic genes AP1, LFY and SEP3 in emerging floral meristems to establish a floral identity and prevent inflorescence fate. Up-regulated at the shoot apex by SOC1. {ECO:0000269|PubMed:12609028, ECO:0000269|PubMed:14716314, ECO:0000269|PubMed:17428825, ECO:0000269|PubMed:18339670, ECO:0000269|PubMed:18694458}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJQ9067070.0JQ906707.1 Brassica napus clone AGL24-1 MADS-box protein AGL24 (AGL24) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018461368.11e-137PREDICTED: MADS-box protein AGL24-like isoform X2
SwissprotO827941e-113AGL24_ARATH; MADS-box protein AGL24
TrEMBLA0A397L6441e-134A0A397L644_BRACM; Uncharacterized protein
STRINGBra019221.1-P1e-134(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM145111521
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G24540.13e-96AGAMOUS-like 24
Publications ? help Back to Top
  1. Ramamoorthy R,Phua EE,Lim SH,Tan HT,Kumar PP
    Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae).
    PLoS ONE, 2013. 8(6): p. e67243
    [PMID:23840638]
  2. Lei HJ, et al.
    Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry.
    Gene, 2013. 531(2): p. 158-67
    [PMID:24055423]
  3. Wells CE,Vendramin E,Jimenez Tarodo S,Verde I,Bielenberg DG
    A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch].
    BMC Plant Biol., 2015. 15: p. 41
    [PMID:25848674]
  4. Sacharowski SP, et al.
    SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development.
    Plant Cell, 2015. 27(7): p. 1889-906
    [PMID:26106148]
  5. Sun LM,Zhang JZ,Hu CG
    Characterization and Expression Analysis of PtAGL24, a SHORT VEGETATIVE PHASE/AGAMOUS-LIKE 24 (SVP/AGL24)-Type MADS-Box Gene from Trifoliate Orange (Poncirus trifoliata L. Raf.).
    Front Plant Sci, 2016. 7: p. 823
    [PMID:27375669]