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 RrC3695_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: 228aa    MW: 26711.4 Da    PI: 7.3248
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3695_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF80.21.4e-25958150
                S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
      SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                k+ien + rqvtfskRr g++KKA+ELSvLCda++ +i+fs+tgkly  +
  RrC3695_p1  9 KKIENRTARQVTFSKRRSGVIKKANELSVLCDAQIGLIVFSTTGKLYQHC 58
                68*********************************************987 PP
2K-box43.91e-15831531181
       K-box  11 eakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelq 81 
                 + + e+ ++e++ L++e+ +L+  +R + G dL s+   eL  LeqqLe+s+ k+R++K ++l e  +++ 
  RrC3695_p1  83 NDNREEFCHEIEVLRRETCKLELRLRLYRGHDLASIPPHELDGLEQQLEHSVLKVRERKRRMLEEDNNNMY 153
                 5678999********************************************************99988875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006630.628161IPR002100Transcription factor, MADS-box
SMARTSM004326.9E-38160IPR002100Transcription factor, MADS-box
SuperFamilySSF554552.49E-31291IPR002100Transcription factor, MADS-box
CDDcd002652.79E-41279No hitNo description
PRINTSPR004042.9E-27323IPR002100Transcription factor, MADS-box
PfamPF003195.1E-241056IPR002100Transcription factor, MADS-box
PRINTSPR004042.9E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004042.9E-273859IPR002100Transcription factor, MADS-box
PfamPF014861.2E-1283152IPR002487Transcription factor, K-box
PROSITE profilePS5129710.36286173IPR002487Transcription 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: 228 aa     Download sequence    Send to blast
MGRGKIEIKK IENRTARQVT FSKRRSGVIK KANELSVLCD AQIGLIVFST TGKLYQHCTE  60
PLTMAQVIDR YLQTSGLRLP DPNDNREEFC HEIEVLRRET CKLELRLRLY RGHDLASIPP  120
HELDGLEQQL EHSVLKVRER KRRMLEEDNN NMYRWLHEHR AAVVFQQGGI ETKPGEYQQF  180
LEQVQYYNDH QQQPNSFLQL ATLPSEIDLN YHLHLAQPNL QNDPMANI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-16173171MEF2C
5f28_B1e-16173171MEF2C
5f28_C1e-16173171MEF2C
5f28_D1e-16173171MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the developmental regulation of the endothelium and in the accumulation of proanthocyanidins (PAs) or condensed tannins which give the seed its brown pigmentation after oxidation (PubMed:12368498, PubMed:16080001). Necessary for the normal activation of the BANYULS promoter in the endothelium body (PubMed:12368498). Is required, together with AGL11/STK for the maternal control of endothelium formation, which is essential for female gametophyte development and fertilization, and seed formation (PubMed:22176531). Interacts genetically with AGL1/SHP1 and AGL5/SHP2 in a partially antagonistic manner and represses AGL1/SHP1, AGL5/SHP2, and AGL8/FUL during flower development. Is essential for the coordination of cell divisions in ovule, seed coat development and endosperm formation (PubMed:27776173). Mediates the crosstalk between endothelium and nucellus to ensure proper seed formation. Functions redundantly with AGL63/GOA to repress nucellus growth and promote its degeneration. Represses the negative regulator of autophagy and programmed cell death HVA22D in the proximal nucellus (PubMed:27233529). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269|PubMed:12368498, ECO:0000269|PubMed:16080001, ECO:0000269|PubMed:22176531, ECO:0000269|PubMed:27233529, ECO:0000269|PubMed:27776173}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHM4499900.0HM449990.1 Brassica napus cultivar DH12075 MADS-box DNA-binding domain transcription factor (TT16.3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018437861.11e-162PREDICTED: protein TRANSPARENT TESTA 16-like isoform X1
SwissprotQ8RYD91e-118TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLA0A3P6DUZ11e-153A0A3P6DUZ1_BRAOL; Uncharacterized protein
STRINGBo2g160980.11e-153(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM65062543
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.31e-123MIKC_MADS family protein
Publications ? help Back to Top
  1. Kim K,Jiang K,Teng SL,Feldman LJ,Huang H
    Using biologically interrelated experiments to identify pathway genes in Arabidopsis.
    Bioinformatics, 2012. 28(6): p. 815-22
    [PMID:22271267]
  2. Rhodes DH, et al.
    Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm.
    J. Agric. Food Chem., 2014. 62(45): p. 10916-27
    [PMID:25272193]
  3. Xu W, et al.
    Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds.
    Plant Cell, 2016. 28(6): p. 1343-60
    [PMID:27233529]
  4. Ehlers K, et al.
    The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana.
    PLoS ONE, 2016. 11(10): p. e0165075
    [PMID:27776173]
  5. Coen O, et al.
    Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds.
    Development, 2017. 144(8): p. 1490-1497
    [PMID:28348169]
  6. Xu W, et al.
    TRANSPARENT TESTA 16 and 15 act through different mechanisms to control proanthocyanidin accumulation in Arabidopsis testa.
    J. Exp. Bot., 2017. 68(11): p. 2859-2870
    [PMID:28830101]
  7. Fiume E,Coen O,Xu W,Lepiniec L,Magnani E
    Developmental patterning of sub-epidermal cells in the outer integument of Arabidopsis seeds.
    PLoS ONE, 2017. 12(11): p. e0188148
    [PMID:29141031]