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 XP_009136371.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MIKC_MADS
Protein Properties Length: 256aa    MW: 29998.8 Da    PI: 6.6819
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009136371.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF81.17.5e-262575151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    krien + rqvtfskRr g++KK +ELSvLCda + +i+fs tgkl ey+s
  XP_009136371.1 25 KRIENRTSRQVTFSKRRSGLIKKTHELSVLCDAHIGLIVFSATGKLTEYCS 75
                    79***********************************************96 PP
2K-box60.75.7e-211011871399
           K-box  13 kaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                      +e+l+qe++ L++e+ +L+  qR + G dL s+   eL  LeqqLe+s+ k+R++Knell +q+e+l +k ++l+ +n ++ ++l 
  XP_009136371.1 101 GQEELYQEIEVLRRETCKLELRQRPYHGHDLASIPPHELDALEQQLEHSVLKVRERKNELLQQQLENLSRKRRMLEVDNSNMYRRLH 187
                     5789***************************************************************************99988765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006630.7821777IPR002100Transcription factor, MADS-box
SMARTSM004321.2E-391776IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.79E-3118104IPR002100Transcription factor, MADS-box
CDDcd002656.87E-431895No hitNo description
PRINTSPR004043.5E-281939IPR002100Transcription factor, MADS-box
PROSITE patternPS0035001973IPR002100Transcription factor, MADS-box
PfamPF003198.6E-242673IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-283954IPR002100Transcription factor, MADS-box
PRINTSPR004043.5E-285475IPR002100Transcription factor, MADS-box
PfamPF014865.7E-20100186IPR002487Transcription factor, K-box
PROSITE profilePS5129713.677102192IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008360Biological Processregulation of cell shape
GO:0019252Biological Processstarch biosynthetic process
GO:0043068Biological Processpositive regulation of programmed cell death
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0080155Biological Processregulation of double fertilization forming a zygote and endosperm
GO:2000029Biological Processregulation of proanthocyanidin biosynthetic process
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: 256 aa     Download sequence    Send to blast
MNPEEEEGVN KRKRGEMGRG KIEIKRIENR TSRQVTFSKR RSGLIKKTHE LSVLCDAHIG  60
LIVFSATGKL TEYCSDPSKM PQLIERYLQT NGLRLPDPND GQEELYQEIE VLRRETCKLE  120
LRQRPYHGHD LASIPPHELD ALEQQLEHSV LKVRERKNEL LQQQLENLSR KRRMLEVDNS  180
NMYRRLHEHG TAMEFQQAGI ETKPGEYQQF LEQVQYYNEH QQQQPPNSVL QLATLPSEID  240
PNYHLQLAQP NLQNDN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-181791173MEF2C
5f28_B2e-181791173MEF2C
5f28_C2e-181791173MEF2C
5f28_D2e-181791173MEF2C
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1168173SRKRRM
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during seed development.
UniprotTISSUE SPECIFICITY: Expressed in buds, flowers and immature seeds, but not in roots, stems, leaves, seedlings or siliques valves. Expression in seed coat is confined to the endothelium layer.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009136371.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU1920280.0EU192028.1 Brassica napus MADS-box DNA-binding domain transcription factor (TT16.1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009136371.10.0PREDICTED: protein TRANSPARENT TESTA 16 isoform X1
SwissprotQ8RYD91e-136TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLA0A3P5ZPI60.0A0A3P5ZPI6_BRACM; Uncharacterized protein
STRINGBra013028.1-P1e-176(Brassica rapa)
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
AT5G23260.21e-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]