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_009141461.1
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: 239aa    MW: 28198.9 Da    PI: 7.416
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009141461.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF79.13.2e-25959151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    k+ienk+ rqvtfskRrng++KK  ELSvLCda + +i+fs+tgkl  y+s
  XP_009141461.1  9 KKIENKTSRQVTFSKRRNGLIKKTRELSVLCDAHIGLIVFSTTGKLTQYCS 59
                    68***********************************************96 PP
2K-box423.9e-15871611594
           K-box  15 eslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 
                       l++e++ L++e+ +L+  +R + G dL s+   eL+ LeqqLe+s++k+R++K++l      +l +k+++l+++n+++
  XP_009141461.1  87 DDLRHEIEILRRETCKLELRLRPYHGHDLASIPPHELEGLEQQLEHSVRKVRERKQQL-----GNLSRKKRMLEDDNNNM 161
                     57899**************************************************865.....66777777777777765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.1E-38160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.445161IPR002100Transcription factor, MADS-box
CDDcd002653.82E-42279No hitNo description
SuperFamilySSF554551.83E-30285IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-27323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.9E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-273859IPR002100Transcription factor, MADS-box
PfamPF014862.5E-1585165IPR002487Transcription factor, K-box
PROSITE profilePS5129711.7786171IPR002487Transcription 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: 239 aa     Download sequence    Send to blast
MGRGKIEIKK IENKTSRQVT FSKRRNGLIK KTRELSVLCD AHIGLIVFST TGKLTQYCSE  60
HSNMPQLIDR YLTKEGLQLP DLNDDRDDLR HEIEILRRET CKLELRLRPY HGHDLASIPP  120
HELEGLEQQL EHSVRKVRER KQQLGNLSRK KRMLEDDNNN MYRWLHDEHR TGVEFQQAGI  180
ETKPMEYQQF LEQVQYYNDH HQQQSSVLQL PTLPSEIDLS YHLQLAQPNL QNDPTTKVD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-17171169MEF2C
5f28_B4e-17171169MEF2C
5f28_C4e-17171169MEF2C
5f28_D4e-17171169MEF2C
Search in ModeBase
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_009141461.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHM4499890.0HM449989.1 Brassica napus cultivar DH12075 MADS-box DNA-binding domain transcription factor (TT16.4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009141461.11e-177PREDICTED: protein TRANSPARENT TESTA 16-like isoform X3
RefseqXP_022572833.11e-177protein TRANSPARENT TESTA 16 isoform X3
SwissprotQ8RYD91e-126TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLM4ECJ71e-176M4ECJ7_BRARP; Uncharacterized protein
STRINGBra026507.1-P1e-177(Brassica rapa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.11e-116MIKC_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]