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_013618046.1
Organism
Brassica oleracea
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: 258aa    MW: 30627.7 Da    PI: 7.7073
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013618046.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF79.81.8e-252574150
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                    k+ien + rqvtfskRr g++KKA+ELSvLCda + +i+fs tgkly  +
  XP_013618046.1 25 KKIENRTARQVTFSKRRSGVIKKAHELSVLCDAHIGLIVFSATGKLYQHC 74
                    68*********************************************987 PP
2K-box622.4e-21991831195
           K-box  11 eakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLr 95 
                     + + e+ ++e++ L++e+ +L+  qR + G dL s+   eL +LeqqLe+s+ kiR++Knel+ +q+e+l +k ++l+e+n+++ 
  XP_013618046.1  99 NDNREEFCHEIEVLRRETCKLELRQRIYRGHDLASIPPHELDELEQQLEHSVLKIRQRKNELMQQQLENLSRKRRMLEEDNNNMY 183
                     5678999**************************************************************************9875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006630.5151777IPR002100Transcription factor, MADS-box
SMARTSM004321.2E-381776IPR002100Transcription factor, MADS-box
CDDcd002652.12E-411895No hitNo description
SuperFamilySSF554551.7E-3018107IPR002100Transcription factor, MADS-box
PRINTSPR004042.8E-271939IPR002100Transcription factor, MADS-box
PfamPF003195.1E-242672IPR002100Transcription factor, MADS-box
PRINTSPR004042.8E-273954IPR002100Transcription factor, MADS-box
PRINTSPR004042.8E-275475IPR002100Transcription factor, MADS-box
PfamPF014863.7E-2099186IPR002487Transcription factor, K-box
PROSITE profilePS5129713.494102192IPR002487Transcription 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: 258 aa     Download sequence    Send to blast
MNPEEEERGN KKKRREMGRG KIEIKKIENR TARQVTFSKR RSGVIKKAHE LSVLCDAHIG  60
LIVFSATGKL YQHCTEPLTM PQLIDRYLQT NGLRLPDPND NREEFCHEIE VLRRETCKLE  120
LRQRIYRGHD LASIPPHELD ELEQQLEHSV LKIRQRKNEL MQQQLENLSR KRRMLEEDNN  180
NMYRWLHGHR ATTEFQQAGI ETKPGEYQQF LEQVQFYNDH QQQPNSFLQL ATLPSEIDLN  240
YHLHLAQPNF QNDPMANI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-171791173MEF2C
5f28_B3e-171791173MEF2C
5f28_C3e-171791173MEF2C
5f28_D3e-171791173MEF2C
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
11014KKKRR
2168173SRKRRM
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_013618046.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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_013618046.10.0PREDICTED: protein TRANSPARENT TESTA 16-like isoform X1
RefseqXP_022551330.10.0protein TRANSPARENT TESTA 16 isoform X1
SwissprotQ8RYD91e-131TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLA0A3P6DUZ10.0A0A3P6DUZ1_BRAOL; Uncharacterized protein
STRINGBo2g160980.10.0(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
AT5G23260.21e-120MIKC_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]