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 Lus10017388
Organism
Linum usitatissimum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum
Family MIKC_MADS
Protein Properties Length: 239aa    MW: 27882.7 Da    PI: 8.8144
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10017388genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF84.56.3e-27959151
                 S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
       SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                 krien++ rqvtfskRrng+lKK +ELSvLCda++ +iifs tgkl  y+s
  Lus10017388  9 KRIENQTTRQVTFSKRRNGLLKKTHELSVLCDAQIGLIIFSATGKLCQYAS 59
                 79*********************************************9986 PP
2K-box65.42.1e-2271160189
        K-box   1 yqkssgks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 
                  yqk++g++  e+   e+  +e+a L+ke+++Lq + R++ Ge++ ++ +++L+qLeqqLe+s++k+R++Knell +q+e+l++k +e+++
  Lus10017388  71 YQKATGTRiPEHDSREQVLNEIAVLRKETKQLQVSMRRYTGEEMANIPFQDLEQLEQQLERSVTKVRDRKNELLQQQLENLRRKIQENRS 160
                  7888888876667788999******************************************************************99876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.3E-38160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.417161IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.1E-31279IPR002100Transcription factor, MADS-box
CDDcd002659.24E-42276No hitNo description
PRINTSPR004044.1E-28323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.7E-231057IPR002100Transcription factor, MADS-box
PRINTSPR004044.1E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004044.1E-283859IPR002100Transcription factor, MADS-box
PfamPF014862.2E-1981158IPR002487Transcription factor, K-box
PROSITE profilePS5129712.95185173IPR002487Transcription 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: 239 aa     Download sequence    Send to blast
MGRGKITIKR IENQTTRQVT FSKRRNGLLK KTHELSVLCD AQIGLIIFSA TGKLCQYASE  60
PSRMEQIIER YQKATGTRIP EHDSREQVLN EIAVLRKETK QLQVSMRRYT GEEMANIPFQ  120
DLEQLEQQLE RSVTKVRDRK NELLQQQLEN LRRKIQENRS AFEFQQQPQV EPDDAKPLEQ  180
QQFIQLQDQF PFCGEPSSSN TVLQLSTLPP HLNSYHLHLG QSSFQWYVFE RIIAAWLI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-19171169MEF2C
5f28_B1e-19171169MEF2C
5f28_C1e-19171169MEF2C
5f28_D1e-19171169MEF2C
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLus10017388
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021278556.11e-108protein TRANSPARENT TESTA 16
RefseqXP_021278563.11e-108protein TRANSPARENT TESTA 16
SwissprotQ8RYD96e-71TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLA0A061E4151e-106A0A061E415_THECC; K-box region and MADS-box transcription factor family protein isoform 1
STRINGLus100173881e-175(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF49352952
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.36e-55MIKC_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]