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 Potri.005G091100.1
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family MIKC_MADS
Protein Properties Length: 263aa    MW: 30564.9 Da    PI: 8.6623
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.005G091100.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF79.13e-251665251
                        ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        rien++ rqvtfskRr+ +lKK +ELSvLCda++ +iifsstgkl  y+s
  Potri.005G091100.1 16 RIENQTTRQVTFSKRRAVLLKKTHELSVLCDAQIGLIIFSSTGKLCQYCS 65
                        8***********************************************96 PP
2K-box69.31.3e-23891761299
               K-box  12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                            e+l+ ela L+ke + L ++ R + Ged++s+ ++eL  +eq+Le++++k+R +Knell++q+e+l++ke++l+een ++ + ++
  Potri.005G091100.1  89 DRREQLYGELAMLRKESRRLHSNMRCYTGEDMSSIPYEELDAVEQELERAVNKVRHRKNELLHQQLENLRRKERMLEEENSNMYRWIQ 176
                         55688999************************************************************************99987766 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004327.1E-30766IPR002100Transcription factor, MADS-box
PROSITE profilePS5006625.483767IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-23929IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.03E-271184IPR002100Transcription factor, MADS-box
CDDcd002651.26E-351182No hitNo description
PfamPF003196.7E-221663IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-232944IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-234465IPR002100Transcription factor, MADS-box
PfamPF014864.3E-2288175IPR002487Transcription factor, K-box
PROSITE profilePS5129714.40591181IPR002487Transcription 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: 263 aa     Download sequence    Send to blast
MHEVHFGSFA KIAIRRIENQ TTRQVTFSKR RAVLLKKTHE LSVLCDAQIG LIIFSSTGKL  60
CQYCSEGLRM EQIIERYQRM TGTCIPDHDR REQLYGELAM LRKESRRLHS NMRCYTGEDM  120
SSIPYEELDA VEQELERAVN KVRHRKNELL HQQLENLRRK ERMLEEENSN MYRWIQEHRA  180
ALGYQQAAIE ANPVEHQQVL DQFQFCGERP VACFSFQTSL IKLTHTISSL LSPAFKALAS  240
TTEVSKELVR QTKKLQGSSV YN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-151177569MEF2C
5f28_B4e-151177569MEF2C
5f28_C4e-151177569MEF2C
5f28_D4e-151177569MEF2C
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
PlantRegMapPotri.005G091100.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2166823e-67AC216682.1 Populus trichocarpa clone POP024-L07, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_011022027.11e-137PREDICTED: protein TRANSPARENT TESTA 16-like isoform X1
RefseqXP_011022028.11e-137PREDICTED: protein TRANSPARENT TESTA 16-like isoform X1
SwissprotQ8RYD95e-77TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLA0A2K2ADY70.0A0A2K2ADY7_POPTR; Uncharacterized protein
STRINGEOX990961e-116(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF49352952
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.22e-79MIKC_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]