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 GSVIVT01026207001
Organism
Vitis vinifera
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family MIKC_MADS
Protein Properties Length: 219aa    MW: 25844.2 Da    PI: 8.788
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01026207001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF85.82.5e-271059251
                       ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
             SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                       rien++ rqvtfskRr+g+lKK +ELSvLCd+++ +iifsstgk+ ey++
  GSVIVT01026207001 10 RIENQTSRQVTFSKRRAGLLKKTHELSVLCDVQIGLIIFSSTGKMCEYCT 59
                       8***********************************************96 PP
2K-box78.12.2e-2671170199
              K-box   1 yqkssgks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeen 91 
                        yqk +g++  e+   e+ ++el++++ke++ Lqr+ R + GedL+s+ +++L qLeqqLe+s  k+R++Kn+ll +q+++l++ke++l+een
  GSVIVT01026207001  71 YQKVTGTRiPEHDSREQIYNELTRMRKETSRLQRSMRGYTGEDLSSIPYEDLDQLEQQLEHSADKVRARKNQLLQQQLDNLRRKEQMLEEEN 162
                        67777888766677899*************************************************************************** PP

              K-box  92 kaLrkkle 99 
                         ++ + ++
  GSVIVT01026207001 163 SKMYHWIK 170
                        99877665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004326.4E-38160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006629.688161IPR002100Transcription factor, MADS-box
SuperFamilySSF554554.58E-31280IPR002100Transcription factor, MADS-box
CDDcd002656.24E-40276No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-26323IPR002100Transcription factor, MADS-box
PfamPF003195.0E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-262338IPR002100Transcription factor, MADS-box
PRINTSPR004041.1E-263859IPR002100Transcription factor, MADS-box
PfamPF014868.2E-2681169IPR002487Transcription factor, K-box
PROSITE profilePS5129715.72285175IPR002487Transcription 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: 219 aa     Download sequence    Send to blast
MGRGKIAIRR IENQTSRQVT FSKRRAGLLK KTHELSVLCD VQIGLIIFSS TGKMCEYCTE  60
PWRMDQIIER YQKVTGTRIP EHDSREQIYN ELTRMRKETS RLQRSMRGYT GEDLSSIPYE  120
DLDQLEQQLE HSADKVRARK NQLLQQQLDN LRRKEQMLEE ENSKMYHWIK ENRAALDYQQ  180
AAIEVKPVEH HHQMLDQAET LTGEVSQGGS EVWRRRHF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A5e-19171169MEF2C
5f28_B5e-19171169MEF2C
5f28_C5e-19171169MEF2C
5f28_D5e-19171169MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.227820.0flower
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4556041e-100AM455604.2 Vitis vinifera contig VV78X152709.17, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002271905.21e-144PREDICTED: protein TRANSPARENT TESTA 16 isoform X1
RefseqXP_010655915.11e-144PREDICTED: protein TRANSPARENT TESTA 16 isoform X1
RefseqXP_010655916.11e-144PREDICTED: protein TRANSPARENT TESTA 16 isoform X1
SwissprotQ8RYD92e-78TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLF6HIR21e-143F6HIR2_VITVI; Uncharacterized protein
STRINGVIT_10s0042g00820.t011e-144(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.28e-73MIKC_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]