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 Gorai.012G134200.6
Common NameB456_012G134200, LOC105780198
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family MIKC_MADS
Protein Properties Length: 234aa    MW: 27502.3 Da    PI: 7.5439
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.012G134200.6genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF848.9e-27959151
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        krien++ rqvtfskRr+g+lKK +ELSvLCda++ +iifs+tgk+  y++
  Gorai.012G134200.6  9 KRIENQTTRQVTFSKRRAGLLKKTHELSVLCDAQIGLIIFSTTGKMCQYCT 59
                        79**********************************************986 PP
2K-box77.24.1e-2673169398
               K-box   3 kssgks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenk 92 
                         k +g+   e+ + e+l++ela L+ke++ Lq + R++ Ged++s+ ++eL qLe++Le+s+ k+R++Knell +q+++l++ke+ l+een 
  Gorai.012G134200.6  73 KVTGTCiPEHDNREHLYNELAVLRKETRRLQLSMRRYTGEDMSSIPFEELDQLEHELERSVIKVRERKNELLQQQLDNLRRKERILEEENS 163
                         5555555677899*****************************************************************************9 PP

               K-box  93 aLrkkl 98 
                         ++ + +
  Gorai.012G134200.6 164 NMYRWV 169
                         987765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004326.3E-38160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.081161IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.83E-30277IPR002100Transcription factor, MADS-box
CDDcd002655.74E-40276No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004047.5E-27323IPR002100Transcription factor, MADS-box
PfamPF003193.5E-231057IPR002100Transcription factor, MADS-box
PRINTSPR004047.5E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004047.5E-273859IPR002100Transcription factor, MADS-box
PfamPF014861.0E-2381169IPR002487Transcription factor, K-box
PROSITE profilePS5129715.57185175IPR002487Transcription 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: 234 aa     Download sequence    Send to blast
MGRGKIPIKR IENQTTRQVT FSKRRAGLLK KTHELSVLCD AQIGLIIFST TGKMCQYCTE  60
GYRMEQIIER YQKVTGTCIP EHDNREHLYN ELAVLRKETR RLQLSMRRYT GEDMSSIPFE  120
ELDQLEHELE RSVIKVRERK NELLQQQLDN LRRKERILEE ENSNMYRWVQ EHRAAIEYQQ  180
GGMEAKPVEH QQVVDQFSFF GEPSSVLQLA TIPQQFQSYQ LQLAQPNLQD SNV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-18171169MEF2C
5f28_B4e-18171169MEF2C
5f28_C4e-18171169MEF2C
5f28_D4e-18171169MEF2C
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHM2364430.0HM236443.1 Gossypium hirsutum MADS27 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012459843.11e-173PREDICTED: protein TRANSPARENT TESTA 16-like
RefseqXP_016679920.11e-173PREDICTED: protein TRANSPARENT TESTA 16-like
SwissprotQ8RYD96e-96TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLA0A0D2TP001e-172A0A0D2TP00_GOSRA; Uncharacterized protein
TrEMBLA0A1U8IP791e-172A0A1U8IP79_GOSHI; protein TRANSPARENT TESTA 16-like
STRINGEOX990961e-162(Theobroma cacao)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.21e-91MIKC_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. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  3. 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]
  4. Xu W, et al.
    Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds.
    Plant Cell, 2016. 28(6): p. 1343-60
    [PMID:27233529]
  5. 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]
  6. 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]
  7. 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]
  8. 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]