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.003G163900.3
Common NameB456_003G163900
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: 163aa    MW: 18702.4 Da    PI: 10.3456
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.003G163900.3genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF95.23e-30959151
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        krien   rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++gklye+ss
  Gorai.003G163900.3  9 KRIENAASRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSTRGKLYEFSS 59
                        79***********************************************96 PP
2K-box61.53.4e-21871591183
               K-box  11 eakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkk 83 
                         ++++++ +++++ + k+ie L++++ +llG++Le++sl+eL+qLe++Le+sl++iR++Kn l+++qie+l++ 
  Gorai.003G163900.3  87 DQNTQNEKEDAQSMAKKIELLENSKQKLLGNGLEPCSLNELNQLETNLERSLSRIRERKNLLFRQQIEKLKQE 159
                         789*******************************************************************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.1E-38160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.539161IPR002100Transcription factor, MADS-box
SuperFamilySSF554557.46E-32373IPR002100Transcription factor, MADS-box
CDDcd002659.07E-41371No hitNo description
PRINTSPR004044.3E-31323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003194.4E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-313859IPR002100Transcription factor, MADS-box
PfamPF014861.2E-1889160IPR002487Transcription factor, K-box
PROSITE profilePS5129712.08490162IPR002487Transcription 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: 163 aa     Download sequence    Send to blast
MVRGKTQMKR IENAASRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFST RGKLYEFSSA  60
SMSKTIERYE KREKDNTGIN NKLAAVDQNT QNEKEDAQSM AKKIELLENS KQKLLGNGLE  120
PCSLNELNQL ETNLERSLSR IRERKNLLFR QQIEKLKQEV NH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-20169169MEF2C
5f28_B3e-20169169MEF2C
5f28_C3e-20169169MEF2C
5f28_D3e-20169169MEF2C
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Mostly expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. Also present in rosette leaves and seedlings and, to a lesser extent, in cauline leaves and flowers. Enriched in apices including the shoot apical meristem and developing leaf primordia. {ECO:0000269|PubMed:11115127, ECO:0000269|PubMed:12837945, ECO:0000269|PubMed:12949148, ECO:0000269|PubMed:16778081}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. {ECO:0000269|PubMed:16778081}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Maintained at very low levels by the polycomb-group (PcG) proteins MSI1, CLF, and EMF2 via histone methylation (H3K27me3). Derepressed upon cold treatment (vernalization). {ECO:0000269|PubMed:16778081}.
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_012471885.11e-109PREDICTED: agamous-like MADS-box protein AGL19 isoform X1
RefseqXP_012471886.11e-109PREDICTED: agamous-like MADS-box protein AGL19 isoform X2
RefseqXP_012471887.11e-109PREDICTED: agamous-like MADS-box protein AGL19 isoform X2
RefseqXP_012471888.11e-109PREDICTED: agamous-like MADS-box protein AGL19 isoform X2
SwissprotO827434e-63AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A0D2MPB31e-112A0A0D2MPB3_GOSRA; Uncharacterized protein
STRINGGorai.003G163900.11e-109(Gossypium raimondii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.15e-59AGAMOUS-like 19
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  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. Suter L,Rüegg M,Zemp N,Hennig L,Widmer A
    Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis.
    Plant Physiol., 2014. 166(4): p. 1928-42
    [PMID:25339407]