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 PGSC0003DMP400031037
Organism
Solanum tuberosum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family MIKC_MADS
Protein Properties Length: 143aa    MW: 16303 Da    PI: 10.244
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400031037genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF82.92e-26959151
                          S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
                SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                          kri++k  rqv f+kRr+g+lKKA+E+S+LCd++vav+i+s++g+l+e+ss
  PGSC0003DMP400031037  9 KRIQDKNCRQVAFCKRRKGLLKKAKEISILCDVDVAVVIISNRGRLHEFSS 59
                          79***********************************************96 PP
2K-box33.61.6e-12561183092
                 K-box  30 nLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenk 92 
                           +  +++R+l   + + L++ +L +Le++L+++l ++Rs+K++l+le  ++l +k  ++++++k
  PGSC0003DMP400031037  56 EFSSNNRQLEETNADGLTVTDLIHLENELQTALIQVRSRKTHLMLECAKDLHEKIASIKKNTK 118
                           5567888888889999**************************************999888765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004325.8E-32160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006628.525161IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.83E-25164IPR002100Transcription factor, MADS-box
PRINTSPR004046.6E-24323IPR002100Transcription factor, MADS-box
PfamPF003194.6E-221057IPR002100Transcription factor, MADS-box
PRINTSPR004046.6E-242338IPR002100Transcription factor, MADS-box
PRINTSPR004046.6E-243859IPR002100Transcription factor, MADS-box
PROSITE profilePS512977.46240125IPR002487Transcription factor, K-box
PfamPF014862.1E-954117IPR002487Transcription 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: 143 aa     Download sequence    Send to blast
MGRRKVEIKR IQDKNCRQVA FCKRRKGLLK KAKEISILCD VDVAVVIISN RGRLHEFSSN  60
NRQLEETNAD GLTVTDLIHL ENELQTALIQ VRSRKTHLML ECAKDLHEKI ASIKKNTKVN  120
EMSDLPAPHI FCGQQRVTLN FL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P3e-15161161Myocyte-specific enhancer factor 2B
1tqe_Q3e-15161161Myocyte-specific enhancer factor 2B
1tqe_R3e-15161161Myocyte-specific enhancer factor 2B
1tqe_S3e-15161161Myocyte-specific enhancer factor 2B
6c9l_A3e-15161161Myocyte-specific enhancer factor 2B
6c9l_B3e-15161161Myocyte-specific enhancer factor 2B
6c9l_C3e-15161161Myocyte-specific enhancer factor 2B
6c9l_D3e-15161161Myocyte-specific enhancer factor 2B
6c9l_E3e-15161161Myocyte-specific enhancer factor 2B
6c9l_F3e-15161161Myocyte-specific enhancer factor 2B
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the negative regulation of flowering time, probably through the photoperiodic and vernalization pathways; more efficient in cv. Landsberg erecta than in cv. Columbia background. Prevents premature flowering (PubMed:12724541, PubMed:25339407). Involved in the modulation of vernalization impact on flowering according to genotype acclimation to altitude (PubMed:25339407). {ECO:0000269|PubMed:12724541, ECO:0000269|PubMed:25339407}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400031037
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed during vernalization (PubMed:12724541). Regulated by HAM1 and HAM2 via epigenetic modification of chromatins at H4K5 acetylation during flowering (PubMed:23273925). {ECO:0000269|PubMed:12724541, ECO:0000269|PubMed:23273925}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9755247e-73HG975524.1 Solanum lycopersicum chromosome ch12, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015170243.12e-88PREDICTED: agamous-like MADS-box protein AGL27 isoform X2
SwissprotQ9LSR71e-27AGL70_ARATH; Agamous-like MADS-box protein AGL70
TrEMBLM1BI807e-99M1BI80_SOLTU; Uncharacterized protein
STRINGSolyc12g087830.1.12e-77(Solanum lycopersicum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G65060.16e-30MIKC_MADS family protein
Publications ? help Back to Top
  1. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
    [PMID:18426584]
  2. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  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]
  4. Nasim Z,Fahim M,Ahn JH
    Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay.
    Front Plant Sci, 2017. 8: p. 191
    [PMID:28261246]