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 Sopim10g017640.0.1
Organism
Solanum pimpinellifolium
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; Lycopersicon
Family M-type_MADS
Protein Properties Length: 62aa    MW: 7032.22 Da    PI: 11.236
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopim10g017640.0.1genomeCSHLView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF91.83.3e-291059251
                        ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        rien + rqvtfskRrng+lKKA+ELSvLCda+v ++i+s+++klye+s+
  Sopim10g017640.0.1 10 RIENATSRQVTFSKRRNGLLKKAFELSVLCDAQVGLVILSPRDKLYEFST 59
                        8***********************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006629.969161IPR002100Transcription factor, MADS-box
SMARTSM004321.3E-37160IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-28323IPR002100Transcription factor, MADS-box
CDDcd002657.22E-34360No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.44E-27360IPR002100Transcription factor, MADS-box
PfamPF003195.5E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004041.5E-283859IPR002100Transcription factor, MADS-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 62 aa     Download sequence    Send to blast
MVRGKTEMRR IENATSRQVT FSKRRNGLLK KAFELSVLCD AQVGLVILSP RDKLYEFSTS  60
R*
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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9755222e-99HG975522.1 Solanum lycopersicum chromosome ch10, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004248574.16e-36MADS-box protein SOC1-like isoform X1
RefseqXP_025883671.16e-36MADS-box protein SOC1-like isoform X1
RefseqXP_025883672.15e-36MADS-box protein SOC1-like isoform X2
SwissprotO827432e-32AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLA0A3Q7IDM61e-34A0A3Q7IDM6_SOLLC; Uncharacterized protein
STRINGSolyc10g017640.1.14e-37(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA4024625
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G22950.17e-35AGAMOUS-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. 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]