PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sopim08g080100.0.1
Organism
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 MIKC_MADS
Protein Properties Length: 225aa    MW: 25839 Da    PI: 9.7598
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopim08g080100.0.1genomeCSHLView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF94.64.5e-30959151
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        krien + rqvtfskRr g+lKKA+ELSvLCdaeva+i+fs++gklye+ss
  Sopim08g080100.0.1  9 KRIENATSRQVTFSKRRSGLLKKAFELSVLCDAEVALIVFSPKGKLYEFSS 59
                        79***********************************************96 PP

2K-box63.21e-21881741399
               K-box  13 kaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                         ++e+l++e+a + +++e L+ ++R+llG +Les ++ eLq++e+qLeksl++iR++Kn l++eqi +l++ ek l +en +L+kk +
  Sopim08g080100.0.1  88 TTEHLKEEVATMTRKLEFLEDSKRKLLGHGLESSTFDELQKVEEQLEKSLSNIRARKNLLFKEQIAQLKEEEKILLKENVDLKKKCQ 174
                         6899********************************************************************************975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004327.1E-41160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.735161IPR002100Transcription factor, MADS-box
PRINTSPR004049.8E-31323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.57E-32373IPR002100Transcription factor, MADS-box
CDDcd002654.39E-43375No hitNo description
PfamPF003196.8E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004049.8E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004049.8E-313859IPR002100Transcription factor, MADS-box
PfamPF014863.1E-2288174IPR002487Transcription factor, K-box
PROSITE profilePS5129713.53289179IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010048Biological Processvernalization response
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
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: 225 aa     Download sequence    Send to blast
MVRGKTELKR IENATSRQVT FSKRRSGLLK KAFELSVLCD AEVALIVFSP KGKLYEFSSS  60
STNKTIERYQ KNEKSLGRLN RKLTDQLTTE HLKEEVATMT RKLEFLEDSK RKLLGHGLES  120
STFDELQKVE EQLEKSLSNI RARKNLLFKE QIAQLKEEEK ILLKENVDLK KKCQVLPLTL  180
TPVPLVEKDV ERQIMEVETE LFIGLPETRK SSYCPNLNTL PTLL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A9e-19187188MEF2C
5f28_B9e-19187188MEF2C
5f28_C9e-19187188MEF2C
5f28_D9e-19187188MEF2C
Search in ModeBase
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
GenBankAC2441952e-96AC244195.1 Solanum lycopersicum strain Heinz 1706 chromosome 8 clone hba-6a9 map 8, complete sequence.
GenBankHG9754472e-96HG975447.1 Solanum pennellii chromosome ch08, complete genome.
GenBankHG9755202e-96HG975520.1 Solanum lycopersicum chromosome ch08, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004245665.11e-158agamous-like MADS-box protein AGL19
SwissprotO827436e-73AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBLM1C2V71e-146M1C2V7_SOLTU; Uncharacterized protein
STRINGSolyc08g080100.2.11e-157(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
AT4G22950.13e-68AGAMOUS-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]