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 Solyc08g080100.2.1
Common NameLOC101250432
Organism
Solanum lycopersicum
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
Solyc08g080100.2.1genomeITAGView 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
  Solyc08g080100.2.1  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 +
  Solyc08g080100.2.1  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
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.228790.0leaf
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc08g080100.2.1
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2441956e-98Solanum lycopersicum strain Heinz 1706 chromosome 0 clone hba-6a9 map 0, complete sequence
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
Representative plantOGRP1617761
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. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]
  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]