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 Solyc01g093960.2.1
Common NameLOC101268317
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: 253aa    MW: 28608.5 Da    PI: 8.372
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc01g093960.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF97.84.5e-31958150
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                        krienk+nrqvtfskRrng+lKKA+ELSvLC+aeva+iifss+gklye+ 
  Solyc01g093960.2.1  9 KRIENKINRQVTFSKRRNGLLKKAYELSVLCEAEVALIIFSSRGKLYEFG 58
                        79**********************************************95 PP
2K-box1027.9e-3480169998
               K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                           e++++s++qe++kLk++ e Lqr+qRhllGedL+ Ls+keLq+Le+qLe +l + R++K+++++eq+eel++ke+ l + nk+L+ k+
  Solyc01g093960.2.1  80 CGERETQSWYQEVSKLKAKFEALQRTQRHLLGEDLGALSVKELQNLEKQLEGALAQARQRKTQIMMEQMEELRRKERHLGDVNKQLKIKV 169
                         67899*********************************************************************************9886 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004322.8E-40160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.095161IPR002100Transcription factor, MADS-box
CDDcd002654.41E-43272No hitNo description
SuperFamilySSF554552.22E-32277IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004043.7E-32323IPR002100Transcription factor, MADS-box
PfamPF003192.2E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004043.7E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004043.7E-323859IPR002100Transcription factor, MADS-box
PfamPF014862.7E-3082169IPR002487Transcription factor, K-box
PROSITE profilePS5129716.63685175IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009553Biological Processembryo sac development
GO:0009911Biological Processpositive regulation of flower development
GO:0010094Biological Processspecification of carpel identity
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0010582Biological Processfloral meristem determinacy
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048455Biological Processstamen formation
GO:0048459Biological Processfloral whorl structural organization
GO:0048509Biological Processregulation of meristem development
GO:0048833Biological Processspecification of floral organ number
GO:0080060Biological Processintegument development
GO:0080112Biological Processseed growth
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: 253 aa     Download sequence    Send to blast
MGRGRVELKR IENKINRQVT FSKRRNGLLK KAYELSVLCE AEVALIIFSS RGKLYEFGSA  60
GITKTLERYQ RCCLNPQDNC GERETQSWYQ EVSKLKAKFE ALQRTQRHLL GEDLGALSVK  120
ELQNLEKQLE GALAQARQRK TQIMMEQMEE LRRKERHLGD VNKQLKIKVS LELSSFEGEG  180
QGVPFPWSNC NASLDEAGSS TFHVHHSQSN HMDCDLPDPV LQIGYHQYMA ADGASGSRNM  240
AVESNIIHGW GL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A1e-22761704102Developmental protein SEPALLATA 3
4ox0_B1e-22761704102Developmental protein SEPALLATA 3
4ox0_C1e-22761704102Developmental protein SEPALLATA 3
4ox0_D1e-22761704102Developmental protein SEPALLATA 3
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.133640.0cell culture| flower
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in flowers and seeds. {ECO:0000269|Ref.1}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in flower development. {ECO:0000250|UniProtKB:Q0HA25}.
Function -- GeneRIF ? help Back to Top
  1. The pivotal role of SlAGL6 in controlling the transition from the state of 'ovary arrest' to fertilization-triggered fruit set.
    [PMID: 27862876]
  2. down-regulation causes parthenocarpy and low seed set
    [PMID: 29699487]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00315DAPTransfer from AT2G45650Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc01g093960.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001348459.10.0AGAMOUS-like MADS-box protein AGL6
RefseqXP_015084442.10.0MADS-box transcription factor 6 isoform X1
SwissprotQ8LLR11e-133MADS3_VITVI; Agamous-like MADS-box protein MADS3
TrEMBLA0A3Q7EKL10.0A0A3Q7EKL1_SOLLC; Uncharacterized protein
STRINGSolyc01g093960.2.10.0(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
AT2G45650.11e-102AGAMOUS-like 6
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. Jaillon O, et al.
    The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Nature, 2007. 449(7161): p. 463-7
    [PMID:17721507]
  3. Díaz-Riquelme J,Lijavetzky D,Martínez-Zapater JM,Carmona MJ
    Genome-wide analysis of MIKCC-type MADS box genes in grapevine.
    Plant Physiol., 2009. 149(1): p. 354-69
    [PMID:18997115]
  4. Grimplet J,Martínez-Zapater JM,Carmona MJ
    Structural and functional annotation of the MADS-box transcription factor family in grapevine.
    BMC Genomics, 2016. 17: p. 80
    [PMID:26818751]
  5. Klap C, et al.
    Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function.
    Plant Biotechnol. J., 2017. 15(5): p. 634-647
    [PMID:27862876]
  6. Takisawa R, et al.
    The parthenocarpic gene Pat-k is generated by a natural mutation of SlAGL6 affecting fruit development in tomato (Solanum lycopersicum L.).
    BMC Plant Biol., 2018. 18(1): p. 72
    [PMID:29699487]