PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc01g087990.2.1
Common NameLOC101260573
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: 272aa    MW: 30847 Da    PI: 6.0061
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc01g087990.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF885.1e-28959151
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        k ien  nrqvtfskRr+g+lKKA ELSvLCd evaviifsstgkl+e+ss
  Solyc01g087990.2.1  9 KLIENLNNRQVTFSKRRAGLLKKAGELSVLCDSEVAVIIFSSTGKLFEFSS 59
                        569**********************************************96 PP
2K-box57.46.4e-20951869100
               K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                         ++++  ++ q+e++ Lk+e+ +L+ +q +llG+dL+ + l+eL+ Le+qL+++l  i+++K+ell++q+e+++k+e++   e ++Lr+++e
  Solyc01g087990.2.1  95 QQTHVLKQEQKEVDSLKDELAKLKMKQQRLLGKDLNGMGLNELRLLEHQLNEGLLAIKERKEELLIQQLEYSRKQEERSALECETLRRQVE 185
                         4444568899*******************************************************************************98 PP

               K-box 100 e 100
                         e
  Solyc01g087990.2.1 186 E 186
                         7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.314161IPR002100Transcription factor, MADS-box
SMARTSM004323.9E-40160IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.53E-31274IPR002100Transcription factor, MADS-box
CDDcd002657.05E-40275No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004049.8E-28323IPR002100Transcription factor, MADS-box
PfamPF003191.4E-241157IPR002100Transcription factor, MADS-box
PRINTSPR004049.8E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004049.8E-283859IPR002100Transcription factor, MADS-box
PfamPF014862.6E-1496184IPR002487Transcription factor, K-box
PROSITE profilePS5129712.508100190IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010047Biological Processfruit dehiscence
GO:0010262Biological Processsomatic embryogenesis
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048577Biological Processnegative regulation of short-day photoperiodism, flowering
GO:0060862Biological Processnegative regulation of floral organ abscission
GO:0060867Biological Processfruit abscission
GO:0071365Biological Processcellular response to auxin stimulus
GO:2000692Biological Processnegative regulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042803Molecular Functionprotein homodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 272 aa     Download sequence    Send to blast
MGRGKIDIKL IENLNNRQVT FSKRRAGLLK KAGELSVLCD SEVAVIIFSS TGKLFEFSST  60
SMKQTLSRYN KCVASTDNSA VEKKSEDNEQ PQLQQQTHVL KQEQKEVDSL KDELAKLKMK  120
QQRLLGKDLN GMGLNELRLL EHQLNEGLLA IKERKEELLI QQLEYSRKQE ERSALECETL  180
RRQVEELRGL FPLSASLPPP FLEYDRPLEK KYSILKESKE SLDSDTACED GVDDEDSNTT  240
LQLGLPTICR KRKRTEQESP SSNSENQVGS K*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-21169169MEF2C
5f28_B2e-21169169MEF2C
5f28_C2e-21169169MEF2C
5f28_D2e-21169169MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.176760.0fruit
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the reproductive phase, accumulates in immature buds and at the base of the floral organs, and in the receptacle, ovules, anther filaments, and stigma and style of open flowers. Accumulates before fertilization in the cytoplasm in the cells of the egg apparatus and moves into the nucleus during early stages of development following fertilization in the suspensor, embryo, and endosperm, mainly double fertilization derived tissues (at protein level). Highly expressed in developing embryos. In young seedlings, present in the shoot and root apices, lateral root primordia and throughout the vascular system. {ECO:0000269|PubMed:10318690, ECO:0000269|PubMed:10662856, ECO:0000269|PubMed:15686521, ECO:0000269|PubMed:17521410, ECO:0000269|PubMed:8953767}.
UniprotTISSUE SPECIFICITY: Expressed at low levels in flowers and siliques. Also present in seedlings. Detected during embryogenesis and accumulates during early seed development (at protein level). Expressed in shoot apices and the base of leaf petioles. {ECO:0000269|PubMed:10318690, ECO:0000269|PubMed:10662856, ECO:0000269|PubMed:12837945, ECO:0000269|PubMed:12949148, ECO:0000269|PubMed:15686521, ECO:0000269|PubMed:16028119, ECO:0000269|PubMed:17521410, ECO:0000269|PubMed:8953767}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the negative regulation of flowering, probably through the photoperiodic pathway. Acts as both an activator and a repressor of transcription. Binds DNA in a sequence-specific manner in large CArG motif 5'-CC (A/T)8 GG-3'. Participates probably in the regulation of programs active during the early stages of embryo development. Prevents premature perianth senescence and abscission, fruits development and seed desiccation. Stimulates the expression of at least DTA4, LEC2, FUS3, ABI3, AT4G38680/CSP2 and GRP2B/CSP4. Can enhance somatic embryo development in vitro. {ECO:0000269|PubMed:10318690, ECO:0000269|PubMed:10662856, ECO:0000269|PubMed:12226488, ECO:0000269|PubMed:12743119, ECO:0000269|PubMed:14615187, ECO:0000269|PubMed:15084721, ECO:0000269|PubMed:15686521, ECO:0000269|PubMed:17521410, ECO:0000269|PubMed:18305206, ECO:0000269|PubMed:19269998, ECO:0000269|PubMed:19767455, ECO:0000269|PubMed:8953767}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00508DAPTransfer from AT5G13790Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc01g087990.2.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin (2,4-D). Feedback loop leading to direct down-regulation by itself. {ECO:0000269|PubMed:15686521}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0142200.0Lycopersicon esculentum clone 133400R, mRNA sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004229674.10.0agamous-like MADS-box protein AGL15 isoform X2
SwissprotQ388472e-68AGL15_ARATH; Agamous-like MADS-box protein AGL15
TrEMBLA0A3Q7F3700.0A0A3Q7F370_SOLLC; Uncharacterized protein
STRINGSolyc01g087990.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA87752226
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G13790.12e-64AGAMOUS-like 15
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. Zheng Q,Zheng Y,Perry SE
    Decreased GmAGL15 expression and reduced ethylene synthesis may contribute to reduced somatic embryogenesis in a poorly embryogenic cultivar of Glycine max.
    Plant Signal Behav, 2014.
    [PMID:23838957]
  3. Perry SE,Zheng Q,Zheng Y
    Transcriptome analysis indicates that GmAGAMOUS-Like 15 may enhance somatic embryogenesis by promoting a dedifferentiated state.
    Plant Signal Behav, 2016. 11(7): p. e1197463
    [PMID:27302197]
  4. Cosio C, et al.
    The class III peroxidase PRX17 is a direct target of the MADS-box transcription factor AGAMOUS-LIKE15 (AGL15) and participates in lignified tissue formation.
    New Phytol., 2017. 213(1): p. 250-263
    [PMID:27513887]
  5. Zheng Q,Zheng Y,Ji H,Burnie W,Perry SE
    Gene Regulation by the AGL15 Transcription Factor Reveals Hormone Interactions in Somatic Embryogenesis.
    Plant Physiol., 2016. 172(4): p. 2374-2387
    [PMID:27794101]
  6. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]