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 Solyc02g093280.2.1
Common NameLOC101266791
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 bHLH
Protein Properties Length: 379aa    MW: 41871.5 Da    PI: 4.8002
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc02g093280.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH505.2e-16146192455
                         HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                 HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                          hn  E+rRR+riN+++  L++l+P++      K +Ka++L +A+eY+k+Lq
  Solyc02g093280.2.1 146 VHNLSEKRRRSRINEKMKALQKLIPNS-----NKTDKASMLDEAIEYLKQLQ 192
                         6*************************7.....5******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474592.75E-20139202IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.101.3E-19139202IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088817.981142191IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000835.30E-17145196No hitNo description
PfamPF000101.8E-13146192IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003538.5E-18148197IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0009409Biological Processresponse to cold
GO:0010114Biological Processresponse to red light
GO:0010154Biological Processfruit development
GO:0010187Biological Processnegative regulation of seed germination
GO:0048440Biological Processcarpel development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 379 aa     Download sequence    Send to blast
MANNNVYYHN ANFSLTDPDP EPDDISVFLR HILLPSSSSS SSSSNFMALK SNEMQYSSSL  60
PHLMPNNNQQ GNLSSMMNSS ACGIFSSSYG VCNGATTVSS SSVGTIDYDP DEYECESEDG  120
TEDLGAEASV QPPSRNTSKR SRAAEVHNLS EKRRRSRINE KMKALQKLIP NSNKTDKASM  180
LDEAIEYLKQ LQLQVQMLTM RNGLNMYPLG LPRMLQQNQL SHQKVGLCEG NAFTNAKVAG  240
NLQVNQDASL NAIFNPTENC TETKVTPPIT MSNINRSDSA FELESSMNIH LDPFQLSRST  300
SKEIWREDDL PLYGMNELTT KTASTGSNLA FSVPLDTDAS NLKRSTREAC LLRYQFGAVN  360
ETNLDCDQLL SQQLYSNF*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.102260.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO74112100.0
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During flower initiation, expressed in the peripheral zone of the shoot apical meristem. Confined to the anlagen of successive flower buds yet to arise. Later expressed in abaxial and adaxial sepal primordia, but not in sepals. When sepals initiate, localized in the region interior to them. Within the gynoecium, detected in the initiating and developing medial regions, and then in the developing septum and stigma. SPT expression also occurs in sub-regions of developing ovules, and in the wall and dehiscence zone of the maturing fruit. As the petals develop, becomes restricted to the adaxial epidermis. In stamen expression increase in the vicinity of the archesporial cells and in cells undergoing divisions to produce sporogenous and secondary parietal cells of the anther locules. Expressed in the tapetum and microspore mother cells until the initiation of meiosis. Also detected in stomium and filaments. {ECO:0000269|PubMed:11245574}.
UniprotTISSUE SPECIFICITY: Expressed in lateral root caps, young leaves, stipules, maturing pith cells of the stem, differentiating vascular cells, shoot apical meristems and flowers. {ECO:0000269|PubMed:11245574}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269|PubMed:10225997, ECO:0000269|Ref.8}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00035PBMTransfer from AT4G36930Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc02g093280.2.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269|PubMed:11245574}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2153730.0Solanum lycopersicum chromosome 2 clone C02HBa0064B17, complete sequence
GenBankAC2154800.0Solanum lycopersicum chromosome 2 clone C02SLm0055O24, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010315963.10.0transcription factor SPATULA isoform X1
SwissprotQ9FUA42e-42SPT_ARATH; Transcription factor SPATULA
TrEMBLK4BDC40.0K4BDC4_SOLLC; Uncharacterized protein
STRINGSolyc02g093280.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA98502227
Representative plantOGRP25816128
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36930.12e-44bHLH family protein
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. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  3. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
    [PMID:25018763]
  4. Moubayidin L,Ostergaard L
    Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development.
    Curr. Biol., 2014. 24(22): p. 2743-8
    [PMID:25455035]
  5. Pfannebecker KC,Lange M,Rupp O,Becker A
    Seed Plant-Specific Gene Lineages Involved in Carpel Development.
    Mol. Biol. Evol., 2017. 34(4): p. 925-942
    [PMID:28087776]
  6. Zumajo-Cardona C,Ambrose BA,Pabón-Mora N
    Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae).
    Evodevo, 2017. 8: p. 5
    [PMID:28331573]
  7. Reyes-Olalde JI, et al.
    The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium.
    PLoS Genet., 2017. 13(4): p. e1006726
    [PMID:28388635]
  8. Wu M, et al.
    SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis.
    Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385
    [PMID:29966653]