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 Solyc10g086640.1.1
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 TALE
Protein Properties Length: 259aa    MW: 29316.2 Da    PI: 8.7963
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc10g086640.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox30.65.6e-101511881954
                         HHH..SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
            Homeobox  19 Fek..nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                         Fe   ++yp+ +++  LAk++gL+ +qV++WF N R +
  Solyc10g086640.1.1 151 FEHflHPYPTDSDKVMLAKQTGLSRNQVSNWFINARVR 188
                         664459******************************87 PP
2BELL94.21.2e-3041111272
                BELL   2 rqelqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                         ++e+ +  +kL+s+l+eV++rYk y+eqlq v+ssFe vag+g+a p+++l lka+S+hFrcL  ai++q+
  Solyc10g086640.1.1  41 NHEHMRNNSKLISMLDEVHRRYKEYYEQLQGVVSSFESVAGVGNASPFANLSLKALSKHFRCLIKAICDQM 111
                         57888999************************************************************995 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005741.5E-136109IPR006563POX domain
PfamPF075267.0E-2733107IPR006563POX domain
PROSITE profilePS5007111.985129192IPR001356Homeobox domain
SMARTSM003896.4E-10132196IPR001356Homeobox domain
CDDcd000869.74E-13132193No hitNo description
SuperFamilySSF466891.28E-17134200IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.604.5E-28135196IPR009057Homeodomain-like
PfamPF059203.5E-19149188IPR008422Homeobox KN domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 259 aa     Download sequence    Send to blast
MSHNKAEEIS LELMQDISGI YAHKLLQDHH HSLGTMDEVS NHEHMRNNSK LISMLDEVHR  60
RYKEYYEQLQ GVVSSFESVA GVGNASPFAN LSLKALSKHF RCLIKAICDQ MKSCDGIGKG  120
NYNNLERGGY VWRPQRGLPE RAVTVLRAWL FEHFLHPYPT DSDKVMLAKQ TGLSRNQVSN  180
WFINARVRVW KPMVEEIHML ETNKSSSHIN NNDPEMNLSS SGGVSLTLGL HHQNNNKALS  240
FPRNAARRFG IDPNNIIA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4xrm_A6e-17138196563Homeobox protein Meis2
4xrm_B6e-17138196563Homeobox protein Meis2
5bng_A5e-17138196159Homeobox protein Meis2
5bng_B5e-17138196159Homeobox protein Meis2
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during late heart stage embryo in the SAM region between the two developing cotyledons. Expression is initially down-regulated in incipient floral primordia but a strong expression is subsequently detected in the central region of young floral primordia and the inner whorl of developing flowers. In fruit, is expressed in the replum of developing ovaries. {ECO:0000269|PubMed:12874117}.
UniprotTISSUE SPECIFICITY: Predominantly expressed in stems, inflorescences and flowers. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that is involved in the preservation of the spiral phyllotactic arrangement leading to a regular pattern of organ initiation. Required for maintenance of stem cell fate in the shoot apical meristem, and is essential for specifying floral primordia and establishing early internode patterning events during inflorescence development. Acts as transcription repressor of AG expression in floral and inflorescence meristems. Is also responsive of the nuclear import of SHOOT MERISTEMLESS (STM). In the fruit, plays a central role in patterning by negatively regulating SHP expression in order to prevent replum cells from adopting a valve margin cell fate. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989, ECO:0000269|PubMed:15120075, ECO:0000269|PubMed:15155890, ECO:0000269|PubMed:16741748}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc10g086640.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010312363.10.0BEL1-like homeodomain protein 9 isoform X4
SwissprotQ9LZM81e-71BLH9_ARATH; BEL1-like homeodomain protein 9
TrEMBLA0A3Q7INH40.0A0A3Q7INH4_SOLLC; Uncharacterized protein
STRINGSolyc10g086640.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA35202237
Representative plantOGRP13316172
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G02030.11e-73TALE 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. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  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. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86
    [PMID:26417006]
  5. Andrés F, et al.
    Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE.
    Plant Physiol., 2015. 169(3): p. 2187-99
    [PMID:26417007]
  6. Bencivenga S,Serrano-Mislata A,Bush M,Fox S,Sablowski R
    Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis.
    Dev. Cell, 2016. 39(2): p. 198-208
    [PMID:27666746]
  7. Sehra B,Franks RG
    Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development.
    Front Plant Sci, 2017. 8: p. 1712
    [PMID:29085379]
  8. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]