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 Solyc05g005090.2.1
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: 321aa    MW: 36695.9 Da    PI: 4.5452
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc05g005090.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox27.55.2e-092632952355
                         SS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
            Homeobox  23 rypsaeereeLAkklgLterqVkvWFqNrRake 55 
                         +yp+++++  LA+++gL+ +q+ +WF N+R ++
  Solyc05g005090.2.1 263 PYPTEADKNSLAESTGLDPKQINNWFINQRKRH 295
                         8*****************************885 PP
2ELK31.34.6e-11215236122
                 ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                         ELK++LlrK++++L+sLk EFs
  Solyc05g005090.2.1 215 ELKDRLLRKFGSHLSSLKLEFS 236
                         9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012559.3E-1888132IPR005540KNOX1
PfamPF037901.5E-2090131IPR005540KNOX1
SMARTSM012561.3E-25138189IPR005541KNOX2
PfamPF037911.0E-24141188IPR005541KNOX2
PROSITE profilePS5121310.196215235IPR005539ELK domain
PfamPF037891.3E-7215236IPR005539ELK domain
SMARTSM011888.4E-6215236IPR005539ELK domain
PROSITE profilePS5007112.908235298IPR001356Homeobox domain
SuperFamilySSF466891.24E-19236309IPR009057Homeodomain-like
SMARTSM003891.5E-13237302IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.602.8E-28240299IPR009057Homeodomain-like
CDDcd000866.19E-12247299No hitNo description
PfamPF059202.7E-17255294IPR008422Homeobox KN domain
PROSITE patternPS000270273296IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010073Biological Processmeristem maintenance
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 321 aa     Download sequence    Send to blast
MDDEIMYGFN STRDDYADKA LMSPENLMMQ TEYNNFHNYT NSSIMFGSDP IQLSSEQTLQ  60
NNIYRGNCCG GSGSGGDNNN NNDEDGSNII KAKILSHPYY PKLLNAYIDC QKVGAPAGIV  120
NLLEEIRQQN DFRKPNATCL CIGADPELDE FMETYCDILL KYKSDLSRPF DEATTFLNKI  180
EMQLGNLCKD DDEEEEEELS CGDASSSMRR SEDNELKDRL LRKFGSHLSS LKLEFSKKKK  240
KGKLPKEARQ MLLAWWDDHF RWPYPTEADK NSLAESTGLD PKQINNWFIN QRKRHWKPSE  300
NMQLAVMDNL SAQFFSSDVD *
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in torpedo stage embryos at the boundaries between the presumptive SAM and the cotyledons. Later expressed between the cotyledons and the meristem, and between the cotyledons. In seedlings, localised in stipules and at the boundaries between the SAM and the emerging primordia. Expressed at the site of lateral roots. {ECO:0000269|PubMed:16798887}.
UniprotTISSUE SPECIFICITY: Expressed predominantly in shoot apices of seedlings, and, to a lower extent, in rosette leaves. {ECO:0000269|PubMed:11311158}.
Functional Description ? help Back to Top
Source Description
UniProtPlays a role in meristem function. Contributes to the shoot apical meristem (SAM) maintenance and organ separation by controlling boundary establishment in embryo in a CUC1, CUC2 and STM-dependent manner. Involved in maintaining cells in an undifferentiated, meristematic state. Probably binds to the DNA sequence 5'-TGAC-3'. {ECO:0000269|PubMed:16798887}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc05g005090.2.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Seems to be repressed by AS2 and AS1 but induced by STM, CUC1 and CUC2. {ECO:0000269|PubMed:11311158, ECO:0000269|PubMed:16798887}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2123080.0Solanum lycopersicum cv. Heinz 1706, chromosome 5 BAC clone C05SLe0101I15, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001233927.10.0knotted 3 protein
SwissprotQ84JS61e-110KNAT6_ARATH; Homeobox protein knotted-1-like 6
TrEMBLA0A3Q7H4G70.0A0A3Q7H4G7_SOLLC; Uncharacterized protein
STRINGSolyc05g005090.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA7532480
Representative plantOGRP16717148
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G23380.13e-97KNOTTED1-like homeobox gene 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. 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. 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]