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 Solyc11g069240.1.1
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 C2H2
Protein Properties Length: 450aa    MW: 50087.3 Da    PI: 9.6335
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc11g069240.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.2e-053254123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        ++C++C+k F r  nL+ H r H
  Solyc11g069240.1.1 32 FVCEICNKGFQRDQNLQLHRRGH 54
                        89*******************88 PP
2zf-C2H212.10.00062109131123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H + +
  Solyc11g069240.1.1 109 WKCEKCSKKYAVQSDWKAHSKIC 131
                         58*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.26E-73154No hitNo description
Gene3DG3DSA:3.30.160.601.4E-53154IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121717.0E-53254IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0173254IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9493254IPR007087Zinc finger, C2H2
PROSITE patternPS0002803454IPR007087Zinc finger, C2H2
SMARTSM003558874104IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.3E-596130IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.26E-7104129No hitNo description
SMARTSM00355140109129IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 450 aa     Download sequence    Send to blast
MMSNDGLSCS MRDPNAEVIA LSPKSLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL  60
KQRNNKEVIK KKVYICPEKS CVHHDPSRAL GDLTGVKKHY SRKHGEKKWK CEKCSKKYAV  120
QSDWKAHSKI CGTREYKCDC GTLFSRKDSF ITHRAFCDAL AEESTRFTSI QTAVNLNNLR  180
NQLINGGIST NLQQQQQMSG NISQLMGLGS LDPSNQLNLD HGQKSRLPLW LHHENSNYGN  240
PNDFLSTPST TTSTLPHELV QVAPHANMLG SSSLHKNNNN NNNNQWFVND DGGDAIITTS  300
SSMLMPRVLK EEEENKTLSP MYYNNSHMSA TALLQIAAQI GSTRSNNNSP LFSNQFGLMT  360
SSSLSMKNSS SSSSASNVAI HENVQGNNGL LIGATNSTTF VANNANTLMM MQDKGKQGNL  420
TRDFLGGGRN EKRLFLQQTH EMAKFENNK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-37105170368Zinc finger protein JACKDAW
5b3h_F5e-37105170368Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}.
UniprotTISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc11g069240.1.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2124370.0Solanum lycopersicum chromosome 11 clone C11HBa0161D01, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004251118.10.0protein indeterminate-domain 9
SwissprotQ700D21e-109IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A3Q7IZY40.0A0A3Q7IZY4_SOLLC; Uncharacterized protein
STRINGSolyc11g069240.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10324350
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-96C2H2-like zinc finger 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. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  3. Hirano Y, et al.
    Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
    Nat Plants, 2017. 3: p. 17010
    [PMID:28211915]
  4. Kobayashi A,Miura S,Kozaki A
    INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
    Plant Mol. Biol., 2017. 94(1-2): p. 1-13
    [PMID:28324206]
  5. Long Y, et al.
    In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
    Nature, 2017. 548(7665): p. 97-102
    [PMID:28746306]
  6. Bustillo-Avendaño E, et al.
    Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
    Plant Physiol., 2018. 176(2): p. 1709-1727
    [PMID:29233938]