PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc09g007550.2.1
Common NameLOC101250621
Organism
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: 460aa    MW: 51314.6 Da    PI: 9.7749
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc09g007550.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.32.7e-056183123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        + C++C+k F r  nL+ H r H
  Solyc09g007550.2.1 61 FICEICNKGFQRDQNLQLHRRGH 83
                        89*******************88 PP

2zf-C2H214.10.00014138160123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H +t+
  Solyc09g007550.2.1 138 WKCEKCSKKYAVQSDWKAHTKTC 160
                         58*******************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.2E-56083IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.65E-76083No hitNo description
SMARTSM003550.0226183IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8456183IPR007087Zinc finger, C2H2
PfamPF121715.4E-56183IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806383IPR007087Zinc finger, C2H2
SMARTSM00355110103133IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-4126159IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.65E-7133158No hitNo description
SMARTSM00355130138158IPR015880Zinc 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: 460 aa     Download sequence    Send to blast
MMSGDLFSIH QQQHQQVLVE QNPNPKANSS SKKRRNLPGT PDPDAEVIAI SPKTLMATNR  60
FICEICNKGF QRDQNLQLHR RGHNLPWKLK QRNKQEIVKK KVYICPEKSC VHHDPSRALG  120
DLTGIKKHFS RKHGEKKWKC EKCSKKYAVQ SDWKAHTKTC GTREYKCDCG TLFSRKDSFI  180
THRAFCDALA EESARITTTN NLNFNQQQQQ PVGVSQIGTS FAQDFTSMTT VNPLHQHQQK  240
PRLSLWLNQA NNNMSSQSSN LFGLPDHHMV QIPSHNMFGT NQILNPTPTT TTTTNTNTNT  300
NTPATPNPPI PMSATALLQK AAQMGSTKST PNYFSNTFGV MHSSSSPSSN NTTQIFNNNE  360
IHQAFAKQTE DYNQTENILI NGCPNMNSSV NSKAINLDQA LLQTGGMHNQ NVHFNLHNSL  420
TRDFLGMGNE GGQPFLPQEL AKFASINSAM GLSHYSTGH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-38134203372Zinc finger protein JACKDAW
5b3h_F6e-38134203372Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.142440.0flower| fruit| leaf
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
PlantRegMapSolyc09g007550.2.1
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
GenBankEF5768130.0Solanum lycopersicum chromosome 9 clone C09HBa0072G22, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004246670.10.0zinc finger protein JACKDAW isoform X1
SwissprotQ700D21e-129IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A3Q7HWE30.0A0A3Q7HWE3_SOLLC; Uncharacterized protein
STRINGSolyc09g007550.2.10.0(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-101C2H2-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-AvendaƱo 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]