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 Potri.006G129300.2
Common NamePOPTR_0006s13130g
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family C2H2
Protein Properties Length: 487aa    MW: 53261 Da    PI: 9.3501
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.006G129300.2genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.22.9e-054163123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        + C++C+k F r  nL+ H r H
  Potri.006G129300.2 41 FICEICNKGFQRDQNLQLHRRGH 63
                        89*******************88 PP

2zf-C2H212.80.00036117139123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H +t+
  Potri.006G129300.2 117 WKCEKCSKKYAVQSDWKAHSKTC 139
                         58*****************9998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.3E-54063IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.58E-74063No hitNo description
SMARTSM003550.0224163IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8454163IPR007087Zinc finger, C2H2
PfamPF121715.8E-54163IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002804363IPR007087Zinc finger, C2H2
SMARTSM0035510082112IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-4105138IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.58E-7112137No hitNo description
SMARTSM00355140117137IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010075Biological Processregulation of meristem growth
GO:0045604Biological Processregulation of epidermal cell differentiation
GO:0048364Biological Processroot development
GO:0051302Biological Processregulation of cell division
GO:0003676Molecular Functionnucleic acid binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 487 aa     Download sequence    Send to blast
MYKTYFKLNS SQINCFYVVF TDPDAEVIAL SPKSLMATNR FICEICNKGF QRDQNLQLHR  60
RGHNLPWKLK QRTNKEVRKK VYICPEKTCV HHDPSRALGD LTGIKKHFSR KHGEKKWKCE  120
KCSKKYAVQS DWKAHSKTCG TREYKCDCGT LFSRKDSFIT HRAFCDALAE ESARITSVPA  180
AANLNFRNDT VDLPHGFPDR PGVPDIAGIP QFNSGFGPDF SGMTPGNSLG ADQQKPGLSL  240
WLNQATSPIS PNLNLYVPSS SSGLPEMVQM GSANLYGSSS TANFGNLTLS GLPHGLKEEG  300
SSKANMVNTS ASLYSDSIQN KQSKPAAVPN MSATALLQKA AQMGSTRSNQ SFFGNNYGLM  360
NCSSSSPTTN PISLNQNPNE LHQVFQNVKQ TAAESLTTTN STVAMSDAMM GTSSNLDQLM  420
MQTSGKLQND QTQLKHQRGS NSIESGLTRD FLGMSSESSR PFLPQDLAKF ASISSAMSLN  480
HFTVNP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-38113178368Zinc finger protein JACKDAW
5b3h_F3e-38113178368Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
16779KLKQRTNKEVRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.9040.0bud| 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00485DAPTransfer from AT5G03150Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.006G129300.2
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006381470.10.0zinc finger protein JACKDAW
SwissprotQ700D21e-126IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLU5GCW40.0U5GCW4_POPTR; C2H2 family protein
STRINGPOPTR_0006s13130.10.0(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-116C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  2. 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]
  3. 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]
  4. 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]
  5. 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]