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 Potri.006G129300.1
Common NamePOPTR_0006s13130g
Organism
Populus trichocarpa
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: 513aa    MW: 55603.4 Da    PI: 9.6197
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.006G129300.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.13.1e-056789123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        + C++C+k F r  nL+ H r H
  Potri.006G129300.1 67 FICEICNKGFQRDQNLQLHRRGH 89
                        89*******************88 PP
2zf-C2H212.70.00038143165123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H +t+
  Potri.006G129300.1 143 WKCEKCSKKYAVQSDWKAHSKTC 165
                         58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576674.77E-76689No hitNo description
Gene3DG3DSA:3.30.160.601.4E-56689IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121716.2E-56789IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.8456789IPR007087Zinc finger, C2H2
SMARTSM003550.0226789IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SMARTSM00355100108138IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-4131164IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.77E-7138163No hitNo description
SMARTSM00355140143163IPR015880Zinc 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: 513 aa     Download sequence    Send to blast
MMSGDAFSLP SSIAGFAQDQ NNANPNPSPK TNPNQAAKRK RNLPGTPDPD AEVIALSPKS  60
LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLKQRTN KEVRKKVYIC PEKTCVHHDP  120
SRALGDLTGI KKHFSRKHGE KKWKCEKCSK KYAVQSDWKA HSKTCGTREY KCDCGTLFSR  180
KDSFITHRAF CDALAEESAR ITSVPAAANL NFRNDTVDLP HGFPDRPGVP DIAGIPQFNS  240
GFGPDFSGMT PGNSLGADQQ KPGLSLWLNQ ATSPISPNLN LYVPSSSSGL PEMVQMGSAN  300
LYGSSSTANF GNLTLSGLPH GLKEEGSSKA NMVNTSASLY SDSIQNKQSK PAAVPNMSAT  360
ALLQKAAQMG STRSNQSFFG NNYGLMNCSS SSPTTNPISL NQNPNELHQV FQNVKQTAAE  420
SLTTTNSTVA MSDAMMGTSS NLDQLMMQTS GKLQNDQTQL KHQRGSNSIE SGLTRDFLGM  480
SSESSRPFLP QDLAKFASIS SAMSLNHFTV NP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-38139204368Zinc finger protein JACKDAW
5b3h_F2e-38139204368Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
193105KLKQRTNKEVRKK
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.006G129300.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006381470.10.0zinc finger protein JACKDAW
SwissprotQ700D21e-135IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLU5GCW40.0U5GCW4_POPTR; C2H2 family protein
STRINGPOPTR_0006s13130.10.0(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF18134275
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-125C2H2-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-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]