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.016G088500.2
Common NamePOPTR_0016s08990g
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: 406aa    MW: 44606.2 Da    PI: 9.7951
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.016G088500.2genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.52.3e-056385123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        + C++C+k F r  nL+ H r H
  Potri.016G088500.2 63 FICEICNKGFQRDQNLQLHRRGH 85
                        89*******************88 PP

2zf-C2H213.10.00029139161123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H +t+
  Potri.016G088500.2 139 WKCEKCSKKYAVQSDWKAHSKTC 161
                         58*****************9998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.0E-56285IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.3E-76285No hitNo description
PfamPF121714.6E-56385IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.8456385IPR007087Zinc finger, C2H2
SMARTSM003550.0226385IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806585IPR007087Zinc finger, C2H2
SMARTSM00355110104134IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.609.5E-5127160IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.3E-7134159No hitNo description
SMARTSM00355140139159IPR015880Zinc 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: 406 aa     Download sequence    Send to blast
MMSGDAFSLP SLIAGFAQDQ NNANPKPNPN PVAKRKRNLP GTPDPDAEVI ALSPKTLMAT  60
NRFICEICNK GFQRDQNLQL HRRGHNLPWK LKQRTNKEVR KKVYICPEKT CVHHDSSRAL  120
GDLTGIKKHF SRKHGEKKWK CEKCSKKYAV QSDWKAHSKT CGTREYKCDC GTLFSRKDSF  180
ITHRAFCDAL ADESARITSV QDTDLNFRND TVNLPHGFSN RPGVPDIAGI SQFSAGFRPD  240
FSGMTAVPMS ATALLQKAAQ MGSTRSNQPF FGNSYGLMSS SSSSSPTTNP ISLNQNPNEL  300
YHVFQNVKQP ASESLTATYN SVAMSDAVMG TSSNLDQLVM QTSGNLQNDP TQLKLQRGSN  360
STESGLTRDF LGMSSESGRL FLPHDLAKFA SISSAMSSNH FTANH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-38135200368Zinc finger protein JACKDAW
5b3h_F4e-38135200368Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
189101KLKQRTNKEVRKK
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
PlantRegMapPotri.016G088500.2
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017615264.10.0PREDICTED: zinc finger protein JACKDAW-like isoform X2
SwissprotQ700D21e-124IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A1U8IX111e-178A0A1U8IX11_GOSHI; zinc finger protein JACKDAW-like
STRINGPOPTR_0016s08990.10.0(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-109C2H2-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]