PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Spipo23G0035700
Organism
Spirodela polyrhiza
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Araceae; Lemnoideae; Spirodela
Family C2H2
Protein Properties Length: 214aa    MW: 24255.8 Da    PI: 10.2254
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Spipo23G0035700genomeMIPS/IBISView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.71e-056587123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     + C++C+k F r  nL+ H r H
  Spipo23G0035700 65 FICEICNKGFQRDQNLQLHRRGH 87
                     89*******************88 PP
2zf-C2H216.42.6e-05142164123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      +kC +C+k +  +s+ k Hi+ +
  Spipo23G0035700 142 WKCDKCSKKYAVQSDWKAHIKIC 164
                      58******************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.604.4E-66487IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.62E-86487No hitNo description
SMARTSM003550.0226587IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8456587IPR007087Zinc finger, C2H2
PfamPF121712.0E-56587IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806787IPR007087Zinc finger, C2H2
SMARTSM0035578107137IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.7E-6130163IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.62E-8137162No hitNo description
SMARTSM0035583142162IPR015880Zinc 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: 214 aa     Download sequence    Send to blast
SPHLPWDSIM NQKTLTLIRS SSQRQPGRPG SSPELQSLDT SRVNTDPDAE VIALSPKTLM  60
ATNRFICEIC NKGFQRDQNL QLHRRGHNLP WKLKQRTGKE VVRKKVYVCP EKSCVHHDPS  120
RALGDLTGIK KHYSRKHGEK KWKCDKCSKK YAVQSDWKAH IKICGTREYK CDCGTLFSRK  180
DSFITHRAFC DALTEESARL SSTAVAAATG LSFK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-38138202367Zinc finger protein JACKDAW
5b3h_F1e-38138202367Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
191104KLKQRTGKEVVRKK
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
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_006480617.11e-112zinc finger protein JACKDAW
SwissprotQ700D21e-106IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A067EAZ31e-111A0A067EAZ3_CITSI; Uncharacterized protein
STRINGXP_006480617.11e-112(Citrus sinensis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20238320
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-97C2H2-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]