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 RrC7231_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 436aa    MW: 48072 Da    PI: 10.2553
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC7231_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.2e-05628123
                EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                ++C++C+k F r  nL+ H r H
  RrC7231_p1  6 FVCEICNKGFQRDQNLQLHRRGH 28
                89*******************88 PP
2zf-C2H215.93.6e-0583105123
                 EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                 ykC++C+k +  +s+ k H +t+
  RrC7231_p1  83 YKCEKCSKKYAVQSDWKAHAKTC 105
                 9*******************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.4E-5528IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.8E-8528No hitNo description
SMARTSM003550.017628IPR015880Zinc finger, C2H2-like
PfamPF121716.8E-5628IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.949628IPR007087Zinc finger, C2H2
PROSITE patternPS000280828IPR007087Zinc finger, C2H2
SMARTSM00355734878IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.3E-671104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.8E-878103No hitNo description
SMARTSM003557483103IPR015880Zinc 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: 436 aa     Download sequence    Send to blast
MATNRFVCEI CNKGFQRDQN LQLHRRGHNL PWKLKQRSNK EVIKKKVYIC PIKTCVHHDS  60
SRALGDLTGI KKHYSRKHGE KKYKCEKCSK KYAVQSDWKA HAKTCGTREY KCDCGTLFSR  120
KDSFITHRAF CDALTEEGAR MSSLSNYPAT TTMTTNLNFG NDSHVMNNPN LPHGFIHRGV  180
HHPDINAAIS QFGLGFGHDL TAMHPQGLSD MVQMTSAGNH HLFPLSSSSV LPDFSGHHHN  240
QQFQIPTTST NPNLTLSASS TSQQSSASLP SLQHQTLKDP SFSPLFSSSS ESKQNKPLSP  300
MSATALLQKA AQMGSTRSNS TTAPSIFAGP TMTSTSSAAS PPPRSSSPMM IQQQLNNNFN  360
TNAPREIRNL APPISGVTTS SVDNNHRFQS NRSGMNPVQQ MGLTRDFLGV SNEHHAHQTG  420
HRPFLPQELA RFAPSG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-4179146370Zinc finger protein JACKDAW
5b3h_F3e-4179146370Zinc finger protein JACKDAW
Search in ModeBase
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_018443047.10.0PREDICTED: zinc finger protein JACKDAW
SwissprotQ700D20.0IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLM4CZA20.0M4CZA2_BRARP; Uncharacterized protein
STRINGBra009549.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.10.0C2H2-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]