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 XP_013618949.1
Organism
Brassica oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 500aa    MW: 54965.5 Da    PI: 10.0383
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013618949.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.21.4e-0582104123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     ++C++C+k F r  nL+ H r H
  XP_013618949.1  82 FVCEICNKGFQRDQNLQLHRRGH 104
                     89*******************88 PP
2zf-C2H2156.9e-05159181123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+k +  +s+ k H +t+
  XP_013618949.1 159 FKCEKCSKKYAVQSDWKAHAKTC 181
                     89******************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.6E-581104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576679.1E-881104No hitNo description
PROSITE profilePS5015710.94982104IPR007087Zinc finger, C2H2
PfamPF121718.0E-582104IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.01782104IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SMARTSM0035578124154IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-5147180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576679.1E-8154179No hitNo description
SMARTSM0035592159179IPR015880Zinc 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: 500 aa     Download sequence    Send to blast
MHMIPGDPFS VSSSMGGFVH QEQHLHHLQQ HMPDINPNSN PNPDAKPNSS SAKKKRNQPG  60
TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSNKEVIK  120
KKVYICPIKT CVHHDASRAL GDLTGIKKHY SRKHGEKKFK CEKCSKKYAV QSDWKAHAKT  180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SHPLISTTTN LNFGNDSHVM  240
NNPNLPHGFV HRGVHHPDIN AAISQFGLGF GHDLNAMHAQ GLSEMVQMAP AGSHHLFPDF  300
SGQHHNQQFQ ITMTSTNPNL TLSSSQQTSA SLPSLQQQHQ NLKDTSFSPI FSSSSECKQN  360
KSLSPMSATA LLQKAAQMGS TRSNSTNAPS IFAGATMTSS SSAASHPPPR SSSPMMIQQQ  420
LNNNFNTNVS RENQNLAPPN SGVTTSSVAK NNQFQTNGSG LNPAQQMGLT RDFLGVSNEH  480
HPHRTGHRPS QELARFSPLG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-40155222370Zinc finger protein JACKDAW
5b3h_F4e-40155222370Zinc finger protein JACKDAW
Search in ModeBase
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
PlantRegMapXP_013618949.1
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_013618949.10.0PREDICTED: zinc finger protein JACKDAW-like
RefseqXP_013654673.10.0zinc finger protein JACKDAW
SwissprotQ700D20.0IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A078I4610.0A0A078I461_BRANA; BnaC02g03330D protein
TrEMBLA0A0D3AHK20.0A0A0D3AHK2_BRAOL; Uncharacterized protein
STRINGBo2g003880.10.0(Brassica oleracea)
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]