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 Cagra.1597s0004.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family C2H2
Protein Properties Length: 515aa    MW: 56363.1 Da    PI: 10.1298
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.1597s0004.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.21.5e-0582104123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C++C+k F r  nL+ H r H
  Cagra.1597s0004.1.p  82 FVCEICNKGFQRDQNLQLHRRGH 104
                          89*******************88 PP

2zf-C2H2140.00015159181123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC++C+k +  +s+ k H +t+
  Cagra.1597s0004.1.p 159 WKCEKCSKKYAVQSDWKAHAKTC 181
                          58******************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.11E-781104No hitNo description
Gene3DG3DSA:3.30.160.601.7E-581104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.94982104IPR007087Zinc finger, C2H2
PfamPF121718.2E-582104IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.01782104IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SMARTSM0035578124154IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.8E-5147180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.11E-7154179No hitNo description
SMARTSM00355140159179IPR015880Zinc 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: 515 aa     Download sequence    Send to blast
MQMIPGDPFS ISSSMGGFVH QETHLHHLQQ QIPDLNPNSN PNPNAKPNSS SAKKKRNQPG  60
TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSKQEVIK  120
KKVYICPIKT CVHHDASRAL GDLTGIKKHY SRKHGEKKWK CEKCSKKYAV QSDWKAHAKT  180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL NNNNPVISTS NLNFGNDSNV  240
MNNNPNLPHG FVHRGVHHPD INAAISQFGL GFGHDLSAMH AQGLSEMVQM ASTGNHHLFP  300
SSSSSLPDFS GHQQFQIPTT STNPNLTLSS SSTSQQSSAS LPSLQQHHQT LKDSSFSPLF  360
SSSSENKPNK PLSPMSATAL LQKAAQMGST RSNSTTAPSF FAGPTMTSSS ATASPPPPPP  420
PRSSSPMLIQ QQLNNNFNTI VSRENHNLAS PPLSGVTTNS VDNNPFQLNR SGLNPVQQMG  480
LTRDFLGVSN EHHPHQTSRR PFLPQELARF APLG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-44155224372Zinc finger protein JACKDAW
5b3h_F2e-44155224372Zinc 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.1597s0004.1.p
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ6214940.0AJ621494.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 3 (idz3 gene).
GenBankAJ6304930.0AJ630493.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At5g03150.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010452174.10.0PREDICTED: zinc finger protein JACKDAW-like
SwissprotQ700D20.0IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLR0H9Z40.0R0H9Z4_9BRAS; Uncharacterized protein
STRINGCagra.1597s0004.1.p0.0(Capsella grandiflora)
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-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]