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 AT5G03150.1
Common NameF15A17.180, IDD10, IDZ3, JKD
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; Arabidopsis
Family C2H2
Protein Properties Length: 503aa    MW: 55200.9 Da    PI: 10.2046
Description C2H2-like zinc finger protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G03150.1genomeTAIRView 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
  AT5G03150.1  82 FVCEICNKGFQRDQNLQLHRRGH 104
                  89*******************88 PP

2zf-C2H214.10.00014159181123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  +kC++C+k +  +s+ k H +t+
  AT5G03150.1 159 WKCEKCSKKYAVQSDWKAHAKTC 181
                  58******************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.7E-581104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.85E-781104No hitNo description
PfamPF121718.0E-582104IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.94982104IPR007087Zinc finger, C2H2
SMARTSM003550.01782104IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SMARTSM0035578124154IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.7E-5147180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.85E-7154179No hitNo description
SMARTSM00355140159179IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010075Biological Processregulation of meristem growth
GO:0045604Biological Processregulation of epidermal cell differentiation
GO:0048364Biological Processroot development
GO:0051302Biological Processregulation of cell division
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008270Molecular Functionzinc ion binding
GO:0042803Molecular Functionprotein homodimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0009005anatomyroot
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009046anatomyflower
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001180developmental stageplant proembryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
Sequence ? help Back to Top
Protein Sequence    Length: 503 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 SNNNPVISTT NLNFGNESNV  240
MNNPNLPHGF VHRGVHHPDI NAAISQFGLG FGHDLSAMHA QGLSEMVQMA STGNHHLFPS  300
SSSSLPDFSG HHQFQIPMTS TNPSLTLSSS STSQQTSASL QHQTLKDSSF SPLFSSSSEN  360
KQNKPLSPMS ATALLQKAAQ MGSTRSNSST APSFFAGPTM TSSSATASPP PRSSSPMMIQ  420
QQLNNFNTNV LRENHNRAPP PLSGVSTSSV DNNPFQSNRS GLNPAQQMGL TRDFLGVSNE  480
HHPHQTGRRP FLPQELARFA PLG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-44155224372Zinc finger protein JACKDAW
5b3h_F3e-44155224372Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.15920.0root
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1865196710.0
Genevisible250982_at0.0
Expression AtlasAT5G03150-
AtGenExpressAT5G03150-
ATTED-IIAT5G03150-
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
TAIRJKD is a nuclear-localized putative transcription factor with three zinc finger domains. jkd mutants show a number of root patterning defects including ectopic periclinal divisions in the cortex, increased cell numbers in the cortical and epidermal layers, a disrupted QC marker expression pattern, and disorganized QC and columella cells. jkd mutants also have a reduced number of meristematic cells in their roots. JKD can interact with the SCR and SHR proteins implicated in root patterning, as well as another zinc finger transcription factor, MAGPIE. All of these interactions require the first zinc finger in JKD according to a Y2H assay. There are also transcriptional interactions among these proteins. The initiation of JKD transcription does not appear to depend on SCR and SHR, but later expression in the post-embryonic QC cells and ground tissue initials is reduced in scr and shr mutants. JKD also appears to be required for SCR transcription beginning in the embryo. There is also some evidence that JKD plays a role in promoting the movement of SHR into the nucleus, particularly in QC cells, but this may be indirect.
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}.
Function -- GeneRIF ? help Back to Top
  1. Findings are consistent with a model where JKD induces a signal in every cortex cell that is more abundant in the hair cell position owing to the larger surface contact of cells located over a cleft.
    [PMID: 20356954]
  2. JKD directly regulates SCR and MGP expression in cooperation with SHR, SCR and MGP.
    [PMID: 21935722]
  3. In the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes, each GRAS domain comprises one alpha/beta core subdomain with an alpha-helical cap that mediates heterodimerization by forming an intermolecular helix bundle.
    [PMID: 28211915]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00485DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G03150.1
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
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT3G54220 (A), AT4G37650 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT3G54220(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G50420
IntActSearch Q700D2
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G03150
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
RefseqNP_195935.20.0C2H2-like zinc finger protein
SwissprotQ700D20.0IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A178UG830.0A0A178UG83_ARATH; JKD
STRINGAT5G03150.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Representative plantOGRP9516242
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Gong W, et al.
    Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
    Plant Physiol., 2004. 135(2): p. 773-82
    [PMID:15208423]
  3. Englbrecht CC,Schoof H,B
    Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
    BMC Genomics, 2004. 5(1): p. 39
    [PMID:15236668]
  4. Nawy T, et al.
    Transcriptional profile of the Arabidopsis root quiescent center.
    Plant Cell, 2005. 17(7): p. 1908-25
    [PMID:15937229]
  5. Colasanti J, et al.
    The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.
    BMC Genomics, 2006. 7: p. 158
    [PMID:16784536]
  6. Morita MT, et al.
    A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems.
    Plant J., 2006. 47(4): p. 619-28
    [PMID:16813575]
  7. Welch D, et al.
    Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action.
    Genes Dev., 2007. 21(17): p. 2196-204
    [PMID:17785527]
  8. Hassan H,Scheres B,Blilou I
    JACKDAW controls epidermal patterning in the Arabidopsis root meristem through a non-cell-autonomous mechanism.
    Development, 2010. 137(9): p. 1523-9
    [PMID:20356954]
  9. Koizumi K,Wu S,MacRae-Crerar A,Gallagher KL
    An essential protein that interacts with endosomes and promotes movement of the SHORT-ROOT transcription factor.
    Curr. Biol., 2011. 21(18): p. 1559-64
    [PMID:21924907]
  10. Ogasawara H,Kaimi R,Colasanti J,Kozaki A
    Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT.
    Plant Mol. Biol., 2011. 77(4-5): p. 489-99
    [PMID:21935722]
  11. Yoshida H, et al.
    DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(21): p. 7861-6
    [PMID:24821766]
  12. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  13. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  14. 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]
  15. 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]
  16. 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]
  17. 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]