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 AT1G03840.1
Common NameF11M21.23, IDD3, MGP
Organism
Arabidopsis thaliana
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: 506aa    MW: 55826.2 Da    PI: 8.4443
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G03840.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.64.6e-057292323
                 ETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                 C++Cgk F r  nL+ H r H
  AT1G03840.1 72 CEICGKGFQRDQNLQLHRRGH 92
                 *******************88 PP
2zf-C2H210.90.0014146168123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  +kC++C k++  +s+ k H +t+
  AT1G03840.1 146 WKCEKCAKRYAVQSDWKAHSKTC 168
                  58*****************9998 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-56992IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.75E-66992No hitNo description
PROSITE profilePS5015711.4897092IPR007087Zinc finger, C2H2
PROSITE patternPS0002807292IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.5E-4134167IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.75E-6141166No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000039anatomyshoot axis vascular system
PO:0000045anatomyembryo root
PO:0000060anatomyroot cortex-endodermis initial cell
PO:0000084anatomyplant sperm cell
PO:0006081anatomyprimary root apical meristem
PO:0009005anatomyroot
PO:0009009anatomyplant embryo
PO:0009030anatomycarpel
PO:0020124anatomyroot stele
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 506 aa     Download sequence    Send to blast
MTTEDQTISS SGGYVQSSST TDHVDHHHHD QHESLNPPLV KKKRNLPGNP DPEAEVIALS  60
PKTLMATNRF LCEICGKGFQ RDQNLQLHRR GHNLPWKLKQ RTSKEVRKRV YVCPEKSCVH  120
HHPTRALGDL TGIKKHFCRK HGEKKWKCEK CAKRYAVQSD WKAHSKTCGT REYRCDCGTI  180
FSRRDSFITH RAFCDALAEE TARLNAASHL KSFAATAGSN LNYHYLMGTL IPSPSLPQPP  240
SFPFGPPQPQ HHHHHQFPIT TNNFDHQDVM KPASTLSLWS GGNINHHQQV TIEDRMAPQP  300
HSPQEDYNWV FGNANNHGEL ITTSDSLITH DNNINIVQSK ENANGATSLS VPSLFSSVDQ  360
ITQDANAASV AVANMSATAL LQKAAQMGAT SSTSPTTTIT TDQSAYLQSF ASKSNQIVED  420
GGSDRFFASF GSNSVELMSN NNNGLHEIGN PRNGVTVVSG MGELQNYPWK RRRVDIGNAG  480
GGGQTRDFLG VGVQTICHSS SINGWI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-35142209370Zinc finger protein JACKDAW
5b3h_F4e-35142209370Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1469473KRRRV
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.425160.0root
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible265081_at0.0
Expression AtlasAT1G03840-
AtGenExpressAT1G03840-
ATTED-IIAT1G03840-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
TAIRMGP is a nuclear-localized putative transcription factor with three zinc finger domains. MGP can interact with three proteins implicated in root patterning: SCR, SHR, and JKD in Y2H assays, and these interactions depend on the first zinc finger in MGP. MGP appears to be a direct transcriptional target of SHR and SCR, based on promoter binding assays, though it is not expressed in the QC, based on in situ hybridizations.
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Function -- GeneRIF ? help Back to Top
  1. JKD directly regulates SCR and MGP expression in cooperation with SHR, SCR and MGP.
    [PMID: 21935722]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G03840.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {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)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G50420
IntActSearch Q9ZWA6
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: No visible phenotype. {ECO:0000269|PubMed:21265895}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G03840
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2278370.0AK227837.1 Arabidopsis thaliana mRNA for putative DNA-binding protein, complete cds, clone: RAFL14-40-M12.
GenBankBT0062090.0BT006209.1 Arabidopsis thaliana At1g03840 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_171880.10.0C2H2 and C2HC zinc fingers superfamily protein
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A384LMU10.0A0A384LMU1_ARATH; MGP
TrEMBLC0SUS50.0C0SUS5_ARATH; Uncharacterized protein At1g03840 (Fragment)
STRINGAT1G03840.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM37102660
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. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  3. 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]
  4. 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]
  5. Levesque MP, et al.
    Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
    PLoS Biol., 2006. 4(5): p. e143
    [PMID:16640459]
  6. 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]
  7. 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]
  8. 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]
  9. Seo PJ,Ryu J,Kang SK,Park CM
    Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis.
    Plant J., 2011. 65(3): p. 418-29
    [PMID:21265895]
  10. 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]
  11. 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]
  12. Gaudinier A, et al.
    Enhanced Y1H assays for Arabidopsis.
    Nat. Methods, 2011. 8(12): p. 1053-5
    [PMID:22037706]
  13. 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]
  14. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  15. 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]
  16. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]