PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G03840.2
Common NameF11M21.23, IDD3, MGP
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: 504aa    MW: 55613.9 Da    PI: 8.5561
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G03840.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.64.6e-057090323
                 ETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                 C++Cgk F r  nL+ H r H
  AT1G03840.2 70 CEICGKGFQRDQNLQLHRRGH 90
                 *******************88 PP

2zf-C2H210.90.0014144166123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  +kC++C k++  +s+ k H +t+
  AT1G03840.2 144 WKCEKCAKRYAVQSDWKAHSKTC 166
                  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-56790IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.6E-66790No hitNo description
PROSITE profilePS5015711.4896890IPR007087Zinc finger, C2H2
PROSITE patternPS0002807090IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.5E-4132165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.6E-6139164No 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: 504 aa     Download sequence    Send to blast
MTTEDQTISS SGGYVQSSST TDHVDHHHHD QHESLNPPLV KKKRNLPGNP EAEVIALSPK  60
TLMATNRFLC EICGKGFQRD QNLQLHRRGH NLPWKLKQRT SKEVRKRVYV CPEKSCVHHH  120
PTRALGDLTG IKKHFCRKHG EKKWKCEKCA KRYAVQSDWK AHSKTCGTRE YRCDCGTIFS  180
RRDSFITHRA FCDALAEETA RLNAASHLKS FAATAGSNLN YHYLMGTLIP SPSLPQPPSF  240
PFGPPQPQHH HHHQFPITTN NFDHQDVMKP ASTLSLWSGG NINHHQQVTI EDRMAPQPHS  300
PQEDYNWVFG NANNHGELIT TSDSLITHDN NINIVQSKEN ANGATSLSVP SLFSSVDQIT  360
QDANAASVAV ANMSATALLQ KAAQMGATSS TSPTTTITTD QSAYLQSFAS KSNQIVEDGG  420
SDRFFASFGS NSVELMSNNN NGLHEIGNPR NGVTVVSGMG ELQNYPWKRR RVDIGNAGGG  480
GQTRDFLGVG VQTICHSSSI NGWI
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1467471KRRRV
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. Detected only in cells that perform asymmetric cell divisions. {ECO:0000269|PubMed:17785527}.
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). Might be involved in the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527). 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). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722}.
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
PlantRegMapAT1G03840.2
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
GenBankAJ6304760.0AJ630476.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At1g03840.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001030951.10.0zinc finger protein MAGPIE
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLC0SUS50.0C0SUS5_ARATH; Putative uncharacterized protein At1g03840 (Fragment)
STRINGAT1G03840.10.0(Arabidopsis thaliana)
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. 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]