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 AT2G02070.1
Common NameAtIDD5, F5O4.16, IDD5, IDZ2
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: 602aa    MW: 64463.7 Da    PI: 9.3288
Description indeterminate(ID)-domain 5
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G02070.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.13.1e-0581103123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  + C+ C+k F r  nL+ H r H
  AT2G02070.1  81 FICEVCNKGFQREQNLQLHRRGH 103
                  89*******************88 PP
2zf-C2H212.50.00046157179123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  +kC +C+k++  +s+ k H +t+
  AT2G02070.1 157 WKCDKCSKRYAVQSDWKAHSKTC 179
                  58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.606.8E-680103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.74E-780103No hitNo description
PfamPF121713.0E-581103IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.005281103IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.9981103IPR007087Zinc finger, C2H2
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SMARTSM00355110122152IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.0E-5145178IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.74E-7152177No hitNo description
SMARTSM00355140157177IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 602 aa     Download sequence    Send to blast
MAASSSSAAS FFGVRQDDQS HLLPPNSSAA APPPPPPHHQ APLPPLEAPP QKKKRNQPRT  60
PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK  120
VYLCPEPSCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCD KCSKRYAVQS DWKAHSKTCG  180
TKEYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARHPTSLT SLPSHHFPYG QNTNNSNNNA  240
SSMILGLSHM GAPQNLDHQP GDVLRLGSGG GGGGAASRSS SDLIAANASG YFMQEQNPSF  300
HDQQDHHHHH QQGFLAGNNN IKQSPMSFQQ NLMQFSHDNH NSAPSNVFNL SFLSGNNGVT  360
SATSNPNAAA AAAVSSGNLM ISNHYDGENA VGGGGEGSTG LFPNNLMSSA DRISSGSVPS  420
LFSSSMQSPN SAPHMSATAL LQKAAQMGST SSNNNNGSNT NNNNNASSIL RSFGSGIYGE  480
NESNLQDLMN SFSNPGATGN VNGVDSPFGS YGGVNKGLSA DKQSMTRDFL GVGQIVKSMS  540
GSGGFQQQQQ QQQQQQQQQQ HGNSRERVGS SSDSADRSSM NVNTGGGPAS TSPPYGIHHA  600
SF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-33153214364Zinc finger protein JACKDAW
5b3h_F2e-33153214364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.133560.0bud| flower| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible266120_at0.0
Expression AtlasAT2G02070-
AtGenExpressAT2G02070-
ATTED-IIAT2G02070-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305|PubMed:22898356}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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). {ECO:0000269|PubMed:22898356, ECO:0000269|PubMed:24821766}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00255DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G02070.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G50420
IntActSearch Q9ZUL3
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Down-regulation of SS4 during the light period of both short and long day conditions. Deformity of the chloroplasts and their contained starch granules, with an increased number of starch granules per chloroplast. {ECO:0000269|PubMed:22898356}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G02070
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ6214950.0AJ621495.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 2 (idz2 gene).
GenBankAY0561740.0AY056174.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBankBT0012150.0BT001215.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001324413.10.0indeterminate(ID)-domain 5
RefseqNP_178316.10.0indeterminate(ID)-domain 5
SwissprotQ9ZUL30.0IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A178VZR30.0A0A178VZR3_ARATH; IDD5
STRINGAT2G02070.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM43732654
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. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
    [PMID:14576160]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  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. Nakayama N, et al.
    Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens.
    Plant Cell, 2005. 17(9): p. 2486-506
    [PMID:16055634]
  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. Wagner R,Pfannschmidt T
    Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants.
    Gene, 2006. 381: p. 62-70
    [PMID:16934950]
  9. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  10. Jones AM, et al.
    Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.
    J Proteomics, 2009. 72(3): p. 439-51
    [PMID:19245862]
  11. Reiland S, et al.
    Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
    Plant Physiol., 2009. 150(2): p. 889-903
    [PMID:19376835]
  12. Jaspers P, et al.
    Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors.
    Plant J., 2009. 60(2): p. 268-79
    [PMID:19548978]
  13. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  14. Ingkasuwan P, et al.
    Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model.
    BMC Syst Biol, 2012. 6: p. 100
    [PMID:22898356]
  15. 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]
  16. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]