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 AT2G02080.1
Common NameAtIDD4, F5O4.15, IDD4
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: 516aa    MW: 55793.9 Da    PI: 9.6547
Description indeterminate(ID)-domain 4
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G02080.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.84.1e-0583105123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  + C  C+k F r  nL+ H r H
  AT2G02080.1  83 FICDVCNKGFQREQNLQLHRRGH 105
                  89*******************88 PP
2zf-C2H213.30.00024159181123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  +kC++C+k++  +s+ k H +t+
  AT2G02080.1 159 WKCEKCSKRYAVQSDWKAHSKTC 181
                  58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.61E-782105No hitNo description
Gene3DG3DSA:3.30.160.601.0E-582105IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF139126.4E-582105IPR007087Zinc finger, C2H2
SMARTSM003550.006183105IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.92883105IPR007087Zinc finger, C2H2
PROSITE patternPS00028085105IPR007087Zinc finger, C2H2
SMARTSM00355110124154IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.3E-5147180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.61E-7154179No hitNo description
SMARTSM00355130159179IPR015880Zinc 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:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
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: 516 aa     Download sequence    Send to blast
MSSSSYNTSV IPSSSSSAQP FFITSSGTGD NDFNRKDTFM SMIQQPNSSA PPPKKRRNQP  60
GNPNPDAEVV ALSPKTLMAT NRFICDVCNK GFQREQNLQL HRRGHNLPWK LKQKSTKEVK  120
RKVYLCPEPT CVHHDPSRAL GDLTGIKKHY YRKHGEKKWK CEKCSKRYAV QSDWKAHSKT  180
CGTKEYRCDC GTIFSRRDSY ITHRAFCDAL IQETARNPTV SFTSMTAASS GVGSGGIYGR  240
LGGGSALSHH HLSDHPNFGF NPLVGYNLNI ASSDNRRDFI PQSSNPNFLI QSASSQGMLN  300
TTPNNNNQSF MNQHGLIQFD PVDNINLKSS GTNNSFFNLG FFQENTKNSE TSLPSLYSTD  360
VLVHHREENL NAGSNVSATA LLQKATQMGS VTSNDPSALF RGLASSSNSS SVIANHFGGG  420
RIMENDNNGN LQGLMNSLAA VNGGGGSGGS IFDVQFGDNG NMSGSDKLTL DFLGVGGMVR  480
NVNRGGGGGG RGSARGGVSL DGEAKFPEQN YPFGRG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-34155221369Zinc finger protein JACKDAW
5b3h_F7e-34155221369Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.133570.0flower| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible266110_at0.0
Expression AtlasAT2G02080-
AtGenExpressAT2G02080-
ATTED-IIAT2G02080-
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). 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:24821766, ECO:0000305|PubMed:19726569}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00256DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G02080.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by gibberellin. {ECO:0000305|PubMed:17933900}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G14920, AT1G50420
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G02080
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1177330.0AK117733.1 Arabidopsis thaliana At2g02080 mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL17-41-L01.
GenBankBT0058970.0BT005897.1 Arabidopsis thaliana At2g02080 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001325405.10.0indeterminate(ID)-domain 4
RefseqNP_001325406.10.0indeterminate(ID)-domain 4
RefseqNP_001325407.10.0indeterminate(ID)-domain 4
RefseqNP_178317.20.0indeterminate(ID)-domain 4
SwissprotQ8GYC10.0IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBLR0HIV80.0R0HIV8_9BRAS; Uncharacterized protein
STRINGAT2G02080.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM36781759
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. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  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. 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. 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]
  8. Zentella R, et al.
    Global analysis of della direct targets in early gibberellin signaling in Arabidopsis.
    Plant Cell, 2007. 19(10): p. 3037-57
    [PMID:17933900]
  9. 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]
  10. Kakizaki T, et al.
    Coordination of plastid protein import and nuclear gene expression by plastid-to-nucleus retrograde signaling.
    Plant Physiol., 2009. 151(3): p. 1339-53
    [PMID:19726569]
  11. 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]
  12. 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]
  13. Mar
    Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners.
    Plant Physiol., 2014. 166(2): p. 1022-32
    [PMID:25118255]
  14. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]