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 LOC_Os03g60430.2
Common NameAP2D2, LOC4334582, OJ1754_E06.6
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family AP2
Protein Properties Length: 435aa    MW: 47276.8 Da    PI: 7.9709
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g60430.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP254.53e-17117166155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV++++++grW+++I+d      + k+++lg f+ta  Aa+a+++a+ k++g
  LOC_Os03g60430.2 117 SQYRGVTFYRRTGRWESHIWD------CgKQVYLGGFDTAHAAARAYDRAAIKFRG 166
                       78*******************......55************************998 PP
2AP2422.3e-13209259155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpseng...krkrfslgkfgtaeeAakaaiaarkkleg 55 
                       s+++GV+ +k  grW+A+       g    +k+++lg f+t+ eAa+a+++a+ +++g
  LOC_Os03g60430.2 209 SKFRGVTLHK-CGRWEAR---M---GqllGKKYIYLGLFDTEVEAARAYDRAAIRFNG 259
                       79********.7******...5...334336**********99**********99987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000181.63E-11117176No hitNo description
PfamPF008471.9E-9117166IPR001471AP2/ERF domain
SuperFamilySSF541715.43E-16117175IPR016177DNA-binding domain
PROSITE profilePS5103217.622118174IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.2E-17118175IPR001471AP2/ERF domain
SMARTSM003802.5E-31118180IPR001471AP2/ERF domain
CDDcd000182.49E-26209269No hitNo description
SuperFamilySSF541711.05E-16209267IPR016177DNA-binding domain
PfamPF008471.1E-8209259IPR001471AP2/ERF domain
PROSITE profilePS5103216.041210267IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.104.4E-16210267IPR001471AP2/ERF domain
SMARTSM003806.7E-33210273IPR001471AP2/ERF domain
PRINTSPR003679.6E-6211222IPR001471AP2/ERF domain
PRINTSPR003679.6E-6249269IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 435 aa     Download sequence    Send to blast
MLLDLNVESP ERSGTSSSSV LNSGDAGGGG GGGGGGGLFR FDLLASSPDD DECSGEQHQL  60
PAASGIVTRQ LLPPPPPAAP SPAPAWQPPR RAAEDAALAQ RPVVAKKTRR GPRSRSSQYR  120
GVTFYRRTGR WESHIWDCGK QVYLGGFDTA HAAARAYDRA AIKFRGLEAD INFNLSDYED  180
DLKQMRNWTK EEFVHILRRQ STGFARGSSK FRGVTLHKCG RWEARMGQLL GKKYIYLGLF  240
DTEVEAARAY DRAAIRFNGR EAVTNFEPAS YNVDALPDAG NEAIVDGDLD LDLRISQPNA  300
RDSKSDVATT GLQLTCDSPE SSNITVHQPM GSSPQWTVHH QSTPLPPQHQ RLYPSHCLGF  360
LPNLQERPMD RRPELGPMPF PTQAWQMQAP SHLPLLHAAA SSGFSAGAGA GVAAATRRQP  420
PFPADHPFYF PPTA*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.590850.0callus| flower| panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1166405810.0
Expression AtlasQ84TB5-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected in developing branch and spikelet meristems at very early stages of inflorescence formation, and is maintained uniformly in the spikelet meristems until floral organs initiation. Present in some floral organ primordia. {ECO:0000269|PubMed:22003982}.
UniprotTISSUE SPECIFICITY: Highly expressed in developing panicles and in young seedlings (PubMed:20017947, PubMed:22003982). Present at low levels at all developmental stages (PubMed:22003982). {ECO:0000269|PubMed:20017947, ECO:0000269|PubMed:22003982}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor (By similarity). Involved in spikelet transition (Probable). Together with SNB, controls synergistically inflorescence architecture and floral meristem establishment via the regulation of spatio-temporal expression of B- and E-function floral organ identity genes in the lodicules and of spikelet meristem genes (PubMed:22003982). Prevents lemma and palea elongation as well as grain growth (PubMed:28066457). {ECO:0000250|UniProtKB:P47927, ECO:0000269|PubMed:22003982, ECO:0000269|PubMed:28066457, ECO:0000305|PubMed:26631749}.
Function -- GeneRIF ? help Back to Top
  1. IDS1 directly associates with GCC-box motifs in promoter regions of abiotic stress responsive genes. IDS1 physically interacts with the transcription corepressor TPR1 and the histone deacetylase HDA1.
    [PMID: 30061119]
  2. The findings illustrate an epigenetic mechanism by which IDS1 modulates salt stress signaling as well as salt tolerance in rice.
    [PMID: 30061119]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00615PBMTransfer from AT2G28550Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g60430.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Target of miR172 microRNA mediated cleavage, particularly during floral organ development. {ECO:0000269|PubMed:22003982, ECO:0000305|PubMed:20017947, ECO:0000305|PubMed:26631749, ECO:0000305|PubMed:28066457}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g60430
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6851130.0AY685113.1 Oryza sativa (japonica cultivar-group) transcription factor AP2D2 (AP2D2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015628369.10.0floral homeotic protein APETALA 2 isoform X1
SwissprotQ84TB50.0AP22_ORYSJ; APETALA2-like protein 2
TrEMBLA0A0E0GVM10.0A0A0E0GVM1_ORYNI; Uncharacterized protein
STRINGONIVA03G40610.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP24483890
Representative plantOGRP4971784
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36920.22e-90AP2 family protein
Publications ? help Back to Top
  1. Lee DY,An G
    Two AP2 family genes, supernumerary bract (SNB) and Osindeterminate spikelet 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice.
    Plant J., 2012. 69(3): p. 445-61
    [PMID:22003982]
  2. Ren D, et al.
    MULTI-FLORET SPIKELET1, which encodes an AP2/ERF protein, determines spikelet meristem fate and sterile lemma identity in rice.
    Plant Physiol., 2013. 162(2): p. 872-84
    [PMID:23629832]
  3. Wang L, et al.
    Coordinated regulation of vegetative and reproductive branching in rice.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(50): p. 15504-9
    [PMID:26631749]
  4. Dai Z,Wang J,Zhu M,Miao X,Shi Z
    OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice.
    Front Plant Sci, 2016. 7: p. 1891
    [PMID:28066457]
  5. Cheng X, et al.
    INDETERMINATE SPIKELET1 Recruits Histone Deacetylase and a Transcriptional Repression Complex to Regulate Rice Salt Tolerance.
    Plant Physiol., 2018. 178(2): p. 824-837
    [PMID:30061119]