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_Os03g60430.1
Common NameLOC4334582, Os03g0818800, OSNPB_030818800
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: 431aa    MW: 46771.2 Da    PI: 7.973
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g60430.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP254.52.9e-17117166155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV++++++grW+++I+d      + k+++lg f+ta  Aa+a+++a+ k++g
  LOC_Os03g60430.1 117 SQYRGVTFYRRTGRWESHIWD------CgKQVYLGGFDTAHAAARAYDRAAIKFRG 166
                       78*******************......55************************998 PP
2AP2378.4e-12209253149
               AP2   1 sgykGVrwdkkrgrWvAeIrdpseng...krkrfslgkfgtaeeAakaaiaa 49 
                       s+++GV+ +k  grW+A+       g    +k+++lg f+t+ eAa+aai++
  LOC_Os03g60430.1 209 SKFRGVTLHK-CGRWEAR---M---GqllGKKYIYLGLFDTEVEAARAAIRF 253
                       79********.7******...5...334336**********99*******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000181.42E-11117176No hitNo description
PfamPF008471.9E-9117166IPR001471AP2/ERF domain
SuperFamilySSF541715.3E-16117175IPR016177DNA-binding domain
SMARTSM003802.5E-31118180IPR001471AP2/ERF domain
PROSITE profilePS5103217.622118174IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.103.1E-17118175IPR001471AP2/ERF domain
PfamPF008471.7E-7209253IPR001471AP2/ERF domain
SuperFamilySSF541712.48E-11209263IPR016177DNA-binding domain
CDDcd000181.09E-20209265No hitNo description
SMARTSM003801.8E-24210269IPR001471AP2/ERF domain
PROSITE profilePS5103210.376210263IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.102.5E-9210263IPR001471AP2/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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009037anatomylemma
PO:0001047developmental stagelemma development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 431 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
DTEVEAARAA IRFNGREAVT NFEPASYNVD ALPDAGNEAI VDGDLDLDLR ISQPNARDSK  300
SDVATTGLQL TCDSPESSNI TVHQPMGSSP QWTVHHQSTP LPPQHQRLYP SHCLGFLPNL  360
QERPMDRRPE LGPMPFPTQA WQMQAPSHLP LLHAAASSGF SAGAGAGVAA ATRRQPPFPA  420
DHPFYFPPTA *
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 AtlasA0A0P0W4R4-
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_Os03g60430.1
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
GenBankCT8365220.0CT836522.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCFA250P08, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015628370.10.0floral homeotic protein APETALA 2 isoform X2
SwissprotQ84TB50.0AP22_ORYSJ; APETALA2-like protein 2
TrEMBLA0A0P0W4R40.0A0A0P0W4R4_ORYSJ; Os03g0818800 protein
STRINGOS03T0818800-000.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36920.22e-85AP2 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]