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_Os07g13170.1
Common NameLOC4342787, Os07g0235800, P0407H12.124
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: 437aa    MW: 47438.9 Da    PI: 7.3059
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os07g13170.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP254.53e-17121170155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV++++++grW+++I+d      + k+++lg f+ta  Aa+a+++a+ k++g
  LOC_Os07g13170.1 121 SQYRGVTFYRRTGRWESHIWD------CgKQVYLGGFDTAHAAARAYDRAAIKFRG 170
                       78*******************......55************************998 PP
2AP242.51.7e-13213263155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpseng...krkrfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV+ +k  grW+A+       g    +k+++lg f+++ eAa+a+++a+ +++g
  LOC_Os07g13170.1 213 SKYRGVTLHK-CGRWEAR---M---GqllGKKYIYLGLFDSEIEAARAYDRAAIRFNG 263
                       89********.7******...5...334336**********99**********99987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541715.1E-16121179IPR016177DNA-binding domain
PfamPF008471.9E-9121170IPR001471AP2/ERF domain
PROSITE profilePS5103217.82122178IPR001471AP2/ERF domain
SMARTSM003803.1E-31122184IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.104.7E-17122178IPR001471AP2/ERF domain
CDDcd000185.72E-11122177No hitNo description
CDDcd000181.10E-26213273No hitNo description
PfamPF008474.0E-9213263IPR001471AP2/ERF domain
SuperFamilySSF541716.54E-17213272IPR016177DNA-binding domain
PROSITE profilePS5103216.107214271IPR001471AP2/ERF domain
SMARTSM003804.2E-33214277IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.105.6E-16214271IPR001471AP2/ERF domain
PRINTSPR003671.8E-6215226IPR001471AP2/ERF domain
PRINTSPR003671.8E-6253273IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 437 aa     Download sequence    Send to blast
MVLDLNVESP GGSAATSSSS TPPPPPDGGG GGYFRFDLLG GSPDEDGCSS PVMTRQLFPS  60
PSAVVALAGD GSSTPPLTMP MPAAAGEGPW PRRAADLGVA QSQRSPAGGK KSRRGPRSRS  120
SQYRGVTFYR RTGRWESHIW DCGKQVYLGG FDTAHAAARA YDRAAIKFRG LDADINFNLN  180
DYEDDLKQMR NWTKEEFVHI LRRQSTGFAR GSSKYRGVTL HKCGRWEARM GQLLGKKYIY  240
LGLFDSEIEA ARAYDRAAIR FNGREAVTNF DPSSYDGDVL PETDNEVVDG DIIDLNLRIS  300
QPNVHELKSD GTLTGFQLNC DSPEASSSVV TQPISPQWPV LPQGTSMSQH PHLYASPCPG  360
FFVNLREVPM EKRPELGPQS FPTSWSWQMQ GSPLPLLPTA ASSGFSTGTV ADAARSPSSR  420
PHPFPGHHQF YFPPTA*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.274710.0callus| leaf| panicle| root
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ8H443
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in the boundary region of the shoot apical meristem (SAM) and the surrounding sheath. Expressed at low levels in vegetative organs, mostly in the sheaths. In inflorescence tissues, observed in the branch meristem and spikelet meristem regions, as well as in their vasculature and surrounding sheath (PubMed:17144896). Accumulates in incipient rudimentary- and empty-glume primordia (PubMed:22003982). Highly abundant in young developing panicles, but becomes later present at low levels in developing panicles and seeds. Found primarily in the boundary region of glume primordia (PubMed:17144896). {ECO:0000269|PubMed:17144896, ECO:0000269|PubMed:22003982}.
UniprotTISSUE SPECIFICITY: Highly expressed in seedlings and developing panicles (PubMed:17144896, PubMed:20017947, PubMed:22003982). Mostly expressed in newly emerging spikelet meristems and, at low levels, in shoots, roots, panicles, mature spikelets and sheaths (PubMed:17144896). {ECO:0000269|PubMed:17144896, 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 IDS1, 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). Regulates the transition from spikelet meristem to floral meristem, spikelet meristem determinancy and the floral organ development (PubMed:17144896). {ECO:0000250|UniProtKB:P47927, ECO:0000269|PubMed:17144896, ECO:0000269|PubMed:22003982, ECO:0000269|PubMed:28066457, ECO:0000305|PubMed:26631749}.
Function -- GeneRIF ? help Back to Top
  1. The identification of the SUPERNUMERARY BRACT (SNB) gene controlling the transition from spikelet meristem to floral meristem and the floral organ development is reported.
    [PMID: 17144896]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os07g13170.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Target of miR172 microRNA mediated cleavage, particularly during floral organ development. {ECO:0000269|PubMed:20017947, ECO:0000269|PubMed:22003982, ECO:0000305|PubMed:26631749, ECO:0000305|PubMed:28066457}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs07g13170
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ3746630.0DQ374663.1 Oryza sativa (japonica cultivar-group) supernumerary bract mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015647891.10.0ethylene-responsive transcription factor RAP2-7 isoform X1
SwissprotQ8H4430.0AP23_ORYSJ; APETALA2-like protein 3
TrEMBLA0A0E0Q5Y60.0A0A0E0Q5Y6_ORYRU; Uncharacterized protein
TrEMBLI1Q9940.0I1Q994_ORYGL; Uncharacterized protein
STRINGOS07T0235800-010.0(Oryza sativa)
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
AT2G28550.31e-93related to AP2.7
Publications ? help Back to Top
  1. Lee DY,Lee J,Moon S,Park SY,An G
    The rice heterochronic gene SUPERNUMERARY BRACT regulates the transition from spikelet meristem to floral meristem.
    Plant J., 2007. 49(1): p. 64-78
    [PMID:17144896]
  2. 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]
  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]