PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os04g55560.3
Common NameLOC9269072, OSJNBa0010D21.13
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: 460aa    MW: 48428.5 Da    PI: 7.0458
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g55560.3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP253.65.7e-17110159155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV++++++grW+++I+d      + k+++lg f+ta  Aa+a+++a+ k++g
  LOC_Os04g55560.3 110 SQYRGVTFYRRTGRWESHIWD------CgKQVYLGGFDTAHAAARAYDRAAIKFRG 159
                       78*******************......55************************997 PP
2AP246.41e-14202252155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV+ +k  grW+A+   +     +k+++lg f+t+eeAa+a+++a+ k +g
  LOC_Os04g55560.3 202 SKYRGVTLHK-CGRWEARMGQF--L-GKKYVYLGLFDTEEEAARAYDRAAIKCNG 252
                       89********.7******5553..2.26**********************99776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541719.15E-16110168IPR016177DNA-binding domain
PfamPF008475.2E-9110159IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.104.2E-17111167IPR001471AP2/ERF domain
SMARTSM003801.8E-31111173IPR001471AP2/ERF domain
PROSITE profilePS5103217.701111167IPR001471AP2/ERF domain
PfamPF008471.0E-10202252IPR001471AP2/ERF domain
SuperFamilySSF541711.96E-18202262IPR016177DNA-binding domain
CDDcd000182.29E-25202262No hitNo description
Gene3DG3DSA:3.30.730.102.4E-17203260IPR001471AP2/ERF domain
SMARTSM003803.0E-33203266IPR001471AP2/ERF domain
PROSITE profilePS5103216.489203260IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010073Biological Processmeristem maintenance
GO:0010093Biological Processspecification of floral organ identity
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 460 aa     Download sequence    Send to blast
MWDLNDSPAA EAAPPPLSPS ADDSGASSSS AAAVVEIPDD ADDDSAAVVV VTRQFFPPAV  60
PGGGGDPAPG NARAGWLRLA GAAPPVAATG PAASAAVSKK SRRGPRSRSS QYRGVTFYRR  120
TGRWESHIWD CGKQVYLGGF DTAHAAARAY DRAAIKFRGV EADINFSLED YEDDLKQMSN  180
LTKEEFVHVL RRQSTGFPRG SSKYRGVTLH KCGRWEARMG QFLGKKYVYL GLFDTEEEAA  240
RAYDRAAIKC NGKDAVTNFD PSIYAGEFEP PAATGDAAEH NLDLSLGSSA GSKRGNVDGG  300
GDDEITGGGG GGAGSDQRVP MAFDLDWQTA AARSTKAKFD QNSNHPQMPP VLQVTHLPFS  360
PRHHHQFLSN GDPGTAGGLS LTIGAGMAGH WPPQQQQGWG NAGGMSWPHP PHPPPPPTNA  420
AAAATATAAA ASSRFPPYIA TQASTWLQKN GFHSLTRPT*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.593061e-156callus| flower| leaf| panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329852001e-156
Expression AtlasQ7XT53-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In developing panicles, highly expressed in the spikelet abscission zone (AZ) and the inner floral organs of 2 mm long spikelets. Later present at weak levels in the apiculus as well as in the palea and lemma to progressively fades out in 8 mm long spikelets. {ECO:0000269|PubMed:22408071}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, leaves, stems, nodes, sheaths, panicles and young spikelets. Accumulates in the spikelet abscission zone (AZ) via a positive regulation by the transcription factor SH4. {ECO:0000269|PubMed:22408071}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor (PubMed:22408071). Involved in spikelet transition and development (PubMed:22408071). Prevents lemma and palea elongation as well as grain growth (PubMed:22408071). Required for seed shattering through specifying abscission zone (AZ) development (PubMed:22408071). {ECO:0000269|PubMed:22408071}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g55560.3
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g55560
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFO0822800.0FO082280.1 Oryza rufipogon (W1943) shattering abortion 1(SHAT1) gene: OR_W1943_CDS_SHAT1, PCR product.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636849.10.0AP2-like ethylene-responsive transcription factor TOE3 isoform X2
SwissprotB8AVJ90.0APL25_ORYSI; APETALA2-like protein 5
TrEMBLA0A0E0DJ660.0A0A0E0DJ66_9ORYZ; Uncharacterized protein
STRINGORGLA04G0237800.10.0(Oryza glaberrima)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36920.23e-90AP2 family protein
Publications ? help Back to Top
  1. Zhou Y, et al.
    Genetic control of seed shattering in rice by the APETALA2 transcription factor shattering abortion1.
    Plant Cell, 2012. 24(3): p. 1034-48
    [PMID:22408071]