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_Os03g56050.1
Common NameOSJNBa0072F13.9
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: 653aa    MW: 67633.9 Da    PI: 7.2685
Description AP2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g56050.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP2392e-12304360155
               AP2   1 sgykGVrwdkkrgrWvAeIrd.pse.ng.krkrfslgkfgtaeeAakaaiaarkkleg 55 
                       s+y+GV++++++gr++A+++d  ++  g  rk  + g ++ +e+Aa+a++ a++k++g
  LOC_Os03g56050.1 304 SQYRGVTRHRWTGRYEAHLWDnSCKkEGqTRKGRQ-GGYDMEEKAARAYDLAALKYWG 360
                       78*******************77776664346655.77******************98 PP
2AP247.93.4e-15403454155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                       s y+GV+++++ grW A+I  +s    +k  +lg+f t eeAa+a++ a+ k++g
  LOC_Os03g56050.1 403 SIYRGVTRHHQHGRWQARIGRVSG---NKDLYLGTFSTQEEAAEAYDVAAIKFRG 454
                       57****************999754...5************************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000188.69E-17304368No hitNo description
SuperFamilySSF541712.55E-14304369IPR016177DNA-binding domain
PfamPF008471.2E-9304360IPR001471AP2/ERF domain
PROSITE profilePS5103217.359305368IPR001471AP2/ERF domain
SMARTSM003808.3E-23305374IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.101.4E-12305369IPR001471AP2/ERF domain
PRINTSPR003673.8E-6306317IPR001471AP2/ERF domain
CDDcd000183.71E-23403464No hitNo description
SuperFamilySSF541717.85E-18403463IPR016177DNA-binding domain
PfamPF008471.7E-10403454IPR001471AP2/ERF domain
SMARTSM003803.9E-34404468IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.101.9E-18404462IPR001471AP2/ERF domain
PROSITE profilePS5103219.137404462IPR001471AP2/ERF domain
PRINTSPR003673.8E-6444464IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007276Biological Processgamete generation
GO:0010492Biological Processmaintenance of shoot apical meristem identity
GO:0042127Biological Processregulation of cell proliferation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 653 aa     Download sequence    Send to blast
MASGNSSSSS GSMAATAGGV GGWLGFSLSP HMATYCAGGV DDVGHHHHHH VHQHQQQHGG  60
GLFYNPAAVA SSFYYGGGHD AVVTSAAGGG SYYGAGFSSM PLKSDGSLCI MEALRGGDQE  120
QQGVVVSASP KLEDFLGAGP AMALSLDNSA FYYGGHGHHQ GHAQDGGAVG GDPHHGGGGF  180
LQCAVIPGAG AGHDAALVHD QSAAAVAAGW AAMHGGGYDI ANAAADDVCA AGPIIPTGGH  240
LHPLTLSMSS AGSQSSCVTV QAAAAGEPYM AMDAVSKKRG GADRAGQKQP VHRKSIDTFG  300
QRTSQYRGVT RHRWTGRYEA HLWDNSCKKE GQTRKGRQGG YDMEEKAARA YDLAALKYWG  360
PSTHINFPLE DYQEELEEMK NMSRQEYVAH LRRKSSGFSR GASIYRGVTR HHQHGRWQAR  420
IGRVSGNKDL YLGTFSTQEE AAEAYDVAAI KFRGLNAVTN FDITRYDVDK ILESSTLLPG  480
ELARRKGKVG DGGGAAAVAD AAAALVQAGN VAEWKMATAA ALPAAARTEQ QQQHGHGGHQ  540
HHDLLPSDAF SVLQDIVSTV DAAGAPPRAP HMSMAATSLG NSREQSPDRG VGGGGGGGVL  600
ATLFAKPAAA SKLYSPVPLN TWASPSPAVS SVPARAGVSI AHLPMFAAWT DA*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.757590.0callus| panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2976017530.0
Expression AtlasQ6AU52-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed at the base of the stem. Expressed in stems. Expressed a low levels in crown roots and seeds (PubMed:21807632). Expressed in the stem region where adventitious (crown) root initiation occurs (PubMed:21481033). {ECO:0000269|PubMed:21481033, ECO:0000269|PubMed:21807632}.
Functional Description ? help Back to Top
Source Description
UniProtActs as positive regulator of adventitious (crown) root formation by promoting its initiation. Promotes adventitious root initiation through repression of cytokinin signaling by positively regulating the two-component response regulator RR1. Regulated by the auxin response factor and transcriptional activator ARF23/ARF1. {ECO:0000269|PubMed:21481033}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00088SELEXTransfer from AT4G37750Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g56050.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by auxin. {ECO:0000269|PubMed:21481033}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g56050
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2417120.0AK241712.1 Oryza sativa Japonica Group cDNA, clone: J065197H24, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025879550.10.0AP2-like ethylene-responsive transcription factor CRL5 isoform X2
SwissprotQ84Z021e-160CRL5_ORYSJ; AP2-like ethylene-responsive transcription factor CRL5
TrEMBLA0A0E0P1U90.0A0A0E0P1U9_ORYRU; Uncharacterized protein
TrEMBLQ6AU520.0Q6AU52_ORYSJ; Putative AP2/EREBP transcription factor
STRINGORUFI03G37050.10.0(Oryza rufipogon)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP94838133
Representative plantOGRP11217209
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37750.11e-129AP2 family protein
Publications ? help Back to Top
  1. Kitomi Y, et al.
    The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling.
    Plant J., 2011. 67(3): p. 472-84
    [PMID:21481033]
  2. Li P,Xue H
    Structural characterization and expression pattern analysis of the rice PLT gene family.
    Acta Biochim. Biophys. Sin. (Shanghai), 2011. 43(9): p. 688-97
    [PMID:21807632]