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_Os05g47650.1
Common NameLOC4339522, Os05g0549800, P0560C03.2
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 RAV
Protein Properties Length: 395aa    MW: 41380.9 Da    PI: 10.055
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os05g47650.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP239.51.4e-1267115155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s+ykGV   + +grW A+I++      r +r++lg+f  + eAa+a++ a+++++g
  LOC_Os05g47650.1  67 SKYKGVVPQP-NGRWGAQIYE------RhQRVWLGTFTGEAEAARAYDVAAQRFRG 115
                       89****9888.8*********......44**********99*************98 PP
2B391.56.4e-29193306192
                       EEEE-..-HHHHTT-EE--HHH.HTT.......................---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHH CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......................ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvk 70 
                       f+k+ tpsdv+k++rlv+pk++ae+h                       g    +++ l +ed  g++W+++++y+++s++yvltkGW++Fvk
  LOC_Os05g47650.1 193 FDKTVTPSDVGKLNRLVIPKQHAEKHfplqlppptttssvaaaadaaagG-GDCKGVLLNFEDAAGKVWKFRYSYWNSSQSYVLTKGWSRFVK 284
                       89***************************888888887777777777643.334999************************************ PP

                       HHT--TT-EEEEEE-SSSEE.. CS
                B3  71 angLkegDfvvFkldgrsefel 92 
                       ++gL +gD v F++   ++++l
  LOC_Os05g47650.1 285 EKGLHAGDAVGFYRAAGKNAQL 306
                       *************765555555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541711.7E-1667123IPR016177DNA-binding domain
PfamPF008472.7E-867115IPR001471AP2/ERF domain
CDDcd000182.50E-2367123No hitNo description
Gene3DG3DSA:3.30.730.101.5E-1968123IPR001471AP2/ERF domain
SMARTSM003803.2E-2668129IPR001471AP2/ERF domain
PROSITE profilePS5103219.86268123IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.101.4E-39184320IPR015300DNA-binding pseudobarrel domain
CDDcd100173.50E-26191298No hitNo description
SuperFamilySSF1019362.62E-28191311IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086312.097193314IPR003340B3 DNA binding domain
PfamPF023624.8E-26193308IPR003340B3 DNA binding domain
SMARTSM010199.2E-21193313IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045892Biological Processnegative regulation 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:0020039anatomyleaf lamina
Sequence ? help Back to Top
Protein Sequence    Length: 395 aa     Download sequence    Send to blast
MDSTSCLLDD ASSGASTGKK AAAAAASKAL QRVGSGASAV MDAAEPGAEA DSGGERRGGG  60
GGKLPSSKYK GVVPQPNGRW GAQIYERHQR VWLGTFTGEA EAARAYDVAA QRFRGRDAVT  120
NFRPLAESDP EAAVELRFLA SRSKAEVVDM LRKHTYLEEL TQNKRAFAAI SPPPPKHPAS  180
SPTSSSAARE HLFDKTVTPS DVGKLNRLVI PKQHAEKHFP LQLPPPTTTS SVAAAADAAA  240
GGGDCKGVLL NFEDAAGKVW KFRYSYWNSS QSYVLTKGWS RFVKEKGLHA GDAVGFYRAA  300
GKNAQLFIDC KVRAKPTTAA AAAAFLSAVA AAAAPPPAVK AIRLFGVDLL TAAAPELQDA  360
GGAAMTKSKR AMDAMAESQA HVVFKKQCIE LALT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A3e-4919031411118DNA-binding protein RAV1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.90641e-133callus| leaf| root| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ6L4H4
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00025PBMTransfer from AT1G68840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os05g47650.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs05g47650
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1307250.0AC130725.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone P0494H05, complete sequence.
GenBankAC1359250.0AC135925.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone P0560C03, complete sequence.
GenBankAC1364920.0AC136492.3 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone P0554F08, complete sequence.
GenBankAP0149610.0AP014961.1 Oryza sativa Japonica Group DNA, chromosome 5, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015637817.10.0AP2/ERF and B3 domain-containing protein Os05g0549800
SwissprotQ6L4H40.0Y5498_ORYSJ; AP2/ERF and B3 domain-containing protein Os05g0549800
TrEMBLA0A0E0HHS80.0A0A0E0HHS8_ORYNI; Uncharacterized protein
STRINGONIVA05G26000.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP45638203
Representative plantOGRP36516108
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G25560.12e-95RAV family protein
Publications ? help Back to Top
  1. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]