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_Os01g49830.1
Common NameLOC4325650, Os01g0693400, P0034C09.44
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: 394aa    MW: 41181.3 Da    PI: 9.3407
Description RAV family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g49830.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP237.75.3e-1280128155
               AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkr.krfslgkfgtaeeAakaaiaarkkleg 55 
                       s++kGV   + +grW A+I++      r +r++lg+f  +++Aa+a++ a+++++g
  LOC_Os01g49830.1  80 SKFKGVVPQP-NGRWGAQIYE------RhQRVWLGTFAGEDDAARAYDVAAQRFRG 128
                       79****9888.8*********......44**********99*************98 PP
2B398.15.4e-31216308186
                       EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                       f+k+ tpsdv+k++rlv+pk++ae+h        g + +++ l +ed  g++W+++++y+++s++yvltkGW++Fvk++gL +gD+v F+++ 
  LOC_Os01g49830.1 216 FDKTVTPSDVGKLNRLVIPKQHAEKHfplqlpsAGGESKGVLLNFEDAAGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKGLHAGDVVGFYRSA 308
                       89*******************************5556799*************************************************9653 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF541714.18E-1680136IPR016177DNA-binding domain
PfamPF008471.4E-780128IPR001471AP2/ERF domain
CDDcd000189.90E-2380136No hitNo description
SMARTSM003803.0E-2681142IPR001471AP2/ERF domain
Gene3DG3DSA:3.30.730.104.5E-1981136IPR001471AP2/ERF domain
PROSITE profilePS5103219.5281136IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.108.5E-38212310IPR015300DNA-binding pseudobarrel domain
CDDcd100173.25E-29214319No hitNo description
SuperFamilySSF1019362.88E-30214309IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086313.662216327IPR003340B3 DNA binding domain
PfamPF023628.3E-28216308IPR003340B3 DNA binding domain
SMARTSM010197.1E-21216324IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009910Biological Processnegative regulation of flower development
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048366Biological Processleaf development
GO:0048527Biological Processlateral root development
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: 394 aa     Download sequence    Send to blast
MDSSSCLVDD TNSGGSSTDK LRALAAAAAE TAPLERMGSG ASAVVDAAEP GAEADSGSGG  60
RVCGGGGGGA GGAGGKLPSS KFKGVVPQPN GRWGAQIYER HQRVWLGTFA GEDDAARAYD  120
VAAQRFRGRD AVTNFRPLAE ADPDAAAELR FLATRSKAEV VDMLRKHTYF DELAQSKRTF  180
AASTPSAATT TASLSNGHLS SPRSPFAPAA ARDHLFDKTV TPSDVGKLNR LVIPKQHAEK  240
HFPLQLPSAG GESKGVLLNF EDAAGKVWRF RYSYWNSSQS YVLTKGWSRF VKEKGLHAGD  300
VVGFYRSAAS AGDDGKLFID CKLVRSTGAA LASPADQPAP SPVKAVRLFG VDLLTAPAPV  360
EQMAGCKRAR DLAATTPPQA AAFKKQCIEL ALV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A2e-4921532213115DNA-binding protein RAV1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
15866GGRVCGGGG
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.80190.0callus| flower| leaf| panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2975974150.0
Expression AtlasQ8RZX9-
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00139DAPTransfer from AT1G13260Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g49830.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
IntActSearch Q8RZX9
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g49830
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2419840.0AK241984.1 Oryza sativa Japonica Group cDNA, clone: J075097P17, full insert sequence.
GenBankAP0034500.0AP003450.3 Oryza sativa Japonica Group genomic DNA, chromosome 1, PAC clone:P0034C09.
GenBankAP0149570.0AP014957.1 Oryza sativa Japonica Group DNA, chromosome 1, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015622542.10.0AP2/ERF and B3 domain-containing protein Os01g0693400
SwissprotQ8RZX90.0Y1934_ORYSJ; AP2/ERF and B3 domain-containing protein Os01g0693400
TrEMBLA0A0E0FRL40.0A0A0E0FRL4_ORYNI; Uncharacterized protein
TrEMBLA0A0E0N1470.0A0A0E0N147_ORYRU; Uncharacterized protein
STRINGORUFI01G30390.10.0(Oryza rufipogon)
STRINGOS01T0693400-010.0(Oryza sativa)
STRINGONIVA01G31290.10.0(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
AT1G68840.21e-106related to ABI3/VP1 2
Publications ? help Back to Top
  1. Cooper B, et al.
    A network of rice genes associated with stress response and seed development.
    Proc. Natl. Acad. Sci. U.S.A., 2003. 100(8): p. 4945-50
    [PMID:12684538]