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_Os04g58000.1
Common NameLOC4337398, Os04g0676600, OsJ_16616, OSJNBa0064G10.6
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 B3
Protein Properties Length: 434aa    MW: 48667.4 Da    PI: 8.3695
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g58000.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B359.65.6e-19299394395
                       EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
                B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                       k+lt+sdv++ gr+v+pk+ ae+h   + ++e+++l++ d +   +W++k+++  ++ks++yvl+  + +Fvk++gL++gD+++++ + ++++
  LOC_Os04g58000.1 299 KELTNSDVGNIGRIVMPKRDAEAHlpALHQREGVMLKMDDfKLETTWNFKYRFwpNNKSRMYVLE-STGGFVKQHGLQTGDIFIIYKS-SESE 389
                       89************************888999********7778*******9989999999**99.9*******************43.3777 PP

                       ..EEE CS
                B3  91 elvvk 95 
                       +lvv+
  LOC_Os04g58000.1 390 KLVVR 394
                       77776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd100172.03E-22296394No hitNo description
Gene3DG3DSA:2.40.330.101.8E-25296396IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.1E-18296393IPR015300DNA-binding pseudobarrel domain
SMARTSM010194.4E-10297399IPR003340B3 DNA binding domain
PROSITE profilePS508639.079297399IPR003340B3 DNA binding domain
PfamPF023623.2E-15299394IPR003340B3 DNA binding 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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0025281anatomypollen
PO:0001059developmental stageJ bicellular pollen stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 434 aa     Download sequence    Send to blast
MADTRGSTSS GGGDDRGREG HDDFTGGGQY NRYHRILEAV PSPLVRRENG VHHQYPTGLI  60
HHPSSTMPVA PCSYVPRYTM VPTSAMLPLQ HHHRQLQISQ ENFQDRVPSN NVAAPHLPSN  120
FQDLRPMCNG PPFMSYGQTA SNRNVLYQNL TPYSFNAWAS NNMPRNPVYT SYHPTAIEDP  180
HATPFHINNH DTDQGFFTVS TSFRVDQSFV HAPSPFPPVS SSSRSFSSAQ ISNGPIDAKK  240
AKKSDIKDQP IVLRRSDTES EKNDELDQTP ASEPSSMSHN SANSTIRFNC REYRVILRKE  300
LTNSDVGNIG RIVMPKRDAE AHLPALHQRE GVMLKMDDFK LETTWNFKYR FWPNNKSRMY  360
VLESTGGFVK QHGLQTGDIF IIYKSSESEK LVVRGEKAIK PNVIMPIVDC SCKNDLNNSE  420
ECGFAISLLT KKT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A5e-352883914106B3 domain-containing transcription factor LEC2
6j9c_D5e-352883914106B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.534770.0callus| flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329828970.0
Expression AtlasQ7XKC5-
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription regulator that binds specifically to the DNA sequence 5'-CATGC-3' of the IDE1 element found in the promoter of the barley iron deficiency-inducible gene IDS2. {ECO:0000269|PubMed:18025467}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g58000.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g58000
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0728740.0AK072874.1 Oryza sativa Japonica Group cDNA clone:J023145I07, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015635183.10.0B3 domain-containing protein Os04g0676600
SwissprotQ7XKC50.0IDEFH_ORYSJ; B3 domain-containing protein Os04g0676600
TrEMBLA0A0E0H7G60.0A0A0E0H7G6_ORYNI; Uncharacterized protein
STRINGOS04T0676600-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP118172835
Representative plantOGRP7881766
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.13e-36B3 family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Kobayashi T, et al.
    The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(48): p. 19150-5
    [PMID:18025467]