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_Os08g01090.2
Common NameB1147B12.12, IDEF1, LOC4344415, Os08g0101000, OsJ_25718
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: 327aa    MW: 36369.7 Da    PI: 7.9382
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os08g01090.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B340.45.1e-13219303383
                       EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS...-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesg...rsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFk 83 
                       k+lt+sdv++ gr+vlpkk ae+    + ++ +  l + d       +W++k++y  ++ks++y+l     eF k +gL++gD+++++
  LOC_Os08g01090.2 219 KELTKSDVGNVGRIVLPKKDAEASlpPLLQRDPLILHMDD--MvlpVTWKFKYRYwpNNKSRMYILD-SAGEFLKTHGLQAGDVIIIY 303
                       899******************9998844445565566666..3446*********777777777777.99***************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd100171.63E-19216314No hitNo description
SuperFamilySSF1019364.58E-16216304IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.5E-20216311IPR015300DNA-binding pseudobarrel domain
SMARTSM010196.1E-7217317IPR003340B3 DNA binding domain
PROSITE profilePS508638.557217319IPR003340B3 DNA binding domain
PfamPF023628.4E-10219303IPR003340B3 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:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0025281anatomypollen
PO:0001015developmental stageK second mitotic division stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 327 aa     Download sequence    Send to blast
MDGWIGAEPP HPHNHNHNHN HNHNIHNSHN HNHNHNAAPH PCHTPTPTPT PRGFADWSAS  60
TSAFTSLAAH SSTAPSNAVH YSFSPCYAFW THYMLNKNAY PTSFPAPHDD HLRLANNNHP  120
RDAPGPASSY GVESFTSPSM APNICTHMPP IEGPISAKED KKPEILPRVV KSSDELETRN  180
SNVEFHSETV GTLPESKQGH DSRATKLLNS GEYQVILRKE LTKSDVGNVG RIVLPKKDAE  240
ASLPPLLQRD PLILHMDDMV LPVTWKFKYR YWPNNKSRMY ILDSAGEFLK THGLQAGDVI  300
IIYKNLAPGK FIIRGEKAIH QQTTNP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A7e-3021430510101B3 domain-containing transcription factor LEC2
6j9c_D7e-3021430510101B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.138090.0callus| flower| leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329926650.0
Expression AtlasQ6Z1Z3-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots. {ECO:0000269|PubMed:18025467}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription regulator involved in iron deficiency response and tolerance. May regulate directly iron transporters or other transcription factors involved in iron-deficiency response. 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}.
Function -- GeneRIF ? help Back to Top
  1. the cellular CSN6 level is decreased during early stages of -Fe to ensure the rapid accumulation of IDEF1, which in turn up-regulates several iron uptake/utilisation-related genes to help overcome -Fe stress in rice.
    [PMID: 27137867]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os08g01090.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated during the early stage of iron deficiency (at protein level). {ECO:0000269|PubMed:27137867}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs08g01090
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1074560.0AK107456.1 Oryza sativa Japonica Group cDNA clone:002-128-C10, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015648159.10.0B3 domain-containing protein IDEF1 isoform X1
SwissprotQ6Z1Z30.0IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A0E0QD760.0A0A0E0QD76_ORYRU; Uncharacterized protein
STRINGORUFI08G00070.20.0(Oryza rufipogon)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.14e-34B3 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]
  3. Kobayashi T, et al.
    The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes.
    Plant J., 2009. 60(6): p. 948-61
    [PMID:19737364]
  4. Kobayashi T, et al.
    The spatial expression and regulation of transcription factors IDEF1 and IDEF2.
    Ann. Bot., 2010. 105(7): p. 1109-17
    [PMID:20197292]
  5. Kobayashi T, et al.
    The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status.
    Plant J., 2012. 69(1): p. 81-91
    [PMID:21880076]
  6. Itai RN,Ogo Y,Kobayashi T,Nakanishi H,Nishizawa NK
    Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots.
    Rice (N Y), 2013. 6(1): p. 16
    [PMID:24280375]
  7. Kobayashi T,Nishizawa NK
    Iron sensors and signals in response to iron deficiency.
    Plant Sci., 2014. 224: p. 36-43
    [PMID:24908504]
  8. Kobayashi T,Nakanishi Itai R,Nishizawa NK
    Iron deficiency responses in rice roots.
    Rice (N Y), 2014. 7(1): p. 27
    [PMID:26224556]
  9. Tan S, et al.
    CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa.
    Sci Rep, 2016. 6: p. 25485
    [PMID:27137867]
  10. Kobayashi T, et al.
    Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots.
    Plant Mol. Biol., 2016. 91(4-5): p. 533-47
    [PMID:27143046]