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_Os01g72370.3
Common NameOs01g0952800, OSNPB_010952800
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 bHLH
Protein Properties Length: 248aa    MW: 26961.5 Da    PI: 5.6763
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g72370.3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH45.61.2e-1469120155
                       CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
               HLH   1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                       r+ +hn+ Er RR+++N+ ++ Lr llP a   +++Kls  +++ ++ +YI +Lq
  LOC_Os01g72370.3  69 RKLSHNAYERDRRKQLNELYSSLRALLPDA---DHTKLSIPTTVSRVLKYIPELQ 120
                       6889**************************...*******************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474594.58E-1667137IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000836.60E-1168124No hitNo description
PROSITE profilePS5088813.77668119IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.102.8E-1369135IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000107.8E-1269120IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003532.6E-974125IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0010106Biological Processcellular response to iron ion starvation
GO:0055072Biological Processiron ion homeostasis
GO:0090575Cellular ComponentRNA polymerase II transcription factor complex
GO:0000977Molecular FunctionRNA polymerase II regulatory region sequence-specific DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000032anatomytetrad of microspores
PO:0001029developmental stageE tetrad stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 248 aa     Download sequence    Send to blast
MEQLFVDDPA FASSMSSLEA DIFSGAGQLP SSPWLDLDLD DDVQDLSMAP TTANAVSSGY  60
GSGGSGSHRK LSHNAYERDR RKQLNELYSS LRALLPDADH TKLSIPTTVS RVLKYIPELQ  120
KQVENLERKK KELTTTSTTN CKPGVLGSQL MSEGMAPIVS ATCINDMEIM VQVSLLSNVA  180
GSVLPLSKCI KVLENEGLHF ISSSTSSGFG NRTFYSIHLQ RSEGTINEEC PAFCERLEKV  240
VRNKAKL*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.218930.0callus| leaf| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329834080.0
Expression AtlasQ0JFZ0-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During seeds germination, detected in embryos. In vegetative tissues under iron-sufficient, restricted almost exclusively to vascular bundles of roots and leaves, and to the root exodermis. In response to iron deficiency, accumulates in all tissues of roots and leaves. {ECO:0000269|PubMed:21331630}.
UniprotTISSUE SPECIFICITY: Expressed constitutively at low levels in the roots (PubMed:16887895, PubMed:21331630). Also observed in flowers, developing seeds, embryos and vascular bundles (PubMed:21331630). {ECO:0000269|PubMed:16887895, ECO:0000269|PubMed:21331630}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that binds to the DNA motif 5'-CACGTGG-3' in the promoter of iron (Fe) deficiency-inducible genes as well as of genes involved in iron homeostasis, thus contributing to basal tolerance to iron deficiency, iron uptake from soil and iron transport, particularly during seed maturation and germination (PubMed:16887895, PubMed:17559517, PubMed:21331630, PubMed:26224556). Promotes the accumulation of mugineic acid family phytosiderophores (MAs) (PubMed:17559517). Required for ethylene-mediated signaling during iron deficiency responses (PubMed:21112958). Improves growth and yield, especially in calcareous soil with low iron availability. Promotes iron concentration in shoots and grain (PubMed:21331630). {ECO:0000269|PubMed:16887895, ECO:0000269|PubMed:17559517, ECO:0000269|PubMed:21112958, ECO:0000269|PubMed:21331630, ECO:0000269|PubMed:26224556}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g72370.3
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Strongly induced in both roots and shoots during iron (Fe) deficiency stress (PubMed:16887895, PubMed:18025467, PubMed:19737364, PubMed:21112958, PubMed:21331630, PubMed:24280375). Ethylene enhances the iron deficiency-mediated induction (PubMed:21112958). Induced by arsenate (AsV25 and AsV50); this induction is repressed by nitric oxide (NO) (PubMed:26793232). Accumulates under cadmium (Cd) stress; this induction is inhibited by the DNA methyltransferase inhibitor 5-aza-2-deoxycytidine (Aza) (PubMed:27412910). {ECO:0000269|PubMed:16887895, ECO:0000269|PubMed:18025467, ECO:0000269|PubMed:19737364, ECO:0000269|PubMed:21112958, ECO:0000269|PubMed:21331630, ECO:0000269|PubMed:24280375, ECO:0000269|PubMed:26793232, ECO:0000269|PubMed:27412910}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g72370
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0733850.0AK073385.1 Oryza sativa Japonica Group cDNA clone:J033041D19, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015612709.11e-161protein IRON-RELATED TRANSCRIPTION FACTOR 2 isoform X1
SwissprotQ0JFZ00.0IRO2_ORYSJ; Protein IRON-RELATED TRANSCRIPTION FACTOR 2
TrEMBLA0A0D3EYS01e-159A0A0D3EYS0_9ORYZ; Uncharacterized protein
TrEMBLA0A0D9YK461e-159A0A0D9YK46_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0CD211e-159A0A0E0CD21_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0FYV71e-159A0A0E0FYV7_ORYNI; Uncharacterized protein
TrEMBLI1NVB21e-159I1NVB2_ORYGL; Uncharacterized protein
STRINGOS01T0952800-010.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G56970.15e-30bHLH family protein
Publications ? help Back to Top
  1. Ogo Y, et al.
    The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions.
    Plant J., 2007. 51(3): p. 366-77
    [PMID:17559517]
  2. 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]
  3. Wu J, et al.
    Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa.
    J. Exp. Bot., 2011. 62(2): p. 667-74
    [PMID:21112958]
  4. Ogo Y, et al.
    OsIRO2 is responsible for iron utilization in rice and improves growth and yield in calcareous soil.
    Plant Mol. Biol., 2011. 75(6): p. 593-605
    [PMID:21331630]
  5. Yang A,Li Y,Xu Y,Xu Y,Zhang WH
    A receptor-like protein RMC is involved in regulation of iron acquisition in rice.
    J. Exp. Bot., 2013. 64(16): p. 5009-20
    [PMID:24014863]
  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. Masuda H,Aung MS,Nishizawa NK
    Iron biofortification of rice using different transgenic approaches.
    Rice (N Y), 2013. 6(1): p. 40
    [PMID:24351075]
  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. Singh AP, et al.
    Nitric Oxide Alleviated Arsenic Toxicity by Modulation of Antioxidants and Thiol Metabolism in Rice (Oryza sativa L.).
    Front Plant Sci, 2015. 6: p. 1272
    [PMID:26793232]
  10. Yang A,Zhang WH
    A Small GTPase, OsRab6a, is Involved in the Regulation of Iron Homeostasis in Rice.
    Plant Cell Physiol., 2016. 57(6): p. 1271-80
    [PMID:27257291]
  11. Feng SJ, et al.
    Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium.
    Plant Cell Environ., 2016. 39(12): p. 2629-2649
    [PMID:27412910]