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 Oropetium_20150105_13618A
Organism
Oropetium thomaeum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Cynodonteae; Tripogoninae; Oropetium
Family B3
Protein Properties Length: 337aa    MW: 36874.4 Da    PI: 6.6269
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Oropetium_20150105_13618AgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B341.13.3e-13230315384
                                EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEE CS
                         B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvv 81 
                                k+lt+sdv + gr+vlpkk ae+    ++   +  l++ d     +W++k+++  ++ks++y+l+    eFvk +gL++gD ++
  Oropetium_20150105_13618A 230 KELTKSDVANVGRIVLPKKDAEASlpPLVRGDPLILQMDDmVLPITWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDALI 312
                                899******************99999666666656777664445*******99888888888888.99**************** PP

                                EEE CS
                         B3  82 Fkl 84 
                                ++ 
  Oropetium_20150105_13618A 313 IYK 315
                                993 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.3E-20227327IPR015300DNA-binding pseudobarrel domain
CDDcd100171.07E-19227325No hitNo description
SuperFamilySSF1019369.03E-15227316IPR015300DNA-binding pseudobarrel domain
SMARTSM010196.8E-8228328IPR003340B3 DNA binding domain
PfamPF023628.3E-10230316IPR003340B3 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
Sequence ? help Back to Top
Protein Sequence    Length: 337 aa     Download sequence    Send to blast
MGAGNGDAGS GGGLPHQYHQ YQALLAAVQN PNQTLHPFSL PFPFPCGPGA DASPPNAAYH  60
SLTPRGFSDW STSNSAFTSL AGQSAPATTN PPFNYIHSPP HAQWTHYMLN KNAVCSYPAP  120
TEEHAHTLHR THSQDKESGS ATNLGVESFT TMSLGPNICA QMLPMEGSIS TKEAENSEDF  180
PIVVRSSDEM DIRNTREFHR ETVETLPEPK QVHETCNTFT SGDYQVILRK ELTKSDVANV  240
GRIVLPKKDA EASLPPLVRG DPLILQMDDM VLPITWKFKY RFWPNNKSRM YILEAAGEFV  300
KTHGLQAGDA LIIYKNSVPG KFIIRGEKAI QQATNS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A4e-312183163101B3 domain-containing transcription factor LEC2
6j9c_D4e-312183163101B3 domain-containing transcription factor LEC2
Search in ModeBase
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapOropetium_20150105_13618A
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-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0389521e-115BT038952.1 Zea mays full-length cDNA clone ZM_BFb0345D11 mRNA, complete cds.
GenBankEU9715151e-115EU971515.1 Zea mays clone 366455 mRNA sequence.
GenBankJX4285221e-115JX428522.1 Zea mays subsp. mays clone pUT3121 ABI47 ABI3VP1 type transcription factor mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001140504.11e-162putative B3 DNA binding domain family protein
SwissprotQ6Z1Z31e-120IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A0A8XSY41e-164A0A0A8XSY4_ARUDO; Uncharacterized protein
STRINGGRMZM2G125596_P011e-162(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP113462831
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.13e-33B3 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 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. 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]
  4. 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]
  5. 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]
  6. Kobayashi T,Nishizawa NK
    Iron sensors and signals in response to iron deficiency.
    Plant Sci., 2014. 224: p. 36-43
    [PMID:24908504]
  7. Kobayashi T,Nakanishi Itai R,Nishizawa NK
    Iron deficiency responses in rice roots.
    Rice (N Y), 2014. 7(1): p. 27
    [PMID:26224556]
  8. 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]
  9. 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]