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 GRMZM2G405699_P03
Organism
Zea mays
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
Family B3
Protein Properties Length: 180aa    MW: 20060.7 Da    PI: 9.7223
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G405699_P03genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B338.71.8e-12100180379
                        EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-E CS
                 B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDf 79 
                        k+lt+sdv +sgr+vlpkk ae+    +++  +  l++ d      W++k+++  ++ks++y+l+    eFvk +gL++gD+
  GRMZM2G405699_P03 100 KELTKSDVANSGRIVLPKKDAEAGlpPLVQGDPLILQMDDmVLPIIWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDT 180
                        899******************88899666666656676664445*******99888888888888.99*************6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.5E-1797180IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.45E-1397180IPR015300DNA-binding pseudobarrel domain
CDDcd100173.85E-1797180No hitNo description
PROSITE profilePS508638.69898180IPR003340B3 DNA binding domain
PfamPF023626.3E-9100180IPR003340B3 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:0000037anatomyshoot apex
PO:0006310anatomytassel floret
PO:0006339anatomyjuvenile vascular leaf
PO:0006340anatomyadult vascular leaf
PO:0006341anatomyprimary shoot system
PO:0006354anatomyear floret
PO:0006505anatomycentral spike of ear inflorescence
PO:0008018anatomytransition vascular leaf
PO:0009001anatomyfruit
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009054anatomyinflorescence bract
PO:0009066anatomyanther
PO:0009074anatomystyle
PO:0009084anatomypericarp
PO:0009089anatomyendosperm
PO:0020040anatomyleaf base
PO:0020104anatomyleaf sheath
PO:0020126anatomytassel inflorescence
PO:0020127anatomyprimary root
PO:0020136anatomyear inflorescence
PO:0020142anatomystem internode
PO:0020148anatomyshoot apical meristem
PO:0025142anatomyleaf tip
PO:0025287anatomyseedling coleoptile
PO:0001007developmental stagepollen development stage
PO:0001009developmental stageD pollen mother cell meiosis stage
PO:0001052developmental stagevascular leaf expansion stage
PO:0001053developmental stagevascular leaf post-expansion stage
PO:0001083developmental stageinflorescence development stage
PO:0001094developmental stageplant embryo coleoptilar stage
PO:0001095developmental stageplant embryo true leaf formation stage
PO:0001180developmental stageplant proembryo stage
PO:0007001developmental stageearly whole plant fruit ripening stage
PO:0007003developmental stageIL.03 full inflorescence length reached stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
PO:0007015developmental stageradicle emergence stage
PO:0007016developmental stagewhole plant flowering stage
PO:0007022developmental stageseed imbibition stage
PO:0007026developmental stageFL.00 first flower(s) open stage
PO:0007031developmental stagemid whole plant fruit ripening stage
PO:0007032developmental stagewhole plant fruit formation stage up to 10%
PO:0007045developmental stagecoleoptile emergence stage
PO:0007063developmental stageLP.07 seven leaves visible stage
PO:0007065developmental stageLP.05 five leaves visible stage
PO:0007072developmental stageLP.18 eighteen leaves visible stage
PO:0007094developmental stageLP.01 one leaf visible stage
PO:0007101developmental stageLP.09 nine leaves visible stage
PO:0007104developmental stageLP.15 fifteen leaves visible stage
PO:0007106developmental stageLP.03 three leaves visible stage
PO:0007112developmental stage1 main shoot growth stage
PO:0007116developmental stageLP.11 eleven leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007633developmental stageendosperm development stage
PO:0021004developmental stageinflorescence initiation stage
Sequence ? help Back to Top
Protein Sequence    Length: 180 aa     Download sequence    Send to blast
MLMPPPRIMP MPLPTLSLQE LSLIGARPTV PLPHSPPLLP PIHPSTTTSP SLMPYGPITC  60
STRMYPTLLT LHHMSRCAIP TSRISIQKFD SGEYQVILRK ELTKSDVANS GRIVLPKKDA  120
EAGLPPLVQG DPLILQMDDM VLPIIWKFKY RFWPNNKSRM YILEAAGEFV KTHGLQAGDT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A1e-3089179494B3 domain-containing transcription factor LEC2
6j9c_D1e-3089179494B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.984841e-157ovary| shoot
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM2G405699
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGRMZM2G405699_P03
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
GenBankEU9715151e-154EU971515.1 Zea mays clone 366455 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020395340.11e-61B3 domain-containing protein IDEF1 isoform X1
RefseqXP_020395341.11e-61B3 domain-containing protein IDEF1 isoform X2
SwissprotQ6Z1Z36e-53IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A1D6LDA91e-61A0A1D6LDA9_MAIZE; Putative B3 DNA binding domain family protein
STRINGGRMZM2G405699_P012e-61(Zea mays)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G28300.16e-30B3 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]