PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID GRMZM2G405699_P02
Organism
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: 313aa    MW: 34077.9 Da    PI: 6.3879
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G405699_P02genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B337.15.7e-12233313379
                        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_P02 233 KELTKSDVANSGRIVLPKKDAEAGlpPLVQGDPLILQMDDmVLPIIWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDT 313
                        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:2.40.330.104.8E-17230313IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.1E-13230313IPR015300DNA-binding pseudobarrel domain
CDDcd100171.75E-16230313No hitNo description
PROSITE profilePS508638.698231313IPR003340B3 DNA binding domain
PfamPF023622.0E-8233313IPR003340B3 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
Sequence ? help Back to Top
Protein Sequence    Length: 313 aa     Download sequence    Send to blast
MGQMGGPDGD GPHHQYHYQA LLAAVQNPSQ GLHVPLHAGA GAPAAGPGPR PGADADASST  60
HNANATPHSQ PPRAFTDWSA SNSAFAAQPA PATTNTPFHY NLSQSYALWT HYMLNKNVSY  120
STYSTPHEPL RHTHIPDKYS GCAFSLGFDS FTTMSLGPNI CANMTPMERS ISAKEPENSE  180
DLPTVVRSSD EMDTRNSGDV RRDTVDTLPE SKQSHESCAS KFDSGEYQVI LRKELTKSDV  240
ANSGRIVLPK KDAEAGLPPL VQGDPLILQM DDMVLPIIWK FKYRFWPNNK SRMYILEAAG  300
EFVKTHGLQA GDT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A7e-29220312294B3 domain-containing transcription factor LEC2
6j9c_D7e-29220312294B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.984840.0ovary| 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_P02
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
GenBankEU9715150.0EU971515.1 Zea mays clone 366455 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020395341.10.0B3 domain-containing protein IDEF1 isoform X2
SwissprotQ6Z1Z31e-100IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A3L6E7510.0A0A3L6E751_MAIZE; B3 domain-containing protein IDEF1
STRINGGRMZM2G405699_P010.0(Zea mays)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G28300.12e-28B3 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]