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 GRMZM2G125596_P01
Common NameLOC100272565, ZEAMMB73_484810
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: 369aa    MW: 40029.6 Da    PI: 6.8552
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G125596_P01genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B341.52.4e-13264349384
                        EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
                 B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkl 84 
                        k+lt+sdv +sgr+vlpkk ae+    +++  +  l++ d      W++k+++  ++ks++y+l+    eFvk +gL++gD ++++ 
  GRMZM2G125596_P01 264 KELTKSDVANSGRIVLPKKDAEAGlpPLVQGDPLILQMDDmVLPIIWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDALIIYK 349
                        899******************88899666666656676664445*******99888888888888.99****************993 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.57E-14261351IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.9E-20261365IPR015300DNA-binding pseudobarrel domain
CDDcd100171.49E-19261359No hitNo description
SMARTSM010197.6E-8262362IPR003340B3 DNA binding domain
PfamPF023628.5E-10264350IPR003340B3 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: 369 aa     Download sequence    Send to blast
MGQMGGPDGD GDGGAGPHHQ YHYQALLAAV QNPSQGLHPF PLPFHVPLHA GAGAPAAGPG  60
PGADADASTH NANAAHHSQP PRGFTDWSAS NSAFAAVASQ PAPATTNTPF HYNLSQSYAL  120
WTHYMLNKNV SYSTYPTPHE EHPHPLRHTH IQENPHPLRH THIPDKDSGC ASSLGFDSFT  180
TMSLGPNICS HMTPMEGSIS AKEPENSEDL PAIVRSSDEM DTRNSGKVHR DTVGTLPESK  240
QSHESCASVN NKFNSGEYQV ILRKELTKSD VANSGRIVLP KKDAEAGLPP LVQGDPLILQ  300
MDDMVLPIIW KFKYRFWPNN KSRMYILEAA GEFVKTHGLQ AGDALIIYKN SVPGKFIIRG  360
EKSIQQTNP
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A1e-292533504101B3 domain-containing transcription factor LEC2
6j9c_D1e-292533504101B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.807020.0ear| endosperm| meristem| shoot| tassel
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM2G125596
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
PlantRegMapGRMZM2G125596_P01
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
GenBankBT0389520.0BT038952.1 Zea mays full-length cDNA clone ZM_BFb0345D11 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001140504.10.0putative B3 DNA binding domain family protein
SwissprotQ6Z1Z31e-123IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLB4FPB40.0B4FPB4_MAIZE; B3 domain-containing transcription factor LEC2
TrEMBLK0DCT90.0K0DCT9_MAIZE; ABI47 ABI3VP1 type transcription factor (Fragment)
STRINGGRMZM2G125596_P010.0(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP113462831
Representative plantOGRP7881766
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.19e-32B3 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]