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 Bradi3g12910.1.p
Common NameBRADI_3g12910, LOC100820925
Organism
Brachypodium distachyon
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium
Family B3
Protein Properties Length: 350aa    MW: 37995.5 Da    PI: 7.4537
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bradi3g12910.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B345.41.4e-14243327383
                       EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFk 83 
                       k+lt+sdv + gr+vlpkk ae+   ++ ++ ++ l++ d     +W++k+++  ++ks++y+l   + eFvk +gL++gD +v++
  Bradi3g12910.1.p 243 KELTKSDVANVGRIVLPKKDAEAGlpQLCQRDPMILKMDDmVLPVTWKFKYRFwpNNKSRMYILD-STAEFVKTHGLQAGDALVIY 327
                       899******************87788666677878888885555*******99777777777777.9*****************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.9E-20239335IPR015300DNA-binding pseudobarrel domain
CDDcd100175.78E-20240338No hitNo description
SuperFamilySSF1019361.37E-15240328IPR015300DNA-binding pseudobarrel domain
SMARTSM010191.1E-5241341IPR003340B3 DNA binding domain
PfamPF023624.0E-11243327IPR003340B3 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: 350 aa     Download sequence    Send to blast
MGGGDGRHGD GGGGSHPHQF QYQALLAAVH TQNPNHNTLP FPLPPLNGNG PDAPANNAAR  60
HPPAPRGFAD WSASNSAFTS LAAQSTPAAS TAASANNAYH YGVTPCYAFW THYMLNKSGY  120
SYYPPQHQEH LHPFCPDSQQ AKNTGSALSF GVDSFTSTPV APNISLAPNS SAHMPPMEGR  180
LSTREPETSE DVPRVVRRKA GMETRNGGED NCETVDTLPE LNQGHESCAT KLNSGEYEVI  240
LRKELTKSDV ANVGRIVLPK KDAEAGLPQL CQRDPMILKM DDMVLPVTWK FKYRFWPNNK  300
SRMYILDSTA EFVKTHGLQA GDALVIYKNP VPGKFIIRGE KAIQHPTNP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A9e-3023933011102B3 domain-containing transcription factor LEC2
6j9c_D9e-3023933011102B3 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
PlantRegMapBradi3g12910.1.p
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003573243.10.0B3 domain-containing protein IDEF1
SwissprotQ6Z1Z31e-121IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLI1I0790.0I1I079_BRADI; Uncharacterized protein
STRINGBRADI3G12910.10.0(Brachypodium distachyon)
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
AT3G24650.12e-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]