PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Traes_7BL_6183FA9D4.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Triticinae; Triticum
Family B3
Protein Properties Length: 229aa    MW: 25674.2 Da    PI: 6.2491
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Traes_7BL_6183FA9D4.1genomeIWGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B345.61.3e-14125211387
                            EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                     B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                            k+lt+sdv + gr+vlpkk ae+    + ++ ++ l++ d     +W++k+++  ++ks++y+l   ++eFvk +gL++gD ++++  
  Traes_7BL_6183FA9D4.1 125 KELTKSDVANVGRIVLPKKDAEASlpPLCERDPVILQMDDmVLPITWKFKYRFwpNNKSRMYILD-STSEFVKTHGLQAGDALIIY-- 209
                            899******************98888666666766777775555*******99777777777777.9****************998.. PP

                            SS CS
                     B3  86 gr 87 
                            ++
  Traes_7BL_6183FA9D4.1 210 KN 211
                            44 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.16E-16122210IPR015300DNA-binding pseudobarrel domain
CDDcd100172.67E-21122220No hitNo description
Gene3DG3DSA:2.40.330.101.6E-21122217IPR015300DNA-binding pseudobarrel domain
SMARTSM010192.9E-8123222IPR003340B3 DNA binding domain
PfamPF023623.0E-11125215IPR003340B3 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: 229 aa     Download sequence    Send to blast
MLNKNAYSYY PAPNQEHTHH FSLDNNQAKD PGSIPSFGIE SFNTTSLAPN MSAHMPPMEG  60
PLPTKEPEAP EDMPARVATI KDEMDARNGV ELKCETVDAL PELKQGHESC ASKFNSGEYQ  120
VILRKELTKS DVANVGRIVL PKKDAEASLP PLCERDPVIL QMDDMVLPIT WKFKYRFWPN  180
NKSRMYILDS TSEFVKTHGL QAGDALIIYK NPVPGKYIVR GEKAIQQTN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A2e-331122182108B3 domain-containing transcription factor LEC2
6j9c_D2e-331122182108B3 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}.
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
GenBankAK3739020.0AK373902.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv3046N18.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020169706.11e-169B3 domain-containing protein IDEF1-like
SwissprotQ6Z1Z31e-103IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A3B6SGK41e-169A0A3B6SGK4_WHEAT; Uncharacterized protein
TrEMBLA0A446YJQ21e-169A0A446YJQ2_TRITD; Uncharacterized protein
TrEMBLA0A453S4231e-170A0A453S423_AEGTS; Uncharacterized protein
STRINGTraes_7BL_6183FA9D4.11e-172(Triticum aestivum)
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
AT3G24650.12e-35B3 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. Brenchley R, et al.
    Analysis of the bread wheat genome using whole-genome shotgun sequencing.
    Nature, 2012. 491(7426): p. 705-10
    [PMID:23192148]
  6. 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]
  7. Kobayashi T,Nishizawa NK
    Iron sensors and signals in response to iron deficiency.
    Plant Sci., 2014. 224: p. 36-43
    [PMID:24908504]
  8. Kobayashi T,Nakanishi Itai R,Nishizawa NK
    Iron deficiency responses in rice roots.
    Rice (N Y), 2014. 7(1): p. 27
    [PMID:26224556]
  9. 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]
  10. 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]