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 PH01005516G0020
Organism
Phyllostachys heterocycla
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Bambusoideae; Arundinarodae; Arundinarieae; Arundinariinae; Phyllostachys
Family B3
Protein Properties Length: 305aa    MW: 33579.6 Da    PI: 6.7344
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PH01005516G0020genomeICBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B346.75.9e-15198288390
                      EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
               B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                      k+lt+sdv++ gr+vlpkk ae+    + ++ ++ l++ d     +W++k+++  ++ks++y+l   + eFvk +gL++gD+++++ ++   +
  PH01005516G0020 198 KELTKSDVGNVGRIVLPKKDAESSlpPLFERDPVILQMDDmVLPVTWKFKYRFwpNNKSRMYILD-ATGEFVKTHGLQAGDVFIIYKNS-VPG 288
                      899******************99999555667777888885555*******99777777777777.9*****************99333.444 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.57E-17195284IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.4E-22195291IPR015300DNA-binding pseudobarrel domain
CDDcd100174.85E-21195293No hitNo description
SMARTSM010191.5E-9196296IPR003340B3 DNA binding domain
PROSITE profilePS508638.684196298IPR003340B3 DNA binding domain
PfamPF023628.3E-12198289IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009657Biological Processplastid organization
GO:0009733Biological Processresponse to auxin
GO:0009737Biological Processresponse to abscisic acid
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0031930Biological Processmitochondria-nucleus signaling pathway
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0001076Molecular Functiontranscription factor activity, RNA polymerase II transcription factor binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 305 aa     Download sequence    Send to blast
METEVQRSRS TPDGPGTDAS THNAAQQSPI PRGFGDWSAS SGAFTSLGVQ ATPATSNALH  60
HSLPPCYAFW THYMLNKNAY CSYPPAPHQE HAHTLCHNDN RAKDPGPASS FGIESFTTTS  120
LAPNICAHMP PIEGPISAKE TETSEDLPRV VRSSDERETR NSGELKCETI DTFPESKQGH  180
ESCATKFNSG EYQVILRKEL TKSDVGNVGR IVLPKKDAES SLPPLFERDP VILQMDDMVL  240
PVTWKFKYRF WPNNKSRMYI LDATGEFVKT HGLQAGDVFI IYKNSVPGKF IVRGEKAIQQ  300
TANP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A5e-321872844101B3 domain-containing transcription factor LEC2
6j9c_D5e-321872844101B3 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00083PBMTransfer from AT3G24650Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPH01005516G0020
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020169706.11e-163B3 domain-containing protein IDEF1-like
SwissprotQ6Z1Z31e-147IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A287X0N41e-167A0A287X0N4_HORVV; Uncharacterized protein
STRINGEMT276751e-154(Aegilops tauschii)
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. 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]