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 Sof001739
Organism
Saccharum officinarum
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; Saccharinae; Saccharum; Saccharum officinarum complex
Family B3
Protein Properties Length: 374aa    MW: 40787.3 Da    PI: 6.5422
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
gnl|UG|Sof#S17378705PU_unrefUnigeneView CDS
PUT-157a-Saccharum_officinarum-744133732PU_refplantGDBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B341.42.5e-13264355391
                EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS.SEE. CS
         B3   3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr.sefe 91 
                k+lt+sdv +sgr+vlpkk ae+    +++  +  l++ d      W++k+++  ++ks++y+l+    eFvk +gL +gD ++++   + + ++
  Sof001739 264 KELTKSDVANSGRIVLPKKDAEAGlpPLVQGDPLILQMDDmVLPIIWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLXAGDALIIYK--NsEPGK 355
                899******************88899666666656676664445*******99888888888888.99*****************93..335554 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.104.3E-20261367IPR015300DNA-binding pseudobarrel domain
CDDcd100174.87E-19261359No hitNo description
SuperFamilySSF1019362.22E-14261358IPR015300DNA-binding pseudobarrel domain
SMARTSM010193.7E-8262362IPR003340B3 DNA binding domain
PfamPF023621.0E-9264356IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 374 aa     Download sequence    Send to blast
MGQMGGADGD GDGDGGPHHQ YHYQALLAAV QNPSQGLHPF PLPFHLPLHA GAGAPAAGPG  60
ADADASSTHN VHAAPHSQPP RGFTDWSPSN SAFAAVAAQP APATTNTPLH YNLSQPYTLW  120
THYMLNKNVS CSTYPTQHEE NPNPLRHTHI PEENPHPLRH THIPDKDSGC ASSLGFDSFT  180
TMSLGPNICA HMTPMERSIS AKEPENSEDL PAVVRSSDEM DTRNSGEIHH DTVGTLPESK  240
QSHESCASMS NKFNSGEYQV ILRKELTKSD VANSGRIVLP KKDAEAGLPP LVQGDPLILQ  300
MDDMVLPIIW KFKYRFWPNN KSRMYILEAA GEFVKTHGLX AGDALIIYKN SEPGKFIIRG  360
EKSIQQTNPR HNLM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A9e-292533504101B3 domain-containing transcription factor LEC2
6j9c_D9e-292533504101B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sof.45940.0bud| callus| crown| inflorescence| root
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}.
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021321516.10.0B3 domain-containing protein IDEF1 isoform X1
SwissprotQ6Z1Z31e-117IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLC5YLC10.0C5YLC1_SORBI; Uncharacterized protein
STRINGGRMZM2G125596_P010.0(Zea mays)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.17e-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]