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 Pavir.6KG263500.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family B3
Protein Properties Length: 362aa    MW: 38927.5 Da    PI: 6.5471
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6KG263500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B342.41.2e-13256342385
                          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 ++++ +
  Pavir.6KG263500.1.p 256 KELTKSDVANVGRIVLPKKDAEASlpPLVQGDPLILQMDDmVLPVTWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDALIIYKN 342
                          899******************99999666666666777774455*******99888888888888.99****************9933 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.8E-20253350IPR015300DNA-binding pseudobarrel domain
SMARTSM010199.4E-7254354IPR003340B3 DNA binding domain
PROSITE profilePS508638.628254356IPR003340B3 DNA binding domain
SuperFamilySSF1019367.06E-15254342IPR015300DNA-binding pseudobarrel domain
CDDcd100172.16E-19256354No hitNo description
PfamPF023623.6E-10256346IPR003340B3 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: 362 aa     Download sequence    Send to blast
MGQMGGPDGD GRGGAHPHHQ YQALLAAVQN PAQGLHHFPL PFHVPLHQGP PAAGPGPAAD  60
TAASTHNAAP HSQHPRGLAD WSDSSSSAFA SVSAQPAPAT TNAPPVPYNL SQSYALWSHY  120
MLNKNAVPYS SYPAPHEENP HPLRHTHIPP HKDPGSTYSM ETAGSASSLG FDSFTTMSLG  180
PNICAHMSAM EASLPAKEAE NSEDLPTVVR NSDEMDTINS EEVHHDTAAT IPESKPSHES  240
CTTKFNSGEY QVVLRKELTK SDVANVGRIV LPKKDAEASL PPLVQGDPLI LQMDDMVLPV  300
TWKFKYRFWP NNKSRMYILE AAGEFVKTHG LQAGDALIIY KNSVPGKFII RAEKAIQQTN  360
P*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9c_A2e-312453424101B3 domain-containing transcription factor LEC2
6j9c_D2e-312453424101B3 domain-containing transcription factor LEC2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.65590.0callus| leaf| root| stem
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
PlantRegMapPavir.6KG263500.1.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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0389521e-180BT038952.1 Zea mays full-length cDNA clone ZM_BFb0345D11 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025822621.10.0B3 domain-containing protein IDEF1-like isoform X2
SwissprotQ6Z1Z31e-114IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBLA0A2T7D2910.0A0A2T7D291_9POAL; Uncharacterized protein
STRINGPavir.Fa02368.1.p0.0(Panicum virgatum)
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-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]