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.3KG003000.1.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 GRAS
Protein Properties Length: 667aa    MW: 70766.1 Da    PI: 6.4493
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG003000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS406.82e-1242976592374
                 GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetsekn.sseelaalklfsevsPi 90 
                           +lLl+cAe v++++l  a+++L ++ ela+p g+++qR+aayf+eA++arl++s+ +ly+ lpp + +  + + +++aa+++f+ +sP+
  Pavir.3KG003000.1.p 297 LTLLLQCAESVNADNLDDAHQTLLEIAELATPFGTSTQRVAAYFAEAMSARLVSSCLGLYAPLPPASPAAARlHGRVAAAFQVFNGISPL 386
                          579************************************************************77666655548899999********** PP

                 GRAS  91 lkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnv 180
                          +kfsh+taNqaI ea+e+eervHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g+    s ++l++tg+rL++fA++lg+pfef +
  Pavir.3KG003000.1.p 387 VKFSHFTANQAIQEAFEREERVHIIDLDIMQGLQWPGLFHILASRPGGPPRVRLTGLGA----SLDALQATGKRLSDFADTLGLPFEFCA 472
                          ***********************************************************....9************************** PP

                 GRAS 181 lvakrledleleeL..rvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalf 268
                           va++  ++++++L   v ++Ea+aV++ +  h+l+d +++ ++    +L+l+++l Pkvv++veq+++h s+sFl+rf+ea++yysalf
  Pavir.3KG003000.1.p 473 -VAEKAGNVDPDKLlgGVARREAVAVHWLH--HSLYDVTGNDSN----TLWLIQRLAPKVVTMVEQDLSH-SGSFLARFVEAIHYYSALF 554
                          .7************99999**********9..999988888888....**********************.899**************** PP

                 GRAS 269 dsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgsl 358
                          dsl+a+++++s er++vE++ll+rei+nv+a  g +r+ + + +++Wre+l ++GF++++l  +aa+qa+lll +++sdgy++ ee+g+l
  Pavir.3KG003000.1.p 555 DSLDASYGEDSPERHVVEQQLLSREIRNVLAVGGPARTGDVK-FGSWREKLAQSGFRSASLAGSAAAQASLLLGMFPSDGYTLVEENGAL 643
                          ************************************999987.*********************************************** PP

                 GRAS 359 vlgWkdrpLvsvSaWr 374
                           lgWkd  L+++SaWr
  Pavir.3KG003000.1.p 644 KLGWKDLCLLTASAWR 659
                          ***************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098561.586270639IPR005202Transcription factor GRAS
PfamPF035147.0E-122297659IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008356Biological Processasymmetric cell division
GO:0009630Biological Processgravitropism
GO:0009956Biological Processradial pattern formation
GO:0048366Biological Processleaf development
GO:0051457Biological Processmaintenance of protein location in nucleus
GO:0090610Biological Processbundle sheath cell fate specification
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 667 aa     Download sequence    Send to blast
MGSSSLLLFP SSSSAAPPPT ASAAYSHATS SHSLLPPLPS SQDHLLLHYL HLAEHHQESA  60
AAAMVRKRPA PDMDLPPPRR HVTGDLSDVT AAAAGAGGQL PHQSPASAQL PALPTQLQLP  120
AYQQQQQHAE VEAPPAAAGE VAASTTAWVD GIIRDIIGSS GSAGVSIAQL IHNVREIIHP  180
CNPGLASLLE LRLRSLLNAD PAPPPLPHPP ALLHSTPPAA APAVPALPPP HPLPDKRRHD  240
PQQQEEPNPS PQSPKPPTAE ETAAAAAAAA AAAAAAAKER KEEQRRKQRD EEGLHLLTLL  300
LQCAESVNAD NLDDAHQTLL EIAELATPFG TSTQRVAAYF AEAMSARLVS SCLGLYAPLP  360
PASPAAARLH GRVAAAFQVF NGISPLVKFS HFTANQAIQE AFEREERVHI IDLDIMQGLQ  420
WPGLFHILAS RPGGPPRVRL TGLGASLDAL QATGKRLSDF ADTLGLPFEF CAVAEKAGNV  480
DPDKLLGGVA RREAVAVHWL HHSLYDVTGN DSNTLWLIQR LAPKVVTMVE QDLSHSGSFL  540
ARFVEAIHYY SALFDSLDAS YGEDSPERHV VEQQLLSREI RNVLAVGGPA RTGDVKFGSW  600
REKLAQSGFR SASLAGSAAA QASLLLGMFP SDGYTLVEEN GALKLGWKDL CLLTASAWRP  660
IQTPCR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A0.02806603380Protein SCARECROW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.86650.0callus| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In the basal portion of the P3 leaf primordium, expressed continuously within the stomatal row. At later stages, expressed in guard mother cell (GMC)-forming cells and in subsidiary mother cell (SMC) just before asymmetric division. {ECO:0000269|PubMed:12974810}.
UniprotTISSUE SPECIFICITY: Expressed in the root endodermis, in the cortex/endodermal initial and in the quiescent center. Not expressed in the shoot apical meristem itself, but strongly in the L1 layer. {ECO:0000269|PubMed:12974810}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in asmmetric cell division in the cortex/endodermis progenitor cell and in the process of stomata and ligule formation in leaves. {ECO:0000250}.
UniProtProbable transcription factor involved in asmmetric cell division in the cortex/endodermis progenitor cell and in the process of stomata and ligule formation in leaves. {ECO:0000269|PubMed:12974810}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG003000.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0636820.0BT063682.1 Zea mays full-length cDNA clone ZM_BFc0094J16 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025807416.10.0protein SCARECROW-like
SwissprotA2ZHL00.0SCR2_ORYSI; Protein SCARECROW 2
SwissprotQ2QYF30.0SCR2_ORYSJ; Protein SCARECROW 2
TrEMBLA0A3L6PCB60.0A0A3L6PCB6_PANMI; Scarecrow
STRINGORUFI12G01460.10.0(Oryza rufipogon)
STRINGOS12T0122000-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP137138122
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54220.10.0GRAS family protein
Publications ? help Back to Top
  1. Kamiya N, et al.
    Rice globular embryo 4 (gle4) mutant is defective in radial pattern formation during embryogenesis.
    Plant Cell Physiol., 2003. 44(9): p. 875-83
    [PMID:14519768]
  2. Lim J, et al.
    Conservation and diversification of SCARECROW in maize.
    Plant Mol. Biol., 2005. 59(4): p. 619-30
    [PMID:16244911]
  3. Kaur P, et al.
    Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates.
    Funct. Integr. Genomics, 2008. 8(4): p. 375-86
    [PMID:18543009]
  4. Sazuka T, et al.
    A rice tryptophan deficient dwarf mutant, tdd1, contains a reduced level of indole acetic acid and develops abnormal flowers and organless embryos.
    Plant J., 2009. 60(2): p. 227-41
    [PMID:19682283]
  5. Fan T, et al.
    Rice osa-miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors.
    PLoS ONE, 2015. 10(5): p. e0125833
    [PMID:26023934]
  6. Yi J, et al.
    OsMPK6 plays a critical role in cell differentiation during early embryogenesis in Oryza sativa.
    J. Exp. Bot., 2016. 67(8): p. 2425-37
    [PMID:26912801]
  7. Li S, et al.
    Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa.
    Plant Cell, 2016. 28(5): p. 1025-34
    [PMID:27081181]