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.8KG098500.1.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: 188aa    MW: 20303.4 Da    PI: 7.6177
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.8KG098500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS177.97.4e-55117749233
                 GRAS  49 Laarlarsvselykalppsetsekn.sseelaalklfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpe 137
                          ++arl++s+ +ly+ lpp + +  + + +++aa+++f+ +sP++kfsh+taNqaI ea+e+eervHiiD+di+qGlQWp L++ LasRp+
  Pavir.8KG098500.1.p   1 MSARLVSSCLGLYAPLPPASPAAARlHGRVAAAFQVFNGISPLVKFSHFTANQAIQEAFEREERVHIIDLDIMQGLQWPGLFHILASRPG 90 
                          579*************77666655548899999********************************************************* PP

                 GRAS 138 gppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeL..rvkpgEalaVnlvlqlhrlldesvsleserd 225
                          gpp++R+Tg+g+    s ++l++tg+rL++fA++lg+pfef + va++  ++++++L   v ++Ea+aV++ +  h+l+d +++ ++   
  Pavir.8KG098500.1.p  91 GPPRVRLTGLGA----SMDALQATGKRLSDFADTLGLPFEFCA-VAEKAGNVDPDKLlgGVARREAVAVHWLH--HSLYDVTGNDSN--- 170
                          ************....***************************.7************99999**********9..899988888777... PP

                 GRAS 226 evLklvks 233
                           +L+l+++
  Pavir.8KG098500.1.p 171 -TLWLIQR 177
                          .8887766 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098532.9691187IPR005202Transcription factor GRAS
PfamPF035142.5E-521177IPR005202Transcription factor GRAS
Sequence ? help Back to Top
Protein Sequence    Length: 188 aa     Download sequence    Send to blast
MSARLVSSCL GLYAPLPPAS PAAARLHGRV AAAFQVFNGI SPLVKFSHFT ANQAIQEAFE  60
REERVHIIDL DIMQGLQWPG LFHILASRPG GPPRVRLTGL GASMDALQAT GKRLSDFADT  120
LGLPFEFCAV AEKAGNVDPD KLLGGVARRE AVAVHWLHHS LYDVTGNDSN TLWLIQRCLA  180
PLLLHCY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_A1e-93118166242Protein SCARECROW
5b3h_D1e-93118166242Protein 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: Expressed in early stages of lateral root primordium formation, becoming restricted to the endodermal cell lineage at later stages. {ECO:0000269|PubMed:10948251}.
UniprotTISSUE SPECIFICITY: Expressed in the root endodermis and in a single file of cells through the quiescent center. {ECO:0000269|PubMed:10948251}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in establishing and maintaining the correct radial pattern in the root apical meristem. {ECO:0000269|PubMed:10948251}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.8KG098500.1.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
GenBankAF2634570.0AF263457.1 Zea mays SCARECROW (SCR) gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001168484.11e-114protein SCARECROW
RefseqXP_021317511.11e-114protein SCARECROW
SwissprotQ9FUZ71e-115SCR_MAIZE; Protein SCARECROW
TrEMBLA0A1E5UKB11e-118A0A1E5UKB1_9POAL; Protein SCARECROW
TrEMBLC0P5W31e-117C0P5W3_MAIZE; Uncharacterized protein
STRINGSb05g001500.11e-115(Sorghum bicolor)
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
AT3G54220.13e-84GRAS family protein
Publications ? help Back to Top
  1. Lim J, et al.
    Conservation and diversification of SCARECROW in maize.
    Plant Mol. Biol., 2005. 59(4): p. 619-30
    [PMID:16244911]