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.3KG535400.4.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 LSD
Protein Properties Length: 139aa    MW: 14660.7 Da    PI: 8.3742
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG535400.4.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD151.41.8e-164367125
              zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                         Cg+C+t+L+YP+GApsV+Ca+C+++
  Pavir.3KG535400.4.p 43 CGQCQTVLMYPYGAPSVKCAICNFI 67
                         ***********************86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010536.5E-124069IPR005735Zinc finger, LSD1-type
PfamPF069431.6E-144367IPR005735Zinc finger, LSD1-type
Sequence ? help Back to Top
Protein Sequence    Length: 139 aa     Download sequence    Send to blast
MPCSHHRATS RNGDGSTYLW WLPNIIDVYS QCNNLSSIAH VNCGQCQTVL MYPYGAPSVK  60
CAICNFITNI GGHQVPMVRP LPPALPASSG NSYNIPSTSA PTSQSQNVTV VVENPMTVDD  120
KGKLVSNVVV GVTTGGKK*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.72771e-166callus| leaf| root
Functional Description ? help Back to Top
Source Description
UniProtPutative zinc finger that may be involved in programmed cell death and defense response. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG535400.4.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
GenBankKF3146991e-136KF314699.1 Setaria italica clone Si18S 18S ribosomal RNA gene, partial sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025805780.18e-67protein LOL2-like isoform X1
SwissprotQ2QMB33e-48LOL2_ORYSJ; Protein LOL2
TrEMBLA0A3L6RCG12e-66A0A3L6RCG1_PANMI; Protein LOL2-like isoform X1
STRINGPavir.J37999.1.p5e-67(Panicum virgatum)
STRINGPavir.J38598.1.p4e-67(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G20380.71e-15LSD 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. Wu J, et al.
    OsLOL1, a C2C2-type zinc finger protein, interacts with OsbZIP58 to promote seed germination through the modulation of gibberellin biosynthesis in Oryza sativa.
    Plant J., 2014. 80(6): p. 1118-30
    [PMID:25353370]