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.9NG189700.1.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 LSD
Protein Properties Length: 176aa    MW: 18341.2 Da    PI: 8.4401
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9NG189700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD139.59.5e-13731125
              zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                         C+ Crt+L YPrGApsV+Ca+C++V
  Pavir.9NG189700.1.p  7 CHACRTVLLYPRGAPSVCCAVCQAV 31
                         ************************9 PP
2zf-LSD139.96.7e-134670125
              zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                         CggCrtlL+Y+r A  VRC++C+tV
  Pavir.9NG189700.1.p 46 CGGCRTLLMYTRSADTVRCSCCNTV 70
                         ************************9 PP
3zf-LSD1482e-1584108125
              zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                          Cg+C+t+L+YP+GA sV+Ca+C+++
  Pavir.9NG189700.1.p  84 CGHCQTTLMYPYGAHSVKCAICNHI 108
                          ***********************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010531.2E-12434IPR005735Zinc finger, LSD1-type
PfamPF069432.5E-10731IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010532.3E-154373IPR005735Zinc finger, LSD1-type
PfamPF069437.9E-114670IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010533.2E-1181109IPR005735Zinc finger, LSD1-type
PfamPF069431.4E-1384108IPR005735Zinc finger, LSD1-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000303Biological Processresponse to superoxide
GO:0001666Biological Processresponse to hypoxia
GO:0002240Biological Processresponse to molecule of oomycetes origin
GO:0009626Biological Processplant-type hypersensitive response
GO:0009862Biological Processsystemic acquired resistance, salicylic acid mediated signaling pathway
GO:0010104Biological Processregulation of ethylene-activated signaling pathway
GO:0010310Biological Processregulation of hydrogen peroxide metabolic process
GO:0010602Biological Processregulation of 1-aminocyclopropane-1-carboxylate metabolic process
GO:0010618Biological Processaerenchyma formation
GO:0043069Biological Processnegative regulation of programmed cell death
Sequence ? help Back to Top
Protein Sequence    Length: 176 aa     Download sequence    Send to blast
MQSQIVCHAC RTVLLYPRGA PSVCCAVCQA VTTVPPPGLE MAQLICGGCR TLLMYTRSAD  60
TVRCSCCNTV NLVRPVNNIA HVNCGHCQTT LMYPYGAHSV KCAICNHITT TGVNTVAPTP  120
SARPASNGSA YSTSSTSVPK SQPQNVTVVV ENPMTVDDKG KLVSNVVVGV TTGKN*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.64440.0callus| 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.9NG189700.1.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
GenBankEU9750491e-173EU975049.1 Zea mays clone 466017 zinc finger protein LSD2 mRNA, complete cds.
GenBankEU9764861e-173EU976486.1 Zea mays clone 895962 zinc finger protein LSD2 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025796943.11e-121protein LOL3-like
SwissprotQ6ASS27e-95LOL3_ORYSJ; Protein LOL3
TrEMBLA0A3L6S9J31e-120A0A3L6S9J3_PANMI; Uncharacterized protein
STRINGPavir.Ib04023.1.p1e-121(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP134738124
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G20380.71e-50LSD 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]