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.6NG062800.1.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: 152aa    MW: 15740.5 Da    PI: 7.9177
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG062800.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD142.51.1e-133559125
              zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                         C gCr+lL+YP+GA+sV+Ca+C tV
  Pavir.6NG062800.1.p 35 CTGCRNLLMYPAGATSVCCAVCSTV 59
                         9**********************99 PP
2zf-LSD146.75.2e-157498125
              zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                         CggC+tlL+Y rGA+sV+C++C+tV
  Pavir.6NG062800.1.p 74 CGGCHTLLMYIRGATSVQCSCCHTV 98
                         ************************9 PP
3zf-LSD141.81.8e-13112136125
              zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                          Cg+Cr lL+Y +GA+sV+Ca+C++V
  Pavir.6NG062800.1.p 112 CGNCRMLLMYQYGARSVKCAVCNFV 136
                          ***********************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.90.10.102.4E-423133No hitNo description
TIGRFAMsTIGR010536.7E-133262IPR005735Zinc finger, LSD1-type
PfamPF069438.4E-113559IPR005735Zinc finger, LSD1-type
SuperFamilySSF486953.35E-535133IPR011031Multihaem cytochrome
TIGRFAMsTIGR010539.3E-1571100IPR005735Zinc finger, LSD1-type
PfamPF069431.4E-127498IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010534.2E-12109139IPR005735Zinc finger, LSD1-type
PfamPF069431.1E-12112136IPR005735Zinc finger, LSD1-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009814Biological Processdefense response, incompatible interaction
GO:0034052Biological Processpositive regulation of plant-type hypersensitive response
GO:2000121Biological Processregulation of removal of superoxide radicals
Sequence ? help Back to Top
Protein Sequence    Length: 152 aa     Download sequence    Send to blast
MPVPLAPYPT PPVPFTPPNV SFVLQFSGAQ SQLVCTGCRN LLMYPAGATS VCCAVCSTVT  60
AVPAPGTEMA QLVCGGCHTL LMYIRGATSV QCSCCHTVNL AMEVNQVAHV NCGNCRMLLM  120
YQYGARSVKC AVCNFVTSVG ASPGAEQKPS S*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.16940.0leaf| root| stem
Functional Description ? help Back to Top
Source Description
UniProtNegative regulator of programmed cell death and hypersensitive response (HR). Positive regulator of callus differentiation. {ECO:0000269|PubMed:15915636}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6NG062800.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. Down-regulated by dark. {ECO:0000269|PubMed:15915636}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006847710.11e-84protein LSD1 isoform X1
RefseqXP_011624573.11e-84protein LSD1 isoform X1
SwissprotQ0J7V93e-84LSD1_ORYSJ; Protein LSD1
TrEMBLB5KLZ62e-86B5KLZ6_BAMOL; LOL1
STRINGPavir.J40729.1.p1e-104(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
AT1G32540.11e-59lsd one like 1
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]