PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID PGSC0003DMP400036746
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family LSD
Protein Properties Length: 175aa    MW: 18108 Da    PI: 8.394
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400036746genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD138.32.2e-12730124
               zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdt 24
                          C+gCrt+L YPrGA++V+Ca+C++
  PGSC0003DMP400036746  7 CSGCRTMLLYPRGASNVCCAVCNA 30
                          **********************97 PP

2zf-LSD145.21.5e-144670125
               zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                          CggCrtlL+ PrGA sVRC++C+tV
  PGSC0003DMP400036746 46 CGGCRTLLMHPRGANSVRCSCCHTV 70
                          ************************9 PP

3zf-LSD139.11.2e-1284107124
               zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdt 24 
                           Cg+Cr +L+YP GApsV+Ca+C+ 
  PGSC0003DMP400036746  84 CGNCRMMLMYPCGAPSVKCAVCHY 107
                           **********************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
TIGRFAMsTIGR010534.2E-13432IPR005735Zinc finger, LSD1-type
PfamPF069435.4E-11730IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010535.8E-174373IPR005735Zinc finger, LSD1-type
PfamPF069437.9E-134670IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010532.5E-1181110IPR005735Zinc finger, LSD1-type
PfamPF069433.0E-1284108IPR005735Zinc 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: 175 aa     Download sequence    Send to blast
MQSQLMCSGC RTMLLYPRGA SNVCCAVCNA LTPVPPPGME MAQLICGGCR TLLMHPRGAN  60
SVRCSCCHTV NLVPGPNQFA HVYCGNCRMM LMYPCGAPSV KCAVCHYITN VNAGDGRAHA  120
SLNPPNGTAT PASGSSSTAK ARSQNQTVVV QNPMSVDESG KLVSNVVVGV TTTS*
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
PlantRegMapPGSC0003DMP400036746
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKT0364910.0KT036491.1 Solanum tuberosum cultivar Kexin-4 LSD1-like protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006353029.11e-123PREDICTED: protein LSD1
RefseqXP_006353030.11e-123PREDICTED: protein LSD1
RefseqXP_015166652.11e-123PREDICTED: protein LSD1
SwissprotQ6ASS23e-66LOL3_ORYSJ; Protein LOL3
TrEMBLM1BWM11e-121M1BWM1_SOLTU; LSD1-like protein
STRINGPGSC0003DMT4000546161e-122(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA16792467
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G32540.16e-55lsd 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]
  2. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  3. Teper-Bamnolker P, et al.
    Release of apical dominance in potato tuber is accompanied by programmed cell death in the apical bud meristem.
    Plant Physiol., 2012. 158(4): p. 2053-67
    [PMID:22362870]