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 Sobic.007G050100.1.p
Common NameSb07g004050, SORBIDRAFT_07g004050
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family LSD
Protein Properties Length: 144aa    MW: 14804.3 Da    PI: 7.9177
Description LSD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.007G050100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-LSD142.69.9e-142751125
               zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                          C gCr+lL+YP+GA+sV+Ca+C tV
  Sobic.007G050100.1.p 27 CTGCRNLLMYPAGATSVCCAVCSTV 51
                          9**********************99 PP
2zf-LSD146.84.8e-156690125
               zf-LSD1  1 CggCrtlLsYPrGApsVRCalCdtV 25
                          CggC+tlL+Y rGA+sV+C++C+tV
  Sobic.007G050100.1.p 66 CGGCHTLLMYIRGATSVQCSCCHTV 90
                          ************************9 PP
3zf-LSD141.91.7e-13104128125
               zf-LSD1   1 CggCrtlLsYPrGApsVRCalCdtV 25 
                           Cg+Cr lL+Y +GA+sV+Ca+C++V
  Sobic.007G050100.1.p 104 CGNCRMLLMYQYGARSVKCAVCNFV 128
                           ***********************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.90.10.109.5E-422125No hitNo description
TIGRFAMsTIGR010536.1E-132454IPR005735Zinc finger, LSD1-type
SuperFamilySSF486955.86E-527125IPR011031Multihaem cytochrome
PfamPF069437.7E-112751IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010538.5E-156392IPR005735Zinc finger, LSD1-type
PfamPF069431.3E-126690IPR005735Zinc finger, LSD1-type
TIGRFAMsTIGR010533.9E-12101131IPR005735Zinc finger, LSD1-type
PfamPF069431.0E-12104128IPR005735Zinc finger, LSD1-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009814Biological Processdefense response, incompatible interaction
GO:0034051Biological Processnegative regulation of plant-type hypersensitive response
GO:0034052Biological Processpositive regulation of plant-type hypersensitive response
GO:0045595Biological Processregulation of cell differentiation
GO:2000121Biological Processregulation of removal of superoxide radicals
Sequence ? help Back to Top
Protein Sequence    Length: 144 aa     Download sequence    Send to blast
MPVPLAPYPT PPVPFTPPNG AQSQLVCTGC RNLLMYPAGA TSVCCAVCST VTAVPAPGTE  60
MAQLVCGGCH TLLMYIRGAT SVQCSCCHTV NLAMEANQVA HVNCGNCRML LMYQYGARSV  120
KCAVCNFVTS VGASPGAEQK PSS*
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
PlantRegMapSobic.007G050100.1.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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9729821e-145EU972982.1 Zea mays clone 391080 LOL1 mRNA, complete cds.
GenBankFP0916661e-145FP091666.1 Phyllostachys edulis cDNA clone: bphyst007l18, full insert sequence.
GenBankFP0942101e-145FP094210.1 Phyllostachys edulis cDNA clone: bphylf003c20, full insert sequence.
GenBankFP0971061e-145FP097106.1 Phyllostachys edulis cDNA clone: bphyst016n22, full insert sequence.
GenBankFP0978371e-145FP097837.1 Phyllostachys edulis cDNA clone: bphylf033i22, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002445097.19e-99protein LSD1
RefseqXP_004972784.29e-99protein LSD1
RefseqXP_022683193.19e-99protein LSD1
RefseqXP_025820445.19e-99protein LSD1
RefseqXP_025820446.19e-99protein LSD1
RefseqXP_025820447.19e-99protein LSD1
RefseqXP_025820449.19e-99protein LSD1
SwissprotQ0J7V91e-87LSD1_ORYSJ; Protein LSD1
TrEMBLA0A2T7D3S82e-97A0A2T7D3S8_9POAL; Uncharacterized protein
TrEMBLA0A2T8IF352e-97A0A2T8IF35_9POAL; Uncharacterized protein
TrEMBLC5YHD02e-97C5YHD0_SORBI; Uncharacterized protein
TrEMBLK3YK342e-97K3YK34_SETIT; Uncharacterized protein
STRINGPavir.Fa01884.1.p4e-98(Panicum virgatum)
STRINGSi014603m4e-98(Setaria italica)
STRINGSb07g004050.14e-98(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP134738124
Representative plantOGRP11461753
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G32540.31e-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]