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 PGSC0003DMP400061155
Common NameLOC102582468
Organism
Solanum tuberosum
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 NF-YC
Protein Properties Length: 137aa    MW: 14875.3 Da    PI: 11.0647
Description NF-YC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400061155genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YC25.23.4e-08221011896
                 NF-YC  18 nhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavt.rtdifdflvdiv 96 
                             ++P+ari + lk+ +  k++ a aPv+l+   e++ +e+   + + a++ k++ +    i+ a+    +  +fl d+ 
  PGSC0003DMP400061155  22 GLQFPVARIARFLKVGKYAKRVGAGAPVFLAAVLEYLAVEVLELAGIAARNDKKTRIIPRHIQLAIRfDKELNQFLRDVT 101
                           568**************************************999999999999999999999999972455678999975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004143.0E-612122IPR002119Histone H2A
Gene3DG3DSA:1.10.20.101.2E-506120IPR009072Histone-fold
SuperFamilySSF471136.29E-386119IPR009072Histone-fold
CDDcd000741.92E-5611117No hitNo description
PfamPF001259.5E-151289IPR007125Histone H2A/H2B/H3
PRINTSPR006203.2E-441335IPR002119Histone H2A
PROSITE patternPS0004602127IPR032458Histone H2A conserved site
PRINTSPR006203.2E-444257IPR002119Histone H2A
PRINTSPR006203.2E-445770IPR002119Histone H2A
PRINTSPR006203.2E-447185IPR002119Histone H2A
PfamPF162113.1E-1392125IPR032454Histone H2A, C-terminal domain
PRINTSPR006203.2E-4499117IPR002119Histone H2A
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000786Cellular Componentnucleosome
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 137 aa     Download sequence    Send to blast
MAGKGKNLGS NAKRRSRSSK AGLQFPVARI ARFLKVGKYA KRVGAGAPVF LAAVLEYLAV  60
EVLELAGIAA RNDKKTRIIP RHIQLAIRFD KELNQFLRDV TIPNGGVIPR IHNIFLPNNK  120
SNTSKAIADA ADEEED*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5oy7_a2e-5011261126Histone H2A
5oy7_e2e-5011261126Histone H2A
5oy7_G2e-5011261126Histone H2A
5oy7_K2e-5011261126Histone H2A
5oy7_S2e-5011261126Histone H2A
5oy7_W2e-5011261126Histone H2A
5x0x_C2e-5011261126Histone H2A
5x0x_G2e-5011261126Histone H2A
6i84_Q2e-5011261126Histone H2A type 1
6i84_V2e-5011261126Histone H2A type 1
6j99_C2e-5011261126Histone H2A
6j99_G2e-5011261126Histone H2A
6n1z_B2e-5011261126Histone H2A
6n1z_E2e-5011261126Histone H2A
6o96_C2e-5011261126Histone H2A
6o96_G2e-5011261126Histone H2A
6om3_C2e-5011261126Histone H2A
6om3_G2e-5011261126Histone H2A
6om3_O2e-5011261126Histone H2A
6om3_S2e-5011261126Histone H2A
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtCore component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400061155
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754441e-77HG975444.1 Solanum pennellii chromosome ch05, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006341737.11e-93PREDICTED: histone H2A-beta, sperm-like
SwissprotO818265e-60H2A3_ARATH; Probable histone H2A.3
TrEMBLM1DI903e-92M1DI90_SOLTU; Histone H2A
STRINGPGSC0003DMT4000894805e-93(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA16469
Publications ? help Back to Top
  1. Yi H,Sardesai N,Fujinuma T,Chan CW,Gelvin SB
    Constitutive expression exposes functional redundancy between the Arabidopsis histone H2A gene HTA1 and other H2A gene family members.
    Plant Cell, 2006. 18(7): p. 1575-89
    [PMID:16751347]
  2. Sridhar VV, et al.
    Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination.
    Nature, 2007. 447(7145): p. 735-8
    [PMID:17554311]
  3. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]