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 Sopen05g009980.1
Organism
Solanum pennellii
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; Lycopersicon
Family NF-YC
Protein Properties Length: 135aa    MW: 14763.3 Da    PI: 11.0464
Description NF-YC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopen05g009980.1genomespennView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YC29.41.7e-09231021997
             NF-YC  19 helPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavt.rtdifdflvdivp 97 
                        ++P+ari + lk+ +  k++ a aPv+l+   e++ +e+   + + a++ k++ +    i+ a+    + ++fl d+ +
  Sopen05g009980.1  23 LKFPVARIARFLKVGKYAKRVGAGAPVFLAAVLEYLAVEVLELAGVAARNDKKTRITPRHIQLAIRfDQELYQFLRDVTI 102
                       689**************************************99*******************999736789******865 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004142.9E-592122IPR002119Histone H2A
Gene3DG3DSA:1.10.20.105.3E-506120IPR009072Histone-fold
SuperFamilySSF471137.79E-386119IPR009072Histone-fold
CDDcd000743.67E-5511117No hitNo description
PfamPF001251.1E-151289IPR007125Histone H2A/H2B/H3
PRINTSPR006202.6E-441335IPR002119Histone H2A
PROSITE patternPS0004602127IPR032458Histone H2A conserved site
PRINTSPR006202.6E-444257IPR002119Histone H2A
PRINTSPR006202.6E-445770IPR002119Histone H2A
PRINTSPR006202.6E-447185IPR002119Histone H2A
PfamPF162111.5E-1392125IPR032454Histone H2A, C-terminal domain
PRINTSPR006202.6E-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: 135 aa     Download sequence    Send to blast
MAGKGKNLGS NAKRRSRSSK AGLKFPVARI ARFLKVGKYA KRVGAGAPVF LAAVLEYLAV  60
EVLELAGVAA RNDKKTRITP RHIQLAIRFD QELYQFLRDV TIPNGGVIPK IHKILLPDNK  120
SNTSKAVVAA QEEED
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1eqz_A2e-4811261126PROTEIN (HISTONE H2A)
1eqz_E2e-4811261126PROTEIN (HISTONE H2A)
1hq3_A2e-4811261126HISTONE H2A-IV
1hq3_E2e-4811261126HISTONE H2A-IV
1tzy_A2e-4811261126Histone H2A-IV
1tzy_E2e-4811261126Histone H2A-IV
2aro_A2e-4811261126Histone H2A-IV
2aro_E2e-4811261126Histone H2A-IV
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.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754441e-123HG975444.1 Solanum pennellii chromosome ch05, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015075860.13e-93probable histone H2A.3
SwissprotO818262e-58H2A3_ARATH; Probable histone H2A.3
TrEMBLK4BYJ85e-86K4BYJ8_SOLLC; Histone H2A
STRINGSolyc05g014800.1.18e-87(Solanum lycopersicum)
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]