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 Solyc05g014800.1.1
Common NameLOC101263314
Organism
Solanum lycopersicum
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: 136aa    MW: 14972.5 Da    PI: 10.9372
Description NF-YC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc05g014800.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YC28.72.8e-09231021997
               NF-YC  19 helPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavt.rtdifdflvdivp 97 
                          ++ +ari + lk+ + vk++ a aPv+l+   e++ +e+   + + a++ k++ +    i+ a+    + ++fl d+ +
  Solyc05g014800.1.1  23 LKFSVARISRFLKVGKYVKRVGAGAPVFLAAVLEYLAVEVLELAGVAARNDKKTRITPRHIQLAIRfDKELYQFLRDVTI 102
                         57899************************************99*******************999736789******864 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004142.8E-552122IPR002119Histone H2A
SuperFamilySSF471131.5E-375119IPR009072Histone-fold
PfamPF001251.2E-14789IPR007125Histone H2A/H2B/H3
Gene3DG3DSA:1.10.20.103.3E-488125IPR009072Histone-fold
CDDcd000747.43E-5311117No hitNo description
PRINTSPR006205.8E-411335IPR002119Histone H2A
PRINTSPR006205.8E-414257IPR002119Histone H2A
PRINTSPR006205.8E-415770IPR002119Histone H2A
PRINTSPR006205.8E-417185IPR002119Histone H2A
PfamPF162118.3E-1392125IPR032454Histone H2A, C-terminal domain
PRINTSPR006205.8E-4199117IPR002119Histone H2A
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006342Biological Processchromatin silencing
GO:0000786Cellular Componentnucleosome
GO:0000790Cellular Componentnuclear chromatin
GO:0003677Molecular FunctionDNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 136 aa     Download sequence    Send to blast
MAGEWKNLGS NAKRRSRSSK AGLKFSVARI SRFLKVGKYV KRVGAGAPVF LAAVLEYLAV  60
EVLELAGVAA RNDKKTRITP RHIQLAIRFD KELYQFLRDV TIPNCGVIPK IHKILLPNNK  120
SNTSKAVVAA QEEED*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1eqz_A1e-4411261126PROTEIN (HISTONE H2A)
1eqz_E1e-4411261126PROTEIN (HISTONE H2A)
1hq3_A1e-4411261126HISTONE H2A-IV
1hq3_E1e-4411261126HISTONE H2A-IV
1tzy_A1e-4411261126Histone H2A-IV
1tzy_E1e-4411261126Histone H2A-IV
2aro_A1e-4411261126Histone H2A-IV
2aro_E1e-4411261126Histone H2A-IV
6c0w_C2e-4411261127Histone H2A
6c0w_G2e-4411261127Histone H2A
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in meristems and dividing cells. {ECO:0000269|PubMed:16751347}.
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
PlantRegMapSolyc05g014800.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2471631e-125Solanum lycopersicum strain Heinz 1706 chromosome 5 clone slm-47n15 map 5, complete sequence
GenBankAC2472401e-125Solanum lycopersicum strain Heinz 1706 chromosome 5 clone slm-34e19 map 5, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004239194.11e-94histone H2A-beta, sperm-like
SwissprotO818263e-54H2A3_ARATH; Probable histone H2A.3
TrEMBLK4BYJ83e-93K4BYJ8_SOLLC; Histone H2A
STRINGSolyc05g014800.1.14e-94(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA16469
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]
  3. Sridhar VV, et al.
    Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination.
    Nature, 2007. 447(7145): p. 735-8
    [PMID:17554311]