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 Solyc05g014830.1.1
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: 293aa    MW: 33015.9 Da    PI: 10.7515
Description NF-YC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc05g014830.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YC27.28.2e-09221021897
               NF-YC  18 nhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavt.rtdifdflvdivp 97 
                           ++P+ari + lk+ +  k++ a aPv+l+   e++ +e+   + + a++ k++ +    i+ a+    + ++fl d+ +
  Solyc05g014830.1.1  22 SLKFPVARIARFLKVGKYAKRVGAGAPVFLADVLEYLAVEVLELAGIAARNDKKTRITPRHIQLAIRfDKELYQFLRDVTI 102
                         6689**************************************99*******************999736789******875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004141.2E-502122IPR002119Histone H2A
Gene3DG3DSA:1.10.20.108.6E-466120IPR009072Histone-fold
CDDcd000743.27E-5111117No hitNo description
PfamPF001258.1E-151289IPR007125Histone H2A/H2B/H3
PRINTSPR006206.6E-381335IPR002119Histone H2A
SuperFamilySSF471137.49E-3514117IPR009072Histone-fold
PRINTSPR006206.6E-384257IPR002119Histone H2A
PRINTSPR006206.6E-385770IPR002119Histone H2A
PRINTSPR006206.6E-387185IPR002119Histone H2A
PfamPF162111.4E-1092125IPR032454Histone H2A, C-terminal domain
PRINTSPR006206.6E-3899117IPR002119Histone H2A
SMARTSM004141.0E-39159279IPR002119Histone H2A
Gene3DG3DSA:1.10.20.109.6E-40176277IPR009072Histone-fold
SuperFamilySSF471131.3E-29177274IPR009072Histone-fold
PfamPF001253.6E-10179246IPR007125Histone H2A/H2B/H3
PfamPF162119.1E-12249282IPR032454Histone H2A, C-terminal domain
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: 293 aa     Download sequence    Send to blast
MVSEGKNLGS NAKRRSRSSK ASLKFPVARI ARFLKVGKYA KRVGAGAPVF LADVLEYLAV  60
EVLELAGIAA RNDKKTRITP RHIQLAIRFD KELYQFLRDV TILNGGVIQK IHKILQPNNK  120
SNASKAVVAA DCQLRYDLYF TTMHLLMSLR YFGWFEDSSM RLLSCIHHLH RIILFVKASL  180
KFPVARIARF LKVGKYAKHV GAGALVFLVV VLEYLAVEVL ELAGIAERND KKTRITPRHI  240
QLAIRFDKEL YQFLRDVTIP NGGVIPKIHK NFLPHNKSNT SKVVATAQEE ED*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1eqz_A2e-4012851128PROTEIN (HISTONE H2A)
1eqz_E2e-4012851128PROTEIN (HISTONE H2A)
1hq3_A2e-4012851128HISTONE H2A-IV
1hq3_E2e-4012851128HISTONE H2A-IV
1tzy_A2e-4012851128Histone H2A-IV
1tzy_E2e-4012851128Histone H2A-IV
2aro_A2e-4012851128Histone H2A-IV
2aro_E2e-4012851128Histone H2A-IV
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
PlantRegMapSolyc05g014830.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2471637e-92Solanum lycopersicum strain Heinz 1706 chromosome 5 clone slm-47n15 map 5, complete sequence
GenBankAC2472407e-92Solanum 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_004239507.14e-86histone H2A-beta, sperm-like
SwissprotO818261e-50H2A3_ARATH; Probable histone H2A.3
TrEMBLA0A4D6NCD93e-89A0A4D6NCD9_VIGUN; Histone H2A
STRINGSolyc05g014830.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA2782422
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]