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 Solyc04g054150.1.1
Common NameLOC104646961
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-YB
Protein Properties Length: 189aa    MW: 21018.4 Da    PI: 8.1841
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc04g054150.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB173.62e-5425120297
               NF-YB   2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyre 92 
                         +e d+flPianvsrimkk lPanakisk+aketvqecvsefisf+t+easdkcqrekrktingddl+wa++tlGfe+yv plk yl+kyre
  Solyc04g054150.1.1  25 KELDKFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLVWAMTTLGFENYVGPLKGYLNKYRE 115
                         788**************************************************************************************** PP

               NF-YB  93 legek 97 
                          egek
  Solyc04g054150.1.1 116 SEGEK 120
                         **997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.105.7E-5219133IPR009072Histone-fold
SuperFamilySSF471139.63E-4028131IPR009072Histone-fold
PfamPF008085.8E-273094IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006151.4E-185876No hitNo description
PROSITE patternPS0068506177IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006151.4E-187795No hitNo description
PRINTSPR006151.4E-1896114No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 189 aa     Download sequence    Send to blast
MTGKKTLNSS VESPLSSNTS DNFSKELDKF LPIANVSRIM KKSLPANAKI SKEAKETVQE  60
CVSEFISFIT GEASDKCQRE KRKTINGDDL VWAMTTLGFE NYVGPLKGYL NKYRESEGEK  120
NSMARNDETS HEPIITSTNN IIGTSYNNNN NNNNVTNFSL ARPEFIQSYK QNYGENLTSK  180
ANLHGVGW*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4g91_B3e-4525115292Transcription factor HapC (Eurofung)
4g92_B3e-4525115292Transcription factor HapC (Eurofung)
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, nodes, leaf blades, leaf sheaths and young panicles. {ECO:0000269|PubMed:20566706}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of flowering time under long day (LD) conditions. Functions as repressor of flowering, independently of HD1 and GHD7. Controls flowering time by negatively regulating the expression of EHD1 and HD3A (PubMed:20566706, PubMed:21148627). Regulates plant height by promoting cell elongation in the internodes (PubMed:20566706). Component of the NF-Y/HAP transcription factor complex (By similarity). {ECO:0000250, ECO:0000269|PubMed:20566706, ECO:0000269|PubMed:21148627}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc04g054150.1.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Circadian-regulation under long day (LD) conditions. Expression increases in the middle of daytime, peaks around the end of the light period and gradually decreases during the dark period and beginning of daylight. {ECO:0000269|PubMed:26542958}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010319776.11e-137nuclear transcription factor Y subunit B-3-like
SwissprotQ0J7P41e-59HD5_ORYSJ; Nuclear transcription factor Y subunit B-11
TrEMBLA0A3Q7GX101e-135A0A3Q7GX10_SOLLC; Uncharacterized protein
STRINGSolyc04g054150.1.11e-136(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA11124356
Representative plantOGRP16817170
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G14540.15e-61nuclear factor Y, subunit B3
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. Yan WH, et al.
    A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice.
    Mol Plant, 2011. 4(2): p. 319-30
    [PMID:21148627]
  3. Dai X, et al.
    LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).
    J Integr Plant Biol, 2012. 54(10): p. 790-9
    [PMID:22963226]
  4. Kim SK, et al.
    OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice.
    Planta, 2016. 243(3): p. 563-76
    [PMID:26542958]