PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc01g079870.2.1
Organism
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: 259aa    MW: 28475.3 Da    PI: 6.149
Description NF-YC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc01g079870.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YC176.62.4e-55801831101
               NF-YC   1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdi 88 
                         ql++fw++q   ie++tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlr+w+h+eenkrrtl+k+diaaa+trtdi
  Solyc01g079870.2.1  80 QLQTFWANQyqeIEHVTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRAWNHTEENKRRTLQKNDIAAAITRTDI 170
                         89******99999****************************************************************************** PP

               NF-YC  89 fdflvdivprdel 101
                         fdflvdivpr++l
  Solyc01g079870.2.1 171 FDFLVDIVPREDL 183
                         **********987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF471131.08E-3369174IPR009072Histone-fold
PfamPF008082.6E-22102165IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
Gene3DG3DSA:1.10.20.102.7E-38103180IPR009072Histone-fold
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 259 aa     Download sequence    Send to blast
MDQHGNGQPP GIGVVTSSAP IYGAPYQANQ MAGPSPPAVS AGAIQSPQAA GLAASSAQMA  60
QHQLAYQHIH QQQQQQLQQQ LQTFWANQYQ EIEHVTDFKN HSLPLARIKK IMKADEDVRM  120
ISAEAPVVFA RACEMFILEL TLRAWNHTEE NKRRTLQKND IAAAITRTDI FDFLVDIVPR  180
EDLKDEVLAT IPRGTLPVGG PTEGLPFYYG MPPQSAQPIG APGMYMGKPV DQALYAQQPR  240
PYMAQPIWPQ QQQPPSDS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5g49_B2e-6188180395NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1152158RRTLQKN
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.34100.0callus| cell culture| flower| fruit| leaf| root| stem| trichome
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. Present in etiolated seedlings. {ECO:0000269|PubMed:11867211, ECO:0000269|PubMed:17322342}.
Functional Description ? help Back to Top
Source Description
UniProtStimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters (By similarity). Interacts with REF6 to directly regulate SOC1 transcription in response to flowering signals from photoperiod and gibberellic acid pathways (PubMed:25105952). {ECO:0000250, ECO:0000269|PubMed:25105952}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc01g079870.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2466450.0Solanum lycopersicum strain Heinz 1706 chromosome 1 clone slm-49l1 map 1, complete sequence
GenBankBT0129480.0Lycopersicon esculentum clone 114117R, mRNA sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001233820.20.0CONSTANS interacting pr isoform 1
RefseqXP_019067327.10.0CONSTANS interacting protein 2b isoform X1
SwissprotQ8L4B23e-85NFYC9_ARATH; Nuclear transcription factor Y subunit C-9
TrEMBLQ2VY171e-166Q2VY17_SOLLC; CONSTANS interacting protein 2b
STRINGSolyc01g079870.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA34222447
Representative plantOGRP31517117
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G08970.42e-81nuclear factor Y, subunit C9
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. Ben-Naim O, et al.
    The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA.
    Plant J., 2006. 46(3): p. 462-76
    [PMID:16623906]
  3. Hwang YH, et al.
    Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time.
    Plant Cell Rep., 2016. 35(4): p. 857-65
    [PMID:26754793]
  4. Liu X, et al.
    The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis.
    Nat Commun, 2016. 7: p. 12768
    [PMID:27624486]
  5. Myers ZA, et al.
    NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana.
    PLoS Genet., 2016. 12(9): p. e1006333
    [PMID:27685091]
  6. Tang Y, et al.
    Arabidopsis NF-YCs Mediate the Light-Controlled Hypocotyl Elongation via Modulating Histone Acetylation.
    Mol Plant, 2017. 10(2): p. 260-273
    [PMID:27876642]
  7. Zhao H, et al.
    The Arabidopsis thaliana Nuclear Factor Y Transcription Factors.
    Front Plant Sci, 2016. 7: p. 2045
    [PMID:28119722]
  8. Gnesutta N, et al.
    CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer.
    Plant Cell, 2017. 29(6): p. 1516-1532
    [PMID:28526714]
  9. Bi C,Ma Y,Wang XF,Zhang DP
    Overexpression of the transcription factor NF-YC9 confers abscisic acid hypersensitivity in Arabidopsis.
    Plant Mol. Biol., 2017. 95(4-5): p. 425-439
    [PMID:28924726]
  10. Liu X, et al.
    Temporal-Specific Interaction of NF-YC and CURLY LEAF during the Floral Transition Regulates Flowering.
    Plant Physiol., 2018. 177(1): p. 105-114
    [PMID:29599268]