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 LOC_Os02g07450.2
Common NameLOC4328444, OJ1116_A06.31, Os02g0170500, OsHAP5A, OsJ_05556, OSNPB_020170500, P0030G02.21
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family NF-YC
Protein Properties Length: 260aa    MW: 28789.3 Da    PI: 4.6278
Description NF-YC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g07450.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YC178.37.4e-56831871102
             NF-YC   1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifd 90 
                       ql+ fw++q   ie++tdfknh+lPlarikki+kadedv+misaeaPv+++kace+fileltlrsw+h+eenkrrtl+k+diaaa+trtdi+d
  LOC_Os02g07450.2  83 QLREFWANQmeeIEQTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFAKACEVFILELTLRSWMHTEENKRRTLQKNDIAAAITRTDIYD 175
                       89******9777789****************************************************************************** PP

             NF-YC  91 flvdivprdelk 102
                       flvdivprde+k
  LOC_Os02g07450.2 176 FLVDIVPRDEMK 187
                       *********975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF471136.2E-3457177IPR009072Histone-fold
Gene3DG3DSA:1.10.20.102.1E-3797169IPR009072Histone-fold
PfamPF008085.3E-21105168IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0046982Molecular Functionprotein heterodimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 260 aa     Download sequence    Send to blast
MEPSSQPQPV MGVATGGSQA YPPPAAAYPP QAMVPGAPAV VPPGSQPSAP FPTNPAQLSA  60
QHQLVYQQAQ QFHQQLQQQQ QQQLREFWAN QMEEIEQTTD FKNHSLPLAR IKKIMKADED  120
VRMISAEAPV VFAKACEVFI LELTLRSWMH TEENKRRTLQ KNDIAAAITR TDIYDFLVDI  180
VPRDEMKEEG LGLPRVGLPP NVGGAADTYP YYYVPAQQGP GSGMMYGGQQ GHPVTYVWQQ  240
PQEQQEEAPE EQHSLPESS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5g49_B1e-5991183395NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1155161RRTLQKN
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.108760.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ6H707
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:26542958). Component of the NF-Y/HAP transcription factor complex (By similarity). {ECO:0000250, ECO:0000269|PubMed:26542958}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g07450.2
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-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g07450
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2880410.0AB288041.1 Oryza sativa Japonica Group OsHAP5A gene for HAP5 subunit of HAP complex, complete cds.
GenBankAK2434290.0AK243429.1 Oryza sativa Japonica Group cDNA, clone: J100067L16, full insert sequence.
GenBankAP0041130.0AP004113.3 Oryza sativa Japonica Group genomic DNA, chromosome 2, BAC clone:OJ1116_A06.
GenBankAP0048360.0AP004836.2 Oryza sativa Japonica Group genomic DNA, chromosome 2, PAC clone:P0030G02.
GenBankAP0149580.0AP014958.1 Oryza sativa Japonica Group DNA, chromosome 2, cultivar: Nipponbare, complete sequence.
GenBankCP0126100.0CP012610.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 2 sequence.
GenBankHQ1626830.0HQ162683.1 Oryza sativa Japonica Group nuclear transcription factor Y subunit gamma mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015627520.10.0nuclear transcription factor Y subunit C-4-like
RefseqXP_015627522.10.0nuclear transcription factor Y subunit C-4-like
SwissprotQ655V51e-127NFYC4_ORYSJ; Nuclear transcription factor Y subunit C-4
TrEMBLA0A0D3F1A70.0A0A0D3F1A7_9ORYZ; Uncharacterized protein
TrEMBLA0A0D9YMY10.0A0A0D9YMY1_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0G2060.0A0A0E0G206_ORYNI; Uncharacterized protein
TrEMBLA0A0E0NAH20.0A0A0E0NAH2_ORYRU; Uncharacterized protein
TrEMBLA2X1E40.0A2X1E4_ORYSI; Uncharacterized protein
TrEMBLI1NXP30.0I1NXP3_ORYGL; Uncharacterized protein
TrEMBLQ6H7070.0Q6H707_ORYSJ; HAP5 subunit of HAP complex
STRINGOGLUM02G05270.10.0(Oryza glumipatula)
STRINGORUFI02G05530.10.0(Oryza rufipogon)
STRINGOS02T0170500-010.0(Oryza sativa)
STRINGONIVA02G05730.10.0(Oryza nivara)
STRINGORGLA02G0049900.10.0(Oryza glaberrima)
STRINGOBART02G05400.10.0(Oryza barthii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G56170.23e-74nuclear factor Y, subunit C2
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Thirumurugan T,Ito Y,Kubo T,Serizawa A,Kurata N
    Identification, characterization and interaction of HAP family genes in rice.
    Mol. Genet. Genomics, 2008. 279(3): p. 279-89
    [PMID:18193457]
  3. 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]