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_Os02g49370.1
Common NameLOC4330586, OJ1124_G07.19, Os02g0725700, OsHAP3E, OsJ_08218, OSNPB_020725700
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-YB
Protein Properties Length: 255aa    MW: 27147.2 Da    PI: 6.7339
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g49370.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB172.54.7e-5431126297
             NF-YB   2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyrele 94 
                       reqdr++Pianv+rim++vlPa+akis+daket+qecvse+isf+t+ea+++cqre+rkti+++d+lwa++ lGf+dyvepl vyl++yre+e
  LOC_Os02g49370.1  31 REQDRLMPIANVIRIMRRVLPAHAKISDDAKETIQECVSEYISFITGEANERCQREQRKTITAEDVLWAMSRLGFDDYVEPLGVYLHRYREFE 123
                       89******************************************************************************************* PP

             NF-YB  95 gek 97 
                       ge+
  LOC_Os02g49370.1 124 GES 126
                       986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.101.4E-4828128IPR009072Histone-fold
SuperFamilySSF471135.28E-3833134IPR009072Histone-fold
PfamPF008083.9E-2537100IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006152.6E-166482No hitNo description
PROSITE patternPS0068506783IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006152.6E-1683101No hitNo description
PRINTSPR006152.6E-16102120No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0033613Molecular Functionactivating transcription factor binding
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 255 aa     Download sequence    Send to blast
MEAGYPGTAA NGAAADGNGG AQQAAAAPAI REQDRLMPIA NVIRIMRRVL PAHAKISDDA  60
KETIQECVSE YISFITGEAN ERCQREQRKT ITAEDVLWAM SRLGFDDYVE PLGVYLHRYR  120
EFEGESRGVG VGVGAARGDH HHGHVGGMLK SRAQGSMVTH HDMQMHAAMY GGGAVPPPPH  180
PPPHHHAFHQ LMPPHHGQYA PPYDMYGGEH GMAAYYGGMY APGSGGDGSG SSGSGGAGTP  240
QTVNFEHQHP FGYK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5g49_A3e-6129121597NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.88910.0callus
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329930700.0
Expression AtlasQ6ZFM9-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed primarily during seed development. {ECO:0000269|PubMed:12509518}.
UniprotTISSUE SPECIFICITY: Expressed in roots, flowers and developing siliques. Present in etiolated seedlings. {ECO:0000269|PubMed:11250072, ECO:0000269|PubMed:12509518, ECO:0000269|PubMed:17322342}.
Functional Description ? help Back to Top
Source Description
UniProtComponent of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. Plays a role in the regulation of the embryogenesis. Involved in the abscisic acid (ABA) signaling pathway. {ECO:0000269|PubMed:12509518, ECO:0000269|PubMed:17322342}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g49370.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g49370
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2880360.0AB288036.1 Oryza sativa Japonica Group OsHAP3E mRNA for HAP3 subunit of HAP complex, complete cds.
GenBankAK1078610.0AK107861.1 Oryza sativa Japonica Group cDNA clone:002-134-B07, full insert sequence.
GenBankAP0041790.0AP004179.3 Oryza sativa Japonica Group genomic DNA, chromosome 2, BAC clone:OJ1124_G07.
GenBankAP0149580.0AP014958.1 Oryza sativa Japonica Group DNA, chromosome 2, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015624920.10.0nuclear transcription factor Y subunit B-10
SwissprotQ84W666e-66NFYB6_ARATH; Nuclear transcription factor Y subunit B-6
TrEMBLQ6ZFM90.0Q6ZFM9_ORYSJ; HAP3 subunit of HAP complex
STRINGOS02T0725700-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20138331
Representative plantOGRP16817170
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G47670.22e-62nuclear factor Y, subunit B6
Publications ? help Back to Top
  1. 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]
  2. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  3. Kim HU, et al.
    Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues.
    FEBS Open Bio, 2013. 4: p. 25-32
    [PMID:24363987]
  4. Gnesutta N,Saad D,Chaves-Sanjuan A,Mantovani R,Nardini M
    Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants.
    Mol Plant, 2017. 10(4): p. 645-648
    [PMID:27871811]
  5. Li D, et al.
    MYB89 Transcription Factor Represses Seed Oil Accumulation.
    Plant Physiol., 2017. 173(2): p. 1211-1225
    [PMID:27932421]
  6. Zhao H, et al.
    The Arabidopsis thaliana Nuclear Factor Y Transcription Factors.
    Front Plant Sci, 2016. 7: p. 2045
    [PMID:28119722]
  7. Han JD, et al.
    Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program.
    Front Plant Sci, 2017. 8: p. 439
    [PMID:28421087]