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_Os08g07740.1
Common NameHd5, LOC4344784, Os08g0174500, OsHAP3H, OSNPB_080174500
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: 298aa    MW: 29810.7 Da    PI: 6.2351
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os08g07740.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB175.84.3e-5557152297
             NF-YB   2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyrele 94 
                       +eqdrflPianvsrimk+ lPanakisk++ketvqecvsefisfvt+easdkcqrekrktingddllwa++tlGfe yv plk yl++yre+e
  LOC_Os08g07740.1  57 KEQDRFLPIANVSRIMKRSLPANAKISKESKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEAYVGPLKSYLNRYREAE 149
                       89******************************************************************************************* PP

             NF-YB  95 gek 97 
                       gek
  LOC_Os08g07740.1 150 GEK 152
                       997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.101.5E-5054154IPR009072Histone-fold
SuperFamilySSF471135.12E-3859161IPR009072Histone-fold
PfamPF008086.2E-2662126IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006155.2E-1890108No hitNo description
PROSITE patternPS00685093109IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006155.2E-18109127No hitNo description
PRINTSPR006155.2E-18128146No 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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009066anatomyanther
PO:0001004developmental stageanther development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 298 aa     Download sequence    Send to blast
MKSRKSYGHL LSPVGSPPLD NESGEAAAAA AAGGGGCGSS AGYVVYGGGG GGDSPAKEQD  60
RFLPIANVSR IMKRSLPANA KISKESKETV QECVSEFISF VTGEASDKCQ REKRKTINGD  120
DLLWAMTTLG FEAYVGPLKS YLNRYREAEG EKADVLGGAG GAAAARHGEG GCCGGGGGGA  180
DGVVIDGHYP LAGGLSHSHH GHQQQDGGGD VGLMMGGGDA GVGYNAGAGS TTTAFYAPAA  240
TAASGNKAYC GGDGSRVMEF EGIGGEEESG GGGGGGERGF AGHLHGVQWF RLKRNTN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5g49_A2e-4451147197NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO375426740.0
Expression AtlasQ0J7P4-
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
PlantRegMapLOC_Os08g07740.1
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-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs08g07740
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB1246500.0AB124650.1 Oryza sativa Japonica Group Hd5 gene for Heading date 5, complete cds, cultivar:Nipponbare.
GenBankAB1246510.0AB124651.1 Oryza sativa Japonica Group Hd5 mRNA for Heading date 5, complete cds, cultivar:Nipponbare.
GenBankAB2880390.0AB288039.1 Oryza sativa Japonica Group OsHAP3H gene for HAP3 subunit of HAP complex, complete cds.
GenBankAB6932000.0AB693200.1 Oryza sativa Japonica Group Hd5 gene for heading date 5, complete cds, cultivar: Hoshinoyume.
GenBankAB6932020.0AB693202.1 Oryza sativa Japonica Group Hd5 gene for heading date 5, complete cds, cultivar: Italica Liborno.
GenBankAB6932030.0AB693203.1 Oryza sativa Japonica Group Hd5 gene for heading date 5, complete cds, cultivar: Dunghung Shali.
GenBankAB6932040.0AB693204.1 Oryza sativa Japonica Group Hd5 gene for heading date 5, complete cds, cultivar: Arroz da Terra.
GenBankAP0051640.0AP005164.3 Oryza sativa Japonica Group genomic DNA, chromosome 8, BAC clone:OSJNBa0054L03.
GenBankAP0149640.0AP014964.1 Oryza sativa Japonica Group DNA, chromosome 8, cultivar: Nipponbare, complete sequence.
GenBankHM7753960.0HM775396.1 Oryza sativa Japonica Group days to heading 8 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015649101.10.0nuclear transcription factor Y subunit B-11
SwissprotQ0J7P40.0HD5_ORYSJ; Nuclear transcription factor Y subunit B-11
TrEMBLA0A0H5BCL00.0A0A0H5BCL0_ORYSJ; Heading date 5
STRINGOS08T0174500-000.0(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
AT4G14540.18e-59nuclear factor Y, subunit B3
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. Wei X, et al.
    DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously.
    Plant Physiol., 2010. 153(4): p. 1747-58
    [PMID:20566706]
  3. 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]
  4. 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]
  5. Fujino K,Yamanouchi U,Yano M
    Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation.
    Theor. Appl. Genet., 2013. 126(3): p. 611-8
    [PMID:23090144]
  6. 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]