PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os06g17480.1
Common NameLOC4340772, Os06g0285200, OsHAP3D, OSNPB_060285200, P0491D10.32
Organism
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: 251aa    MW: 25965.1 Da    PI: 5.5502
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os06g17480.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB1581.5e-4929123195
             NF-YB   1 vreqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyrel 93 
                       vreqdr++Pianv+rim++vlP +akis+dake++qecvsefisfvt+ea+d+c+re+rkt++++dl+wa+  lGf+dyv pl++yl++ re 
  LOC_Os06g17480.1  29 VREQDRLMPIANVIRIMRRVLPPHAKISDDAKEVIQECVSEFISFVTGEANDRCHREHRKTVTAEDLVWAMDRLGFDDYVPPLTAYLRRMREY 121
                       69******************************************************************************************9 PP

             NF-YB  94 eg 95 
                       eg
  LOC_Os06g17480.1 122 EG 123
                       97 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-4527123IPR009072Histone-fold
SuperFamilySSF471132.95E-3632129IPR009072Histone-fold
PfamPF008082.6E-243699IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006155.1E-136381No hitNo description
PROSITE patternPS0068506682IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006155.1E-1382100No hitNo description
PRINTSPR006155.1E-13101119No 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:0009089anatomyendosperm
PO:0007042developmental stagewhole plant fruit formation stage
PO:0007633developmental stageendosperm development stage
Sequence ? help Back to Top
Protein Sequence    Length: 251 aa     Download sequence    Send to blast
MEPAFPNGGA AAPPPPMAAE QLPPAAAVVR EQDRLMPIAN VIRIMRRVLP PHAKISDDAK  60
EVIQECVSEF ISFVTGEAND RCHREHRKTV TAEDLVWAMD RLGFDDYVPP LTAYLRRMRE  120
YEGGGSGGGG GGGRGAAAAP AVVPPPPPPP PEDAFRYVQV HHPVYAAPGE PVQGYGYPVA  180
MSSALPAPHV HVGVRGGGQH EVFGGGPAPL AVYYGGAPYG EASSRGGCSA ADEGSSSSSA  240
SPAPVGPNYE *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1n1j_A2e-3730120393NF-YB
4awl_B3e-3730120494NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
4csr_A3e-3730120494NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.94950.0panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO375426770.0
Expression AtlasQ5VNF4-
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os06g17480.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs06g17480
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0149620.0AP014962.1 Oryza sativa Japonica Group DNA, chromosome 6, cultivar: Nipponbare, complete sequence.
GenBankAP0047910.0AP004791.3 Oryza sativa Japonica Group genomic DNA, chromosome 6, PAC clone:P0491D10.
GenBankAB2880350.0AB288035.1 Oryza sativa Japonica Group OsHAP3D mRNA for HAP3 subunit of HAP complex, complete cds.
GenBankAK1096600.0AK109660.1 Oryza sativa Japonica Group cDNA clone:002-141-E08, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015642670.11e-178PREDICTED: nuclear transcription factor Y subunit B-9
TrEMBLQ5VNF41e-178Q5VNF4_ORYSJ; HAP3 subunit of HAP complex
STRINGLOC_Os06g17480.11e-177(Oryza sativa Japonica Group)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP16817170
MonocotsOGMP20138331
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G47670.25e-52nuclear 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]