PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

LOC_Os06g17480.1

Common Name

LOC4340772, Os06g0285200, OsHAP3D, OSNPB_060285200, P0491D10.32

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

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_Os06g17480.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YB	158	1.5e-49	29	123	1	95
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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.20.10	1.5E-45	27	123	IPR009072	Histone-fold
SuperFamily	SSF47113	2.95E-36	32	129	IPR009072	Histone-fold
Pfam	PF00808	2.6E-24	36	99	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
PRINTS	PR00615	5.1E-13	63	81	No hit	No description
PROSITE pattern	PS00685	0	66	82	IPR003956	Transcription factor, NFYB/HAP3, conserved site
PRINTS	PR00615	5.1E-13	82	100	No hit	No description
PRINTS	PR00615	5.1E-13	101	119	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046982	Molecular Function	protein heterodimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009089	anatomy	endosperm
PO:0007042	developmental stage	whole plant fruit formation stage
PO:0007633	developmental stage	endosperm 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

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_A	2e-52	29	120	6	97	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.9495	0.0	panicle

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	37542677	0.0
Expression Atlas	Q5VNF4	-

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os06g17480.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os06g17480

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB288035	0.0	AB288035.1 Oryza sativa Japonica Group OsHAP3D mRNA for HAP3 subunit of HAP complex, complete cds.
GenBank	AK109660	0.0	AK109660.1 Oryza sativa Japonica Group cDNA clone:002-141-E08, full insert sequence.
GenBank	AP004791	0.0	AP004791.3 Oryza sativa Japonica Group genomic DNA, chromosome 6, PAC clone:P0491D10.
GenBank	AP014962	0.0	AP014962.1 Oryza sativa Japonica Group DNA, chromosome 6, cultivar: Nipponbare, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015642670.1	1e-177	nuclear transcription factor Y subunit B-10-like
TrEMBL	Q5VNF4	1e-176	Q5VNF4_ORYSJ; HAP3 subunit of HAP complex
STRING	OS06T0285200-01	1e-177	(Oryza sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP201	38	331
Representative plant	OGRP168	17	170

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G47670.2	5e-52	nuclear factor Y, subunit B6

Link Out ? help Back to Top
Phytozome	LOC_Os06g17480.1
Entrez Gene	4340772

Publications ? help Back to Top
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]