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_Os04g58680.1

Common Name

LOC107278593, Os04g0683400, OsHAP5G, OsJ_16673, OSJNBa0032F06.24, OSNPB_040683400

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-YC

Protein Properties

Length: 126aa MW: 13221 Da PI: 9.1825

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os04g58680.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	83.8	1.9e-26	54	116	37	99
NF-YC 37 kmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdflvdivprd 99 +mis eaPv++skacelfi elt r+w + e krrt++k d+aaav++td fdflvd+v d LOC_Os04g58680.1 54 RMISGEAPVVFSKACELFIAELTRRAWAATLEGKRRTVHKEDVAAAVQNTDLFDFLVDVVTAD 116 8**********************************************************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	2.1E-24	18	109	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	3.5E-31	19	101	IPR009072	Histone-fold
Pfam	PF00808	2.6E-12	52	100	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 126 aa Download sequence Send to blast
MRQARPYSAM FAGGVSARTG PHALPLARIK KIMKRSAGDS SVVDGGGGGG GGARMISGEA 60 PVVFSKACEL FIAELTRRAW AATLEGKRRT VHKEDVAAAV QNTDLFDFLV DVVTADLGDD 120 HTDYK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	6e-31	22	113	16	93	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	Q7XPV7

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269\|PubMed:11250072}.
Uniprot	TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269\|PubMed:11250072, ECO:0000269\|PubMed:9662544}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable 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}.
UniProt	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. {ECO:0000250}.
UniProt	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os04g58680.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: 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
PlantRegMap	Retrieve	-

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os04g58680

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB288047	0.0	AB288047.1 Oryza sativa Japonica Group OsHAP5G gene for HAP5 subunit of HAP complex, complete cds.
GenBank	AL606641	0.0	AL606641.3 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0032F06, complete sequence.
GenBank	AP014960	0.0	AP014960.1 Oryza sativa Japonica Group DNA, chromosome 4, cultivar: Nipponbare, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015635297.1	7e-87	nuclear transcription factor Y subunit C-2
Swissprot	Q655V5	2e-29	NFYC4_ORYSJ; Nuclear transcription factor Y subunit C-4
Swissprot	Q8LCG7	4e-30	NFYC2_ARATH; Nuclear transcription factor Y subunit C-2
Swissprot	Q9ZVL3	8e-30	NFYC3_ARATH; Nuclear transcription factor Y subunit C-3
TrEMBL	Q7XPV7	2e-85	Q7XPV7_ORYSJ; HAP5 subunit of HAP complex
STRING	OS04T0683400-00	3e-86	(Oryza sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP11658	33	39
Representative plant	OGRP315	17	117

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G56170.2	6e-31	nuclear factor Y, subunit C2

Link Out ? help Back to Top
Phytozome	LOC_Os04g58680.1
Entrez Gene	107278593

Publications ? help Back to Top
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] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Li S, et al. HEAT-INDUCED TAS1 TARGET1 Mediates Thermotolerance via HEAT STRESS TRANSCRIPTION FACTOR A1a-Directed Pathways in Arabidopsis. Plant Cell, 2014. 26(4): p. 1764-1780 [PMID:24728648] Mei X, et al. Identification and characterization of paternal-preferentially expressed gene NF-YC8 in maize endosperm. Mol. Genet. Genomics, 2015. 290(5): p. 1819-31 [PMID:25851237] 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] Hwang YH, et al. Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time. Plant Cell Rep., 2016. 35(4): p. 857-65 [PMID:26754793] Baud S, et al. Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed. Plant Physiol., 2016. 171(2): p. 1099-112 [PMID:27208266] Liu X, et al. The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis. Nat Commun, 2016. 7: p. 12768 [PMID:27624486] Myers ZA, et al. NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana. PLoS Genet., 2016. 12(9): p. e1006333 [PMID:27685091] 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] Tang Y, et al. Arabidopsis NF-YCs Mediate the Light-Controlled Hypocotyl Elongation via Modulating Histone Acetylation. Mol Plant, 2017. 10(2): p. 260-273 [PMID:27876642] Zhao H, et al. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. Front Plant Sci, 2016. 7: p. 2045 [PMID:28119722] Gnesutta N, et al. CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer. Plant Cell, 2017. 29(6): p. 1516-1532 [PMID:28526714]