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

AT1G54830.3

Common Name

F14C21.41, NFYC3, NF-YC3, T22H22.22

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

NF-YC

Protein Properties

Length: 217aa MW: 24312.2 Da PI: 4.7457

Description

nuclear factor Y, subunit C3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G54830.3	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	178.6	5.7e-56	48	151	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdflvdi 95 ql+sfwe+q iek+tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaavtrtdifdflvdi AT1G54830.3 48 QLQSFWETQfkeIEKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAVTRTDIFDFLVDI 145 89***999999********************************************************************************* PP NF-YC 96 vprdel 101 vpr++l AT1G54830.3 146 VPREDL 151 *986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	2.95E-33	15	142	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	6.1E-38	62	134	IPR009072	Histone-fold
Pfam	PF00808	5.2E-22	70	133	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain

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:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046982	Molecular Function	protein heterodimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001017	developmental stage	M germinated pollen stage
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 217 aa Download sequence Send to blast
MDQQGQSSAM NYGSNPYQTN AMTTTPTGSD HPAYHQIHQQ QQQQLTQQLQ SFWETQFKEI 60 EKTTDFKNHS LPLARIKKIM KADEDVRMIS AEAPVVFARA CEMFILELTL RSWNHTEENK 120 RRTLQKNDIA AAVTRTDIFD FLVDIVPRED LRDEVLGGVG AEAATAAGYP YGYLPPGTAP 180 IGNPGMVMGN PGAYPPNPYM GQPMWQQPGP EQQDPDN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	4e-65	55	148	2	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	120	126	RRTLQKN

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.10845	0.0	flower\| leaf\| root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	264190_at	0.0
Expression Atlas	AT1G54830	-
AtGenExpress	AT1G54830	-
ATTED-II	AT1G54830	-

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

Functional Description ? help Back to Top
Source	Description
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	AT1G54830.3

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

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G72830
IntAct	Search Q9ZVL3

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G54830

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC064840	0.0	AC064840.2 Arabidopsis thaliana chromosome I BAC T24C10 genomic sequence, complete sequence.
GenBank	AC069144	0.0	AC069144.9 Arabidopsis thaliana chromosome 1 BAC F14C21 genomic sequence, complete sequence.
GenBank	AY062775	0.0	AY062775.1 Arabidopsis thaliana Unknown protein (At1g54830; T22H22.22) mRNA, complete cds.
GenBank	AY081654	0.0	AY081654.1 Arabidopsis thaliana unknown protein (At1g54830) mRNA, complete cds.
GenBank	AY087517	0.0	AY087517.1 Arabidopsis thaliana clone 36272 mRNA, complete sequence.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
GenBank	T22H22	0.0	AC005388.1 Sequence of BAC T22H22 from Arabidopsis thaliana chromosome 1, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_175880.1	1e-163	nuclear factor Y, subunit C3
Refseq	NP_849808.1	1e-163	nuclear factor Y, subunit C3
Refseq	NP_974030.1	1e-163	nuclear factor Y, subunit C3
Swissprot	Q9ZVL3	1e-164	NFYC3_ARATH; Nuclear transcription factor Y subunit C-3
TrEMBL	A0A178WGU5	1e-162	A0A178WGU5_ARATH; NF-YC3
STRING	AT1G54830.3	1e-163	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT1G54830.3
Entrez Gene	841922
iHOP	AT1G54830
wikigenes	AT1G54830

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Gusmaroli G,Tonelli C,Mantovani R Regulation of the CCAAT-Binding NF-Y subunits in Arabidopsis thaliana. Gene, 2001. 264(2): p. 173-85 [PMID:11250072] Gusmaroli G,Tonelli C,Mantovani R Regulation of novel members of the Arabidopsis thaliana CCAAT-binding nuclear factor Y subunits. Gene, 2002. 283(1-2): p. 41-8 [PMID:11867211] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Wenkel S, et al. CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell, 2006. 18(11): p. 2971-84 [PMID:17138697] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Kumimoto RW,Zhang Y,Siefers N,Holt BF NF-YC3, NF-YC4 and NF-YC9 are required for CONSTANS-mediated, photoperiod-dependent flowering in Arabidopsis thaliana. Plant J., 2010. 63(3): p. 379-91 [PMID:20487380] Ito J, et al. Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism. J. Proteome Res., 2011. 10(4): p. 1571-82 [PMID:21166475] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] Hackenberg D, et al. Studies on differential nuclear translocation mechanism and assembly of the three subunits of the Arabidopsis thaliana transcription factor NF-Y. Mol Plant, 2012. 5(4): p. 876-88 [PMID:22199235] Calvenzani V, et al. Interactions and CCAAT-binding of Arabidopsis thaliana NF-Y subunits. PLoS ONE, 2012. 7(8): p. e42902 [PMID:22912760] Hou X, et al. Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nat Commun, 2014. 5: p. 4601 [PMID:25105952] 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] 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]