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

AT1G08970.2

Common Name

F7G19.16, HAP5C, NFYC9, NF-YC9

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: 231aa MW: 25639.7 Da PI: 4.8822

Description

nuclear factor Y, subunit C9

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G08970.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	178.8	5.1e-56	58	161	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdflvdi 95 ql++fwe+q iek+tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaavtrtdifdflvdi AT1G08970.2 58 QLQAFWENQfkeIEKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAVTRTDIFDFLVDI 155 89****99999********************************************************************************* PP NF-YC 96 vprdel 101 vpr++l AT1G08970.2 156 VPREDL 161 *986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	1.68E-32	48	152	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	6.9E-38	72	144	IPR009072	Histone-fold
Pfam	PF00808	5.8E-22	80	143	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:0005829	Cellular Component	cytosol
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: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:0025281	anatomy	pollen
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: 231 aa Download sequence Send to blast
MDQQDHGQSG AMNYGTNPYQ TNPMSTTAAT VAGGAAQPGQ LAFHQIHQQQ QQQQLAQQLQ 60 AFWENQFKEI EKTTDFKNHS LPLARIKKIM KADEDVRMIS AEAPVVFARA CEMFILELTL 120 RSWNHTEENK RRTLQKNDIA AAVTRTDIFD FLVDIVPRED LRDEVLGSIP RGTVPEAAAA 180 GYPYGYLPAG TAPIGNPGMV MGNPGGAYPP NPYMGQPMWQ QQAPDQPDQE N

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	3e-64	66	158	3	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	130	136	RRTLQKN

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.22258	0.0	bud\| flower\| inflorescence\| root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	264650_at	0.0
Expression Atlas	AT1G08970	-
AtGenExpress	AT1G08970	-
ATTED-II	AT1G08970	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitous. Present in etiolated seedlings. {ECO:0000269\|PubMed:11867211, ECO:0000269\|PubMed:17322342}.

Functional Description ? help Back to Top
Source	Description
TAIR	heme activated protein (HAP5c)
UniProt	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters (By similarity). Interacts with REF6 to directly regulate SOC1 transcription in response to flowering signals from photoperiod and gibberellic acid pathways (PubMed:25105952). {ECO:0000250, ECO:0000269\|PubMed:25105952}.

Function -- GeneRIF ? help Back to Top
NF-YC9 mediates abscisic acid (ABA) signaling via targeting to and aiding the ABA-responsive transcription factors such as ABI5. [PMID: 28924726] A novel mechanism of the NF-YC9-mediated epigenetic regulation of FT protein activation in photoperiod-induced flowering. [PMID: 29599268]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G08970.2

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

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G09030, AT1G14920, AT1G21970, AT1G28050, AT1G30500, AT1G66350, AT1G72830
IntAct	Search Q8L4B2

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G08970

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK316882	0.0	AK316882.2 Arabidopsis thaliana AT1G08970 mRNA, complete cds, clone: RAFL14-04-L24.
GenBank	AY085860	0.0	AY085860.1 Arabidopsis thaliana clone 1911 mRNA, complete sequence.
GenBank	AY126997	0.0	AY126997.1 Arabidopsis thaliana At1g08970/F7G19_16 mRNA, complete cds.
GenBank	AY143827	0.0	AY143827.1 Arabidopsis thaliana At1g08970/F7G19_16 mRNA, complete cds.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
GenBank	F7G19	0.0	AC000106.1 Sequence of BAC F7G19 from Arabidopsis thaliana chromosome 1, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_172371.1	1e-173	nuclear factor Y, subunit C9
Refseq	NP_849619.1	1e-173	nuclear factor Y, subunit C9
Refseq	NP_973796.1	1e-173	nuclear factor Y, subunit C9
Refseq	NP_973797.1	1e-173	nuclear factor Y, subunit C9
Swissprot	Q8L4B2	1e-174	NFYC9_ARATH; Nuclear transcription factor Y subunit C-9
TrEMBL	A0A384LQG6	1e-172	A0A384LQG6_ARATH; NF-YC9
TrEMBL	B9DFS3	1e-172	B9DFS3_ARATH; AT1G08970 protein
STRING	AT1G08970.4	1e-172	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT1G08970.2
Entrez Gene	837417
iHOP	AT1G08970
wikigenes	AT1G08970

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 novel members of the Arabidopsis thaliana CCAAT-binding nuclear factor Y subunits. Gene, 2002. 283(1-2): p. 41-8 [PMID:11867211] Pollmann S,Neu D,Weiler EW Molecular cloning and characterization of an amidase from Arabidopsis thaliana capable of converting indole-3-acetamide into the plant growth hormone, indole-3-acetic acid. Phytochemistry, 2003. 62(3): p. 293-300 [PMID:12620340] Meyers BC,Kozik A,Griego A,Kuang H,Michelmore RW Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell, 2003. 15(4): p. 809-34 [PMID:12671079] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Devlin PF,Yanovsky MJ,Kay SA A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol., 2003. 133(4): p. 1617-29 [PMID:14645734] Koroleva OA,Tomlinson ML,Leader D,Shaw P,Doonan JH High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions. Plant J., 2005. 41(1): p. 162-74 [PMID:15610358] Ben-Naim O, et al. The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA. Plant J., 2006. 46(3): p. 462-76 [PMID:16623906] 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] Warpeha KM, et al. The GCR1, GPA1, PRN1, NF-Y signal chain mediates both blue light and abscisic acid responses in Arabidopsis. Plant Physiol., 2007. 143(4): p. 1590-600 [PMID:17322342] Kong H, et al. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J., 2007. 50(5): p. 873-85 [PMID:17470057] 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] 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] 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] Bi C,Ma Y,Wang XF,Zhang DP Overexpression of the transcription factor NF-YC9 confers abscisic acid hypersensitivity in Arabidopsis. Plant Mol. Biol., 2017. 95(4-5): p. 425-439 [PMID:28924726] Liu X, et al. Temporal-Specific Interaction of NF-YC and CURLY LEAF during the Floral Transition Regulates Flowering. Plant Physiol., 2018. 177(1): p. 105-114 [PMID:29599268]