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

AT5G12840.3

Common Name

ATHAP2A, AtNFYA1, EMB2220, HAP2A, NFYA1, NF-YA1, T24H18_10

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-YA

Protein Properties

Length: 272aa MW: 30037.9 Da PI: 6.6827

Description

nuclear factor Y, subunit A1

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G12840.3	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	CBFB_NFYA	97.7	1.2e-30	171	227	1	58
CBFB_NFYA 1 deplYVNaKQyqrIlkRRqkRakleeekkldeksrkpylheSRhkhAlrRpRgsgGrF 58 +ep+YVNaKQy++Il+RR++Rak+e e+k+ ++ rkpylheSRhkhA+rR+R+sgGrF AT5G12840.3 171 QEPVYVNAKQYEGILRRRKARAKAELERKV-IRDRKPYLHESRHKHAMRRARASGGRF 227 69**************************.************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00521	4.4E-34	169	230	IPR001289	Nuclear transcription factor Y subunit A
PROSITE profile	PS51152	36.248	170	230	IPR001289	Nuclear transcription factor Y subunit A
Pfam	PF02045	1.3E-27	172	227	IPR001289	Nuclear transcription factor Y subunit A
PRINTS	PR00616	4.0E-23	173	195	IPR001289	Nuclear transcription factor Y subunit A
PROSITE pattern	PS00686	0	175	195	IPR018362	CCAAT-binding factor, conserved site
PRINTS	PR00616	4.0E-23	204	227	IPR001289	Nuclear transcription factor Y subunit A

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010262	Biological Process	somatic embryogenesis
GO:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
GO:0055046	Biological Process	microgametogenesis
GO:0016602	Cellular Component	CCAAT-binding factor complex
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

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:0025281	anatomy	pollen
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:0007131	developmental stage	seedling development stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 272 aa Download sequence Send to blast
MQSKPGRENE EEVNNHHAVQ QPMMYAEPWW KNNSFGVVPQ ARPSGIPSNS SSLDCPNGSE 60 SNDVHSASED GALNGENDGT WKDSQAATSS RSVDNHGMEG NDPALSIRNM HDQPLVQPPE 120 LVGHYIACVP NPYQDPYYGG LMGAYGHQQL GFRPYLGMPR ERTALPLDMA QEPVYVNAKQ 180 YEGILRRRKA RAKAELERKV IRDRKPYLHE SRHKHAMRRA RASGGRFAKK SEVEAGEDAG 240 GRDRERGSAT NSSGSEQVET DSNETLNSSG AP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4awl_A	2e-17	171	227	2	58	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	211	220	RHKHAMRRAR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.5280	0.0	seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	250320_at	0.0
Expression Atlas	AT5G12840	-
AtGenExpress	AT5G12840	-
ATTED-II	AT5G12840	-

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

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a subunit of CCAAT-binding complex, binds to CCAAT box motif present in some plant promoter sequences. One of three members of this class (HAP2A, HAP2B, HAP2C), it is expressed in vegetative and reproductive tissues.
UniProt	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. {ECO:0000250}.

Function -- GeneRIF ? help Back to Top
these results provide evidence that NF-YA1, 5, 6, and 9 play redundant roles in male gametophyte development, embryogenesis, seed development, and post-germinative growth. [PMID: 22933713] NFYA1 is involved in regulation of postgermination growth arrest under salt stress in Arabidopsis. [PMID: 23637805] Here we provide strong support, in the form of genetic and biochemical analyses, that NF-YA, in complex with NF-YB/NF-YC proteins, can directly bind the distal CCAAT box in the FT promoter and are positive regulators of flowering in an FT-dependent manner. [PMID: 27977687]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G12840.3

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

Regulation -- MicroRNA ? help Back to Top
Source	Description
miRTarBase	Regulated by ath-miR169a

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G38140, AT5G50480, AT5G63470, AT1G08970, AT1G54830, AT1G56170

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G12840

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT025801	0.0	BT025801.1 Arabidopsis thaliana At5g12840 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001318552.1	0.0	nuclear factor Y, subunit A1
Refseq	NP_568282.1	0.0	nuclear factor Y, subunit A1
Refseq	NP_974773.1	0.0	nuclear factor Y, subunit A1
Swissprot	Q9LXV5	0.0	NFYA1_ARATH; Nuclear transcription factor Y subunit A-1
TrEMBL	Q1ECD3	0.0	Q1ECD3_ARATH; At5g12840
STRING	AT5G12840.3	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT5G12840.3
Entrez Gene	831124
iHOP	AT5G12840
wikigenes	AT5G12840

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] Zik M,Irish VF Global identification of target genes regulated by APETALA3 and PISTILLATA floral homeotic gene action. Plant Cell, 2003. 15(1): p. 207-22 [PMID:12509532] Stevens R, et al. A CDC45 homolog in Arabidopsis is essential for meiosis, as shown by RNA interference-induced gene silencing. Plant Cell, 2004. 16(1): p. 99-113 [PMID:14660803] Wang XJ,Reyes JL,Chua NH,Gaasterland T Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol., 2004. 5(9): p. R65 [PMID:15345049] Ditt RF, et al. The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens. Mol. Plant Microbe Interact., 2006. 19(6): p. 665-81 [PMID:16776300] 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] Chen NZ, et al. AtHAP3b plays a crucial role in the regulation of flowering time in Arabidopsis during osmotic stress. J. Biochem. Mol. Biol., 2007. 40(6): p. 1083-9 [PMID:18047807] Yazawa K,Kamada H Identification and characterization of carrot HAP factors that form a complex with the embryo-specific transcription factor C-LEC1. J. Exp. Bot., 2007. 58(13): p. 3819-28 [PMID:18057048] Day RC,Herridge RP,Ambrose BA,Macknight RC Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiol., 2008. 148(4): p. 1964-84 [PMID:18923020] 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] Mu J,Tan H,Hong S,Liang Y,Zuo J Arabidopsis transcription factor genes NF-YA1, 5, 6, and 9 play redundant roles in male gametogenesis, embryogenesis, and seed development. Mol Plant, 2013. 6(1): p. 188-201 [PMID:22933713] Li YJ, et al. NFYA1 is involved in regulation of postgermination growth arrest under salt stress in Arabidopsis. PLoS ONE, 2013. 8(4): p. e61289 [PMID:23637805] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] Siriwardana CL, et al. NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T. PLoS Genet., 2016. 12(12): p. e1006496 [PMID:27977687] Zhao H, et al. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. Front Plant Sci, 2016. 7: p. 2045 [PMID:28119722] Edwards D,Murray JA,Smith AG Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiol., 1998. 117(3): p. 1015-22 [PMID:9662544]