PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G12840.3
Common NameATHAP2A, AtNFYA1, EMB2220, HAP2A, NFYA1, NF-YA1, T24H18_10
Organism
Taxonomic ID
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
AT5G12840.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1CBFB_NFYA97.71.2e-30171227158
    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
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005214.4E-34169230IPR001289Nuclear transcription factor Y subunit A
PROSITE profilePS5115236.248170230IPR001289Nuclear transcription factor Y subunit A
PfamPF020451.3E-27172227IPR001289Nuclear transcription factor Y subunit A
PRINTSPR006164.0E-23173195IPR001289Nuclear transcription factor Y subunit A
PROSITE patternPS006860175195IPR018362CCAAT-binding factor, conserved site
PRINTSPR006164.0E-23204227IPR001289Nuclear transcription factor Y subunit A
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010262Biological Processsomatic embryogenesis
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0055046Biological Processmicrogametogenesis
GO:0016602Cellular ComponentCCAAT-binding factor complex
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering 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
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4awl_A1e-17171227258NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1211220RHKHAMRRAR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.52800.0seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible250320_at0.0
Expression AtlasAT5G12840-
AtGenExpressAT5G12840-
ATTED-IIAT5G12840-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:11250072, ECO:0000269|PubMed:9662544}.
Functional Description ? help Back to Top
Source Description
TAIREncodes 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.
UniProtStimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. 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]
  2. NFYA1 is involved in regulation of postgermination growth arrest under salt stress in Arabidopsis.
    [PMID: 23637805]
  3. 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
SourceLink
PlantRegMapAT5G12840.3
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- MicroRNA ? help Back to Top
Source Description
miRTarBaseRegulated by ath-miR169a
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G38140, AT5G50480, AT5G63470, AT1G08970, AT1G54830, AT1G56170
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G12840
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0258010.0BT025801.1 Arabidopsis thaliana At5g12840 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001318552.10.0nuclear factor Y, subunit A1
RefseqNP_568282.10.0nuclear factor Y, subunit A1
RefseqNP_974773.10.0nuclear factor Y, subunit A1
SwissprotQ9LXV50.0NFYA1_ARATH; Nuclear transcription factor Y subunit A-1
TrEMBLQ1ECD30.0Q1ECD3_ARATH; At5g12840
STRINGAT5G12840.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  16. 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]
  17. 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]
  18. Zhao H, et al.
    The Arabidopsis thaliana Nuclear Factor Y Transcription Factors.
    Front Plant Sci, 2016. 7: p. 2045
    [PMID:28119722]
  19. 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]