PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G38880.6
Common NameATHAP3, ATNF-YB1, HAP3, HAP3A, NF-YB1
Organism
Arabidopsis thaliana
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-YB
Protein Properties Length: 112aa    MW: 12446.1 Da    PI: 4.923
Description nuclear factor Y, subunit B1
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G38880.6genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB177.41.4e-5519111193
        NF-YB   1 vreqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyrel 93 
                  vreqdr+lPian+srimkk+lP n+ki+kdak+tvqecvsefisf+tseasdkcq+ekrkt+ngddllwa+atlGfedy+eplk+yl++yre+
  AT2G38880.6  19 VREQDRYLPIANISRIMKKALPPNGKIGKDAKDTVQECVSEFISFITSEASDKCQKEKRKTVNGDDLLWAMATLGFEDYLEPLKIYLARYREV 111
                  69*****************************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.101.3E-5116110IPR009072Histone-fold
SuperFamilySSF471136.52E-3922111IPR009072Histone-fold
PfamPF008087.9E-282589IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006153.0E-215371No hitNo description
PROSITE patternPS0068505672IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006153.0E-217290No hitNo description
PRINTSPR006153.0E-2191109No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009414Biological Processresponse to water deprivation
GO:0005634Cellular Componentnucleus
GO:0016602Cellular ComponentCCAAT-binding factor complex
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000005anatomycultured plant cell
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
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: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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 112 aa     Download sequence    Send to blast
MADTPSSPAG DGGESGGSVR EQDRYLPIAN ISRIMKKALP PNGKIGKDAK DTVQECVSEF  60
ISFITSEASD KCQKEKRKTV NGDDLLWAMA TLGFEDYLEP LKIYLARYRE VW
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1n1j_A3e-4818110193NF-YB
4awl_B3e-4818110294NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
4csr_A3e-4818110294NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.248200.0floral meristem| flower
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible266171_at0.0
Expression AtlasAT2G38880-
AtGenExpressAT2G38880-
ATTED-IIAT2G38880-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. Predominantly expressed in leaves, flowers and siliques. {ECO:0000269|PubMed:11250072, ECO:0000269|PubMed:9662544}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a transcription factor from the nuclear factor Y (NF-Y) family, AtNF-YB1. Confers drought tolerance.
UniProtComponent of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.
Function -- GeneRIF ? help Back to Top
  1. A transcription factor AtNF-YB1, which acts through a previously undescribed mechanism to confer improved performance in Arabidopsis under drought conditions was identified.
    [PMID: 17923671]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00300DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G38880.6
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMap-Retrieve
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G48590, AT3G54390, AT5G15840, AT5G27910, AT5G38140, AT5G50470, AT5G50480, AT5G50490, AT5G63470, AT1G08970, AT1G28050, AT1G54060, AT1G54830, AT1G56170
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G38880
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3188660.0AK318866.1 Arabidopsis thaliana AT2G38880 mRNA, complete cds, clone: RAFL17-11-H19.
GenBankBT0042660.0BT004266.1 Arabidopsis thaliana clone RAFL15-29-F19 (R20926) putative CCAAT-binding transcription factor subunit (At2g38880) mRNA, complete cds.
GenBankBT0055360.0BT005536.1 Arabidopsis thaliana clone U20926 putative CCAAT-binding transcription factor subunit (At2g38880) mRNA, complete cds.
GenBankDQ3333050.0DQ333305.1 Arabidopsis thaliana transcription factor subunit NF-YB1 mRNA, complete cds.
GenBankY137230.0Y13723.1 Arabidopsis thaliana mRNA for Hap3a transcription factor.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001031510.16e-79nuclear factor Y, subunit B1
SwissprotQ9SLG01e-77NFYB1_ARATH; Nuclear transcription factor Y subunit B-1
TrEMBLF4ITZ61e-77F4ITZ6_ARATH; Nuclear factor Y, subunit B1
STRINGCagra.0716s0005.1.p2e-76(Capsella grandiflora)
STRINGAT2G38880.84e-76(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. 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]
  3. Nelson DE, et al.
    Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(42): p. 16450-5
    [PMID:17923671]
  4. G
    Analysis of a post-translational steroid induction system for GIGANTEA in Arabidopsis.
    BMC Plant Biol., 2009. 9: p. 141
    [PMID:19943973]
  5. Ballif J,Endo S,Kotani M,MacAdam J,Wu Y
    Over-expression of HAP3b enhances primary root elongation in Arabidopsis.
    Plant Physiol. Biochem., 2011. 49(6): p. 579-83
    [PMID:21316979]
  6. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  7. 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]
  8. Bienvenut WV, et al.
    Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features.
    Mol. Cell Proteomics, 2012. 11(6): p. M111.015131
    [PMID:22223895]
  9. Calvenzani V, et al.
    Interactions and CCAAT-binding of Arabidopsis thaliana NF-Y subunits.
    PLoS ONE, 2012. 7(8): p. e42902
    [PMID:22912760]
  10. Zhang JJ,Xue HW
    OsLEC1/OsHAP3E participates in the determination of meristem identity in both vegetative and reproductive developments of rice.
    J Integr Plant Biol, 2013. 55(3): p. 232-49
    [PMID:23230849]
  11. 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]
  12. Sato H, et al.
    Arabidopsis DPB3-1, a DREB2A interactor, specifically enhances heat stress-induced gene expression by forming a heat stress-specific transcriptional complex with NF-Y subunits.
    Plant Cell, 2014. 26(12): p. 4954-73
    [PMID:25490919]
  13. 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]