Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G44750.1
Common NameATHD2A, HD2A, HDA3, HDT1, T32N15.8
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 C2H2
Protein Properties Length: 245aa    MW: 26372.2 Da    PI: 4.8568
Description histone deacetylase 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G44750.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
      zf-C2H2   2 kCpdCgksFsrksnLkrHirt.H 23 
                  +C+ C+k+F++   L++H +  H
                  6*****************88766 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF030667.2E-83167No hitNo description
PROSITE profilePS5015710.429218245IPR007087Zinc finger, C2H2
PROSITE patternPS000280220241IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009294Biological ProcessDNA mediated transformation
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010162Biological Processseed dormancy process
GO:0016569Biological Processcovalent chromatin modification
GO:0005730Cellular Componentnucleolus
GO:0003676Molecular Functionnucleic acid binding
GO:0004407Molecular Functionhistone deacetylase activity
GO:0008270Molecular Functionzinc ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
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: 245 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.209500.0flower| root
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G44750-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaves, roots, stems, young plantlets, flowers and siliques. Highest levels in ovules, embryos, shoot apical meristems and first leaves. Also expressed in somatic embryos. {ECO:0000269|PubMed:10792817, ECO:0000269|PubMed:15144374}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a histone deacetylase. Controls the development of adaxial/abaxial leaf polarity. Two lines with RNAi-directed against this gene show reduced Agrobacterium-mediated DNA transformation of the roots.
UniProtProbably mediates the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Required for histone H3 'Lys-9' deacetylation. Involved in rRNA gene silencing in nucleolar dominance. Seems to be implicated in the regulation of genes involved in seeds development. {ECO:0000269|PubMed:10792817, ECO:0000269|PubMed:12694598, ECO:0000269|PubMed:14992728, ECO:0000269|PubMed:15144374}.
Function -- GeneRIF ? help Back to Top
  1. HD2A and HD2C may have different and opposing functions in germination with the glucose/HD2A pathway acting to restrain germination and the HD2C pathway acting to enhance germination.
    [PMID: 21739146]
Cis-element ? help Back to Top
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT5G17430 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G34710(A), AT2G45190(A), AT4G37870(R)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9FVE6
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G44750
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1955450.0AF195545.1 Arabidopsis thaliana putative histone deacetylase (HD2A) mRNA, complete cds.
GenBankAY0653960.0AY065396.1 Arabidopsis thaliana putative histone deacetylase (At3g44750) mRNA, complete cds.
GenBankAY0967290.0AY096729.1 Arabidopsis thaliana putative histone deacetylase (At3g44750) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_566872.11e-177histone deacetylase HDT1
SwissprotQ9FVE61e-179HDT1_ARATH; Histone deacetylase HDT1
TrEMBLF4J3781e-137F4J378_ARATH; Histone deacetylase HDT1
STRINGAT3G44750.11e-177(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP10531129
Publications ? help Back to Top
  1. Wu K,Tian L,Malik K,Brown D,Miki B
    Functional analysis of HD2 histone deacetylase homologues in Arabidopsis thaliana.
    Plant J., 2000. 22(1): p. 19-27
  2. Pandey R, et al.
    Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.
    Nucleic Acids Res., 2002. 30(23): p. 5036-55
  3. Wu K,Tian L,Zhou C,Brown D,Miki B
    Repression of gene expression by Arabidopsis HD2 histone deacetylases.
    Plant J., 2003. 34(2): p. 241-7
  4. Calikowski TT,Meulia T,Meier I
    A proteomic study of the arabidopsis nuclear matrix.
    J. Cell. Biochem., 2003. 90(2): p. 361-78
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Lawrence RJ, et al.
    A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance.
    Mol. Cell, 2004. 13(4): p. 599-609
  7. Zhou C, et al.
    Expression and function of HD2-type histone deacetylases in Arabidopsis development.
    Plant J., 2004. 38(5): p. 715-24
  8. Pendle AF, et al.
    Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions.
    Mol. Biol. Cell, 2005. 16(1): p. 260-9
  9. Ueno Y, et al.
    Histone deacetylases and ASYMMETRIC LEAVES2 are involved in the establishment of polarity in leaves of Arabidopsis.
    Plant Cell, 2007. 19(2): p. 445-57
  10. Crane YM,Gelvin SB
    RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(38): p. 15156-61
  11. Pontes O, et al.
    Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance.
    PLoS ONE, 2007. 2(11): p. e1157
  12. Jones AM, et al.
    Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.
    J Proteomics, 2009. 72(3): p. 439-51
  13. Reiland S, et al.
    Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
    Plant Physiol., 2009. 150(2): p. 889-903
  14. Zhang J,Henagan TM,Gao Z,Ye J
    Inhibition of glyceroneogenesis by histone deacetylase 3 contributes to lipodystrophy in mice with adipose tissue inflammation.
    Endocrinology, 2011. 152(5): p. 1829-38
  15. Colville A, et al.
    Role of HD2 genes in seed germination and early seedling growth in Arabidopsis.
    Plant Cell Rep., 2011. 30(10): p. 1969-79
  16. 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
  17. Luo M, et al.
    HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis.
    J. Exp. Bot., 2012. 63(8): p. 3297-306
  18. Luo M,Wang YY,Liu X,Yang S,Wu K
    HD2 proteins interact with RPD3-type histone deacetylases.
    Plant Signal Behav, 2012. 7(6): p. 608-10
  19. Yano R,Takebayashi Y,Nambara E,Kamiya Y,Seo M
    Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana.
    Plant J., 2013. 74(5): p. 815-28
  20. Waidmann S,Kusenda B,Mayerhofer J,Mechtler K,Jonak C
    A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis.
    Plant Cell, 2014. 26(11): p. 4328-44
  21. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73