PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G03740.1
Common NameF17C15_160, HD2C, HDT3, MED24.1
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: 294aa    MW: 31830.4 Da    PI: 4.5108
Description histone deacetylase 2C
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G03740.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirt.H 23 
                  + C+ C+++F++ + L++H +  H
                  56*****************99877 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5015710.492267294IPR007087Zinc finger, C2H2
PROSITE patternPS000280269290IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0007275Biological Processmulticellular organism development
GO:0009414Biological Processresponse to water deprivation
GO:0009651Biological Processresponse to salt stress
GO:0009737Biological Processresponse to abscisic acid
GO:0016569Biological Processcovalent chromatin modification
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
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:0000003anatomywhole plant
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
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:0025195anatomypollen tube cell
PO:0001016developmental stageL mature pollen stage
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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 294 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.47710.0flower| root| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT5G03740-
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:15144374, ECO:0000269|PubMed:16553900}.
Functional Description ? help Back to Top
Source Description
TAIRHD2-type histone deacetylase HDAC. Involved in the ABA and stress responses. Mediates transcriptional repression
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. Involved in the modulation of abscisic acid and stress-responsive genes. {ECO:0000269|PubMed:12694598, ECO:0000269|PubMed:16553900}.
Function -- GeneRIF ? help Back to Top
  1. AtHD2C can modulate abscisic acid and stress responses.
    [PMID: 16553900]
  2. 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]
  3. HD2C functionally associates with HDA6 and regulates gene expression through histone modifications.
    [PMID: 22368268]
  4. HD2C and BRM act in a common genetic pathway to regulate the Arabidopsis heat stress response.
    [PMID: 27083783]
  5. this study reveals a multifaceted role of HD2C in ribosome biogenesis.
    [PMID: 29343504]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by abscisic acid. {ECO:0000269|PubMed:16553900}.
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 -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9LZR5
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G03740
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF2557120.0AF255712.1 Arabidopsis thaliana putative histone deacetylase HD2c mRNA, complete cds.
GenBankAF3728890.0AF372889.1 Arabidopsis thaliana AT5g03740/F17C15_160 mRNA, complete cds.
GenBankAF5101680.0AF510168.1 Arabidopsis thaliana HDT3 mRNA, complete cds.
GenBankAY1420390.0AY142039.1 Arabidopsis thaliana At5g03740/F17C15_160 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_195994.30.0histone deacetylase 2C
SwissprotQ9LZR50.0HDT3_ARATH; Histone deacetylase HDT3
STRINGAT5G03740.10.0(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. Dangl M,Brosch G,Haas H,Loidl P,Lusser A
    Comparative analysis of HD2 type histone deacetylases in higher plants.
    Planta, 2001. 213(2): p. 280-5
  3. 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
  4. 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
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Zhou C, et al.
    Expression and function of HD2-type histone deacetylases in Arabidopsis development.
    Plant J., 2004. 38(5): p. 715-24
  7. Pendle AF, et al.
    Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions.
    Mol. Biol. Cell, 2005. 16(1): p. 260-9
  8. Stangeland B, et al.
    Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes.
    J. Exp. Bot., 2005. 56(419): p. 2495-505
  9. Pischke MS,Huttlin EL,Hegeman AD,Sussman MR
    A transcriptome-based characterization of habituation in plant tissue culture.
    Plant Physiol., 2006. 140(4): p. 1255-78
  10. Sridha S,Wu K
    Identification of AtHD2C as a novel regulator of abscisic acid responses in Arabidopsis.
    Plant J., 2006. 46(1): p. 124-33
  11. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
  12. Song Y,Wu K,Dhaubhadel S,An L,Tian L
    Arabidopsis DNA methyltransferase AtDNMT2 associates with histone deacetylase AtHD2s activity.
    Biochem. Biophys. Res. Commun., 2010. 396(2): p. 187-92
  13. Van Leene J, et al.
    Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.
    Mol. Syst. Biol., 2010. 6: p. 397
  14. Tamura K,Fukao Y,Iwamoto M,Haraguchi T,Hara-Nishimura I
    Identification and characterization of nuclear pore complex components in Arabidopsis thaliana.
    Plant Cell, 2010. 22(12): p. 4084-97
  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. Khan A, et al.
    The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing.
    Plant J., 2014. 79(1): p. 28-43
  20. Zhong X, et al.
    Molecular mechanism of action of plant DRM de novo DNA methyltransferases.
    Cell, 2014. 157(5): p. 1050-60
  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
  22. Han Z, et al.
    AtHD2D Gene Plays a Role in Plant Growth, Development, and Response to Abiotic Stresses in Arabidopsis thaliana.
    Front Plant Sci, 2016. 7: p. 310
  23. Buszewicz D, et al.
    HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis.
    Plant Cell Environ., 2016. 39(10): p. 2108-22
  24. Chen X, et al.
    Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing.
    Plant Cell, 2018. 30(1): p. 134-152
  25. Huang KC,Lin WC,Cheng WH
    Salt hypersensitive mutant 9, a nucleolar APUM23 protein, is essential for salt sensitivity in association with the ABA signaling pathway in Arabidopsis.
    BMC Plant Biol., 2018. 18(1): p. 40