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 AT5G03740.1
Common NameF17C15_160, HD2C, HDT3, MED24.1
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 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
1zf-C2H215.16.6e-05267290123
                  EEETTTTEEESSHHHHHHHHHH.T CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirt.H 23 
                  + C+ C+++F++ + L++H +  H
  AT5G03740.1 267 FGCKSCTRTFTSEMGLQSHTKAkH 290
                  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: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:0025195anatomypollen tube cell
PO:0025281anatomypollen
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
MEFWGVEVKN GKPLHLDPGL DRLVHISQVA LGESKNNVTE PIQLYVTVGS DKLLIGTLSH  60
EKFPQLSTEI VLERNFALSH TWKNGSVFFS GYKVDASDPE PEDLIDDQLE AAGFKAAPKS  120
AAKQVNFQLP NEDVKAKQDD DADGSEEDSS DDDDSENSGD EEEEKVTAES DSEEDDSSDD  180
EEDDSSEEET PKKPEEPKKR SAEPNSSKNP ASNKKAKFVT PQKTDSKKPH VHVATPHPSK  240
QAGKNSGGGS TGETSKQQQT PKSAGAFGCK SCTRTFTSEM GLQSHTKAKH SAAA
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
Genevisible250912_at0.0
Expression AtlasAT5G03740-
AtGenExpressAT5G03740-
ATTED-IIAT5G03740-
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]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G03740.1
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
PlantRegMapRetrieve-
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
GenBankAY1420390.0AY142039.1 Arabidopsis thaliana At5g03740/F17C15_160 mRNA, complete cds.
GenBankAF5101680.0AF510168.1 Arabidopsis thaliana HDT3 mRNA, complete cds.
GenBankAF3728890.0AF372889.1 Arabidopsis thaliana AT5g03740/F17C15_160 mRNA, complete cds.
GenBankAF2557120.0AF255712.1 Arabidopsis thaliana putative histone deacetylase HD2c 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
TrEMBLD7LWT21e-137D7LWT2_ARALL; Putative uncharacterized protein
STRINGAT5G03740.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM20272667
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
    [PMID:10792817]
  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
    [PMID:11469594]
  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
    [PMID:12466527]
  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
    [PMID:12694598]
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  6. Zhou C, et al.
    Expression and function of HD2-type histone deacetylases in Arabidopsis development.
    Plant J., 2004. 38(5): p. 715-24
    [PMID:15144374]
  7. Pendle AF, et al.
    Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions.
    Mol. Biol. Cell, 2005. 16(1): p. 260-9
    [PMID:15496452]
  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
    [PMID:16014362]
  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
    [PMID:16489130]
  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
    [PMID:16553900]
  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
    [PMID:18775970]
  12. Van Leene J, et al.
    Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.
    Mol. Syst. Biol., 2010. 6: p. 397
    [PMID:20706207]
  13. 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
    [PMID:21189294]
  14. 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
    [PMID:21739146]
  15. 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]
  16. 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
    [PMID:22368268]
  17. 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
    [PMID:22580696]
  18. Zhong X, et al.
    Molecular mechanism of action of plant DRM de novo DNA methyltransferases.
    Cell, 2014. 157(5): p. 1050-60
    [PMID:24855943]
  19. 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
    [PMID:25750178]