PlantTFDB
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 Cagra.9571s0003.1.p
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; Capsella
Family C2H2
Protein Properties Length: 268aa    MW: 28750.8 Da    PI: 5.2889
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.9571s0003.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2140.00015241263223
                          EETTTTEEESSHHHHHHHHHH.T CS
              zf-C2H2   2 kCpdCgksFsrksnLkrHirt.H 23 
                          +C+ C+k+F++   L++H +  H
  Cagra.9571s0003.1.p 241 SCGSCKKTFNSGNALESHNKAkH 263
                          7*****************88766 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF030663.4E-73170No hitNo description
PROSITE profilePS5015710.533240267IPR007087Zinc finger, C2H2
PROSITE patternPS000280242263IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009294Biological ProcessDNA mediated transformation
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010162Biological Processseed dormancy process
GO:0005730Cellular Componentnucleolus
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 268 aa     Download sequence    Send to blast
MEFWGIEVKP GKPVTVETEF DRLIHISQAS LGECKNKKEE TVAVHVKFGD KKLLLGTLST  60
VNIPQIFCDL VFQNDFEISH NGNGSVHFVG YTSPNCADEF GDDDFYDSEE EEEKVPATVT  120
ANGNAAKPKA KPAQVTKNAK AADVDEEDDS DSEGMDFDED EDSEEEEETP TPKKAVSGKK  180
RANEEAPKTP VSSKKAKVAV TPQKTDEKKK GGHTATPHPG KKGAKTPTTA AQSPKSASQI  240
SCGSCKKTFN SGNALESHNK AKHAAAK*
Functional Description ? help Back to Top
Source Description
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.9571s0003.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1955452e-40AF195545.1 Arabidopsis thaliana putative histone deacetylase (HD2A) mRNA, complete cds.
GenBankAY0653962e-40AY065396.1 Arabidopsis thaliana putative histone deacetylase (At3g44750) mRNA, complete cds.
GenBankAY0967292e-40AY096729.1 Arabidopsis thaliana putative histone deacetylase (At3g44750) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023638513.11e-165histone deacetylase HDT1
SwissprotQ9FVE63e-86HDT1_ARATH; Histone deacetylase HDT1
TrEMBLR0FQZ91e-151R0FQZ9_9BRAS; Uncharacterized protein
STRINGCagra.9571s0003.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM20272667
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G44750.24e-84histone deacetylase 3
Publications ? help Back to Top
  1. 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
    [PMID:20331964]
  2. Lee K,Park OS,Jung SJ,Seo PJ
    Histone deacetylation-mediated cellular dedifferentiation in Arabidopsis.
    J. Plant Physiol., 2016. 191: p. 95-100
    [PMID:26724747]
  3. 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
    [PMID:27066015]
  4. Li H, et al.
    Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number.
    Plant Cell, 2017. 29(9): p. 2183-2196
    [PMID:28855334]