PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

GSBRNA2T00012327001

Common Name

GSBRNA2T00012327001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

C2H2

Protein Properties

Length: 328aa MW: 35480.8 Da PI: 4.8507

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00012327001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.8	1.9e-05	300	322	2	23
EETTTTEEESSHHHHHHHHHH.T CS zf-C2H2 2 kCpdCgksFsrksnLkrHirt.H 23 +C+ C+k+F+++ L++H + H GSBRNA2T00012327001 300 SCGSCKKTFNSSNALESHTKAkH 322 6*****************99877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF05764	7.3E-8	165	310	No hit	No description
PROSITE profile	PS50157	10.014	299	327	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	301	322	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 328 aa Download sequence Send to blast
MLMLPMVQFM EKKSSHWIGM EIHLTNNTIT LFHCGLPNED INVDIRQIEI LQMLECLSLG 60 LKNMSDINDD NAMDLLSMLC CEIFDQFMDR DFKEGVEVQA GKPLKVTPGY DSIVHISHAS 120 LGDCKGKKGE AVTLNVKEFE LSHNWGKGSV HFFSLTFNVL CVFTEGGEDF SDSEEEEEVE 180 VPVPVAANGN AAKAVANPKP VTAPDDSDSE GMDEDCSDDE DDSEEEEETP KAETRRKRAH 240 EAAPAPKTPV SAKKAKAAEA TPKKTEEKKK GGPATPHPAK KGGNTPATAT QSPKSASQVS 300 CGSCKKTFNS SNALESHTKA KHSATAK*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.17260	1e-163	seed

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE 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
UniProt	Probably 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
Source	Link
PlantRegMap	GSBRNA2T00012327001

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013583952.1	1e-108	PREDICTED: histone deacetylase HDT1
Swissprot	Q9FVE6	5e-40	HDT1_ARATH; Histone deacetylase HDT1
TrEMBL	A0A078G5W1	0.0	A0A078G5W1_BRANA; BnaC01g23930D protein
TrEMBL	A0A0D3A8I4	0.0	A0A0D3A8I4_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6FSX5	0.0	A0A3P6FSX5_BRAOL; Uncharacterized protein
STRING	Bo1g063760.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2027	26	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G44750.2	2e-15	histone deacetylase 3

Publications ? help Back to Top
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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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] 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] 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]