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

Rsa1.0_05782.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 243aa MW: 25926.5 Da PI: 5.0366

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_05782.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.3	1.3e-05	216	238	2	23
EETTTTEEESSHHHHHHHHHH.T CS zf-C2H2 2 kCpdCgksFsrksnLkrHirt.H 23 +C+ C+k+F+++ L++H + H Rsa1.0_05782.1_g00001.1 216 SCGSCKKTFNSSNALESHTKAkH 238 6*****************99877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF05764	8.3E-7	87	232	No hit	No description
PROSITE profile	PS50157	10.014	215	243	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	217	238	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009294	Biological Process	DNA mediated transformation
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0010162	Biological Process	seed dormancy process
GO:0005730	Cellular Component	nucleolus
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 243 aa Download sequence Send to blast
MEFWGVEVQA GRPLKVTPED GTLVHISHAS LGDCKGKKGE AVTLNVKVGD KKFVMGTLLS 60 ESIPQTCFDM LFDQEFELSH NWGKGREDFS DSEEEEEEEV AATVAANGNA AKGVTKPKPE 120 ADDSDSEGMD EDGSDDEDDS EEEEETPKAE TRRKRAHEVA PGPKTPVSAK KAKAEATPKK 180 TEEKKKGGPA TPHPAKKGGN TPATATQSPK SASQVSCGSC KKTFNSSNAL ESHTKAKHSA 240 TAK

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	Rsa1.0_05782.1_g00001.1

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_013670064.1	1e-115	histone deacetylase HDT1
Swissprot	Q9FVE6	8e-65	HDT1_ARATH; Histone deacetylase HDT1
TrEMBL	A0A398APH0	1e-115	A0A398APH0_BRACM; Uncharacterized protein
STRING	XP_006419104.1	1e-84	(Eutrema salsugineum)

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-38	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] 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]