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

Carubv10001613m

Common Name

CARUB_v10001577mg

Organism

Capsella rubella

Taxonomic ID

81985

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: 292aa MW: 31735.1 Da PI: 4.3884

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10001613m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.9	7.7e-05	266	287	3	23
ETTTTEEESSHHHHHHHHHH.T CS zf-C2H2 3 CpdCgksFsrksnLkrHirt.H 23 C+ C++sF++ + L++H + H Carubv10001613m 266 CKSCTRSFTSEMALQSHTKAkH 287 *****************99877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50157	10.076	264	291	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	266	287	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009414	Biological Process	response to water deprivation
GO:0009651	Biological Process	response to salt stress
GO:0009737	Biological Process	response to abscisic acid
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:0005730	Cellular Component	nucleolus
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 292 aa Download sequence Send to blast
MEFWGVEVKQ GAPLHVDPGV DMLVHISQAA LGENKNNVNE PIKLYLRVKD KKHIIGVLSH 60 DKIPQLATEI VLERNFELSH SWKNGSVFFS GYKVDASDPE NENMTDDGLA VASNEGVKQV 120 NFQLPNEDVQ AKQDDDDDDS EDDSSDDDDD DSSEESGDEE EKTVTAEGDS DEDDSSDDDE 180 EDSSEEDTPI KPEEPKKRSA EANSSKNTAS NKKAKFVTPQ KSESKKPHVH VATPHPSKQA 240 GKNSGGSSNG ESLKQQQTPK SPSHGCKSCT RSFTSEMALQ SHTKAKHSAA A*

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. Involved in the modulation of abscisic acid and stress-responsive genes. {ECO:0000269\|PubMed:12694598, ECO:0000269\|PubMed:16553900}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10001613m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by abscisic acid. {ECO:0000269\|PubMed:16553900}.

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_006288330.1	0.0	histone deacetylase HDT3 isoform X3
Swissprot	Q9LZR5	1e-126	HDT3_ARATH; Histone deacetylase HDT3
TrEMBL	R0HC13	0.0	R0HC13_9BRAS; Uncharacterized protein
STRING	XP_006288331.1	1e-174	(Capsella rubella)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03740.1	2e-67	histone deacetylase 2C

Link Out ? help Back to Top
Phytozome	Carubv10001613m
Entrez Gene	17884343

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] 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 [PMID:24724701] 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] 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 [PMID:27083783] Chen X, et al. Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. Plant Cell, 2018. 30(1): p. 134-152 [PMID:29343504] 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 [PMID:29490615]