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

Csa20g003880.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 334aa MW: 36175.8 Da PI: 5.6151

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa20g003880.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.8	8e-05	306	329	1	23
EEETTTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirt.H 23 + C+ C+++F++ + L++H + H Csa20g003880.1 306 FGCNSCSRTFTSEMGLQSHTKAkH 329 56*****************99877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50157	10.845	306	333	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	308	329	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: 334 aa Download sequence Send to blast
GPFNFIRPRT ALERRIALEP SSSSSHRRLQ AHTTSHDNGV LGLLDSMSRG FGVEVKPNAP 60 LRVNPGEDML VHISQAALGE SKNNVKEPIQ LFVKVVGGEK LIIGNLSHDK FPQLSTELVL 120 EKDFDLSHNW KNGSVFFTGY KVDASDPYPL YYFNICLLYL LKPYKLASDD DDEPAVASDK 180 AEPAVAASGV KQVNFQLPNA EVKAQEDDDE DDSEEDSSDD EEESSDESGD EEPEESKKRS 240 AEANSSKNTA SNKKAKFVTP QKTESKKPHV HIATPHPSKQ AGKNSGGSSN GESSKKQQTP 300 KSAGAFGCNS CSRTFTSEMG LQSHTKAKHS AAA*

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	Csa20g003880.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF255712	1e-116	AF255712.1 Arabidopsis thaliana putative histone deacetylase HD2c mRNA, complete cds.
GenBank	AF372889	1e-116	AF372889.1 Arabidopsis thaliana AT5g03740/F17C15_160 mRNA, complete cds.
GenBank	AF510168	1e-116	AF510168.1 Arabidopsis thaliana HDT3 mRNA, complete cds.
GenBank	AY142039	1e-116	AY142039.1 Arabidopsis thaliana At5g03740/F17C15_160 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010490865.1	1e-145	PREDICTED: histone deacetylase HDT3
Swissprot	Q9LZR5	1e-112	HDT3_ARATH; Histone deacetylase HDT3
TrEMBL	R0GWD3	1e-110	R0GWD3_9BRAS; Uncharacterized protein
STRING	XP_010490865.1	1e-144	(Camelina sativa)

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
AT5G03740.1	1e-52	histone deacetylase 2C

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]