PlantPromoterDB promoter information of AT3G13300.2

Summary of Gene (AT3G13300.2)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G13300 TAIR NCBI
Gene model	AT3G13300.2
Description	Encodes VCS (VARICOSE). Involved in mRNA decapping. VCS forms a mRNA decapping complex with DCP1 (At1g08370) and DCP2 (At5g13570). Unlike DCP2, VCS itself does not have mRNA decapping activity in vitro. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. VCS is also required for leaf development.

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Overview

Focused view (chromosome 3: 4303085-4304284)

`Genome position from initiation codon` `AT3G13290.1 AT3G13300.1 TSS from cDNA TSS information AT3G13300.2 5'->3' (+) Promoter sequence TSS from cDNA TSS information 3'->5' (-) Promoter sequence TSS tag distribution(+) TSS tag distribution(-)`	Your web browser cannot display this window!

ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC

Promoter Summary of AT3G13300.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 2 + 4303885 -200

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	2	+	4303885	-200

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 4303874 -211

TSS clone A clone + 4303875 -210

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	4303874	-211
TSS clone	`A`	clone	+	4303875	-210

Core promoter information

Type Sequence Genome position Position from initiation codon

Strand Start End Start End

initiator Not Available Not Available Not Available

TATA Box None None None

Y Patch CGTCTCTCTCTCTCT + 4303911 4303925 -174 -160

GA None None None

Inr None None None

Type	Sequence	Genome position	Position from initiation codon
		Strand	Start	End	Start	End
initiator	Not Available	Not Available	Not Available
TATA Box	None	None	None
Y Patch	`CGTCTCTCTCTCTCT`	+	4303911	4303925	-174	-160
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Position from initiation codon

Strand Start End Start End

REG TAGGGCCCAATAA + 4303699 4303711 -386 -374

AtREG387 TAGGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG400 AGGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392   GGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352    GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355     GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417      CCCAATAA PPDB Motif GCCCA PLACE Motif

REG TTAAAGGCCCAAAC + 4303718 4303731 -367 -354

AtREG639 TTAAAGGC       PPDB Motif AAACG(C/G) PLACE Motif

AtREG467 TAAAGGCC      PPDB Motif PLACE Motif

AtREG359   AAAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353    AAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356     AGGCCCAA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG373      GGCCCAAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG474       GCCCAAAC PPDB Motif GCCCA PLACE Motif

REG GCCCAATT + 4303824 4303831 -261 -254

AtREG418 GCCCAATT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TAGGGCCCAATAA`		+	4303699	4303711	-386	-374
	AtREG387	`TAGGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG400	`AGGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG392	`GGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TTAAAGGCCCAAAC`		+	4303718	4303731	-367	-354
	AtREG639	`TTAAAGGC`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG467	`TAAAGGCC`		PPDB Motif		PLACE Motif
	AtREG359	`AAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG373	`GGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG474	`GCCCAAAC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GCCCAATT`		+	4303824	4303831	-261	-254
	AtREG418	`GCCCAATT`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box None None None

Y Patch None None None

GA None None None

Inr None None None

Type	Sequence	Genome position	Gene model
		Strand	Start	End
initiator	Not Available	Not Available	Not Available
TATA Box	None	None	None
Y Patch	None	None	None
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG None None None