PlantPromoterDB promoter information of AT3G50820

Summary of Gene (AT3G50820)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G50820 TAIR NCBI
Gene model	AT3G50820
Description	Encodes a protein which is an extrinsic subunit of photosystem II and which has been proposed to play a central role in stabilization of the catalytic manganese cluster. In <i>Arabidopsis thaliana</i> the PsbO proteins are encoded by two genes: <i>psbO1</i> and <i>psbO2</i>. PsbO2 is the minor isoform in the wild-type. Mutants defective in this gene have been shown to be affected in the dephosphorylation of the D1 protein of PSII.

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Overview

Focused view (chromosome 3: 18893311-18892112)

`Genome position from initiation codon` `AT3G50820.1 TSS from cDNA TSS information AT3G50820 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 AT3G50820

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 197 - 18892340 -29

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	197	-	18892340	-29

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 18892389 -78

TSS clone T clone - 18892379 -68

TSS clone A clone - 18892369 -58

TSS clone C clone - 18892368 -57

TSS clone A clone - 18892361 -50

TSS clone A clone - 18892344 -33

TSS clone A clone - 18892339 -28

TSS clone T clone - 18892335 -24

TSS clone A clone - 18892330 -19

TSS clone T clone - 18892327 -16

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	18892389	-78
TSS clone	`T`	clone	-	18892379	-68
TSS clone	`A`	clone	-	18892369	-58
TSS clone	`C`	clone	-	18892368	-57
TSS clone	`A`	clone	-	18892361	-50
TSS clone	`A`	clone	-	18892344	-33
TSS clone	`A`	clone	-	18892339	-28
TSS clone	`T`	clone	-	18892335	-24
TSS clone	`A`	clone	-	18892330	-19
TSS clone	`T`	clone	-	18892327	-16

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 CTTCTCTCC - 18892296 18892304 15 7

Y Patch TCTCTCCTCT - 18892377 18892386 -66 -75

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	`CTTCTCTCC`	-	18892296	18892304	15	7
Y Patch	`TCTCTCCTCT`	-	18892377	18892386	-66	-75
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 AGACACGTGGCT - 18892467 18892478 -156 -167

AtREG470 AGACACGT     ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

AtREG366 GACACGTG    ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC

AtREG382   ACACGTGG   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

AtREG367    CACGTGGC ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

AtREG450     ACGTGGCT ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

REG CACGTCATC - 18892520 18892528 -209 -217

AtREG483 CACGTCAT PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG578 ACGTCATC ABA PPDB Motif ACGT PLACE Motif ACGT

REG TTGAACCG - 18892591 18892598 -280 -287

AtREG640 TTGAACCG PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AGACACGTGGCT`		-	18892467	18892478	-156	-167
	AtREG470	`AGACACGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
	AtREG366	`GACACGTG`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC`
	AtREG382	`ACACGTGG`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACACNNG`
	AtREG367	`CACGTGGC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC`
	AtREG450	`ACGTGGCT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
REG	`CACGTCATC`		-	18892520	18892528	-209	-217
	AtREG483	`CACGTCAT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG578	`ACGTCATC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
REG	`TTGAACCG`		-	18892591	18892598	-280	-287
	AtREG640	`TTGAACCG`		PPDB Motif	`AACCG(G/A)`	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