PlantPromoterDB promoter information of AT3G15840

Summary of Gene (AT3G15840)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G15840 TAIR NCBI
Gene model	AT3G15840
Description	Encodes a chloroplast-targeted protein localized in the stroma that is a novel component essential for NDH-mediated non-photochemical reduction of the plastoquinone pool in chlororespiratory electron transport.

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Overview

Focused view (chromosome 3: 5359418-5358219)

`Genome position from initiation codon` `AT3G15840.1 AT3G15840.2 AT3G15840.3 AT3G15840.4 TSS from cDNA TSS information AT3G15840 5'->3' (-) Promoter sequence AT3G15850.1 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 AT3G15840

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 8 - 5358482 -64

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	8	-	5358482	-64

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 5358499 -81

TSS clone T clone - 5358486 -68

TSS clone T clone - 5358455 -37

TSS clone T clone - 5358452 -34

TSS clone T clone - 5358225 193

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	5358499	-81
TSS clone	`T`	clone	-	5358486	-68
TSS clone	`T`	clone	-	5358455	-37
TSS clone	`T`	clone	-	5358452	-34
TSS clone	`T`	clone	-	5358225	193

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 TCTCCTTCT - 5358457 5358465 -39 -47

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	`TCTCCTTCT`	-	5358457	5358465	-39	-47
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 TGAGCCCATTC - 5358665 5358675 -247 -257

AtREG485 TGAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG372   AGCCCATT PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG643    GCCCATTC PPDB Motif GCCCA PLACE Motif

REG GAATGGGCTTAT - 5358684 5358695 -266 -277

AtREG643 GAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG372 AATGGGCT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378   ATGGGCTT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG426    TGGGCTTA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG462     GGGCTTAT PPDB Motif GCCCA PLACE Motif

REG CAATTGGGCTCA - 5358706 5358717 -288 -299

AtREG647 CAATTGGG     PPDB Motif PLACE Motif

AtREG418 AATTGGGC    PPDB Motif GCCCA PLACE Motif

AtREG402   ATTGGGCT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG533    TTGGGCTC PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG485     TGGGCTCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG CCCAATAT - 5358729 5358736 -311 -318

AtREG509 CCCAATAT PPDB Motif PLACE Motif

REG AAAAGCCC - 5358766 5358773 -348 -355

AtREG409 AAAAGCCC PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TGAGCCCATTC`		-	5358665	5358675	-247	-257
	AtREG485	`TGAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG372	`AGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG643	`GCCCATTC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GAATGGGCTTAT`		-	5358684	5358695	-266	-277
	AtREG643	`GAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG372	`AATGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`ATGGGCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG426	`TGGGCTTA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG462	`GGGCTTAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CAATTGGGCTCA`		-	5358706	5358717	-288	-299
	AtREG647	`CAATTGGG`		PPDB Motif		PLACE Motif
	AtREG418	`AATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG402	`ATTGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG533	`TTGGGCTC`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG485	`TGGGCTCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`CCCAATAT`		-	5358729	5358736	-311	-318
	AtREG509	`CCCAATAT`		PPDB Motif		PLACE Motif
REG	`AAAAGCCC`		-	5358766	5358773	-348	-355
	AtREG409	`AAAAGCCC`		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

TSS clone T clone + 5359060 AT3G15850.1

TSS clone T clone + 5359063 AT3G15850.1

TSS clone peak T clone + 5359067 AT3G15850.1

TSS clone G clone + 5359072 AT3G15850.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	5359060	AT3G15850.1
TSS clone	`T`	clone	+	5359063	AT3G15850.1
TSS clone peak	`T`	clone	+	5359067	AT3G15850.1
TSS clone	`G`	clone	+	5359072	AT3G15850.1

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 CCTCTTCTCTTCCTTCTTTCTCT + 5359047 5359069 AT3G15850.1

Y Patch CTTCTCTTCT + 5359091 5359100 AT3G15850.1

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	`CCTCTTCTCTTCCTTCTTTCTCT`	+	5359047	5359069	AT3G15850.1
Y Patch	`CTTCTCTTCT`	+	5359091	5359100	AT3G15850.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG None None None