PlantPromoterDB promoter information of AT1G78900.2

Summary of Gene (AT1G78900.2)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G78900 TAIR NCBI
Gene model	AT1G78900.2
Description	Encodes catalytic subunit A of the vacuolar ATP synthase. Mutants are devoid of vacuolar ATPase activity as subunit A is encoded only by this gene and show strong defects in male gametophyte development and in Golgi stack morphology.

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Overview

Focused view (chromosome 1: 29659463-29660662)

`Genome position from initiation codon` `AT1G78900.1 TSS from cDNA TSS information AT1G78900.2 5'->3' (+) Promoter sequence AT1G78895.1 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 AT1G78900.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 38 + 29660221 -242

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	38	+	29660221	-242

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 29660184 -279

TSS clone A clone + 29660187 -276

TSS clone T clone + 29660188 -275

TSS clone A clone + 29660191 -272

TSS clone C clone + 29660192 -271

TSS clone T clone + 29660194 -269

TSS clone T clone + 29660198 -265

TSS clone G clone + 29660221 -242

TSS clone T clone + 29660222 -241

TSS clone T clone + 29660241 -222

TSS clone G clone + 29660252 -211

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	29660184	-279
TSS clone	`A`	clone	+	29660187	-276
TSS clone	`T`	clone	+	29660188	-275
TSS clone	`A`	clone	+	29660191	-272
TSS clone	`C`	clone	+	29660192	-271
TSS clone	`T`	clone	+	29660194	-269
TSS clone	`T`	clone	+	29660198	-265
TSS clone	`G`	clone	+	29660221	-242
TSS clone	`T`	clone	+	29660222	-241
TSS clone	`T`	clone	+	29660241	-222
TSS clone	`G`	clone	+	29660252	-211

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 CCTCTCTCTTCTTCTTCTT + 29660202 29660220 -261 -243

Y Patch CTCTTCCT + 29660228 29660235 -235 -228

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	`CCTCTCTCTTCTTCTTCTT`	+	29660202	29660220	-261	-243
Y Patch	`CTCTTCCT`	+	29660228	29660235	-235	-228
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 GGACCCACTTATTGGGCCGTA + 29660017 29660037 -446 -426

AtREG523 GGACCCAC              PPDB Motif GGGACCC PLACE Motif

AtREG611        CTTATTGG       PPDB Motif PLACE Motif

AtREG417         TTATTGGG      PPDB Motif GCCCA PLACE Motif

AtREG355          TATTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG352           ATTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414            TTGGGCCG   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG368             TGGGCCGT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG499              GGGCCGTA PPDB Motif GCCCA PLACE Motif GGGCC

REG ATAAAGCCCAATAA + 29660048 29660061 -415 -402

AtREG601 ATAAAGCC       PPDB Motif PLACE Motif

AtREG365 TAAAGCCC      PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407    AAGCCCAA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG402     AGCCCAAT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG355      GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417       CCCAATAA PPDB Motif GCCCA PLACE Motif

REG TGTCACGTGGCT + 29660068 29660079 -395 -384

AtREG606 TGTCACGT     ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG583 GTCACGTG    PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

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

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GGACCCACTTATTGGGCCGTA`		+	29660017	29660037	-446	-426
	AtREG523	`GGACCCAC`		PPDB Motif	`GGGACCC`	PLACE Motif
	AtREG611	`CTTATTGG`		PPDB Motif		PLACE Motif
	AtREG417	`TTATTGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG355	`TATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`TTGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG368	`TGGGCCGT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG499	`GGGCCGTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`ATAAAGCCCAATAA`		+	29660048	29660061	-415	-402
	AtREG601	`ATAAAGCC`		PPDB Motif		PLACE Motif
	AtREG365	`TAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG402	`AGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TGTCACGTGGCT`		+	29660068	29660079	-395	-384
	AtREG606	`TGTCACGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG583	`GTCACGTG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`
	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`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 4 - 29659923 AT1G78895.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	4	-	29659923	AT1G78895.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone C clone - 29659976 AT1G78895.1

TSS clone G clone - 29659923 AT1G78895.1

TSS clone A clone - 29659911 AT1G78895.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`C`	clone	-	29659976	AT1G78895.1
TSS clone	`G`	clone	-	29659923	AT1G78895.1
TSS clone	`A`	clone	-	29659911	AT1G78895.1

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 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