PlantPromoterDB promoter information of AT4G17040.1

Summary of Gene (AT4G17040.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G17040 TAIR NCBI
Gene model	AT4G17040.1
Description	ATP-dependent Clp protease proteolytic subunit, putative; FUNCTIONS IN: serine-type endopeptidase activity; INVOLVED IN: proteolysis; LOCATED IN: plastid stroma, chloroplast, chloroplast stroma, chloroplast envelope; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase S14, ClpP (InterPro:IPR001907); BEST Arabidopsis thaliana protein match is: ATP-dependent Clp protease proteolytic subunit, putative (TAIR:AT1G09130.2); Has 8307 Blast hits to 8303 proteins in 1647 species: Archae - 0; Bacteria - 4113; Metazoa - 115; Fungi - 50; Plants - 683; Viruses - 6; Other Eukaryotes - 3340 (source: NCBI BLink).

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Overview

Focused view (chromosome 4: 9590297-9589098)

`Genome position from initiation codon` `TSS from cDNA TSS information AT4G17040.1 5'->3' (-) Promoter sequence AT4G17050.1 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 AT4G17040.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 4 - 9589338 -41

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	4	-	9589338	-41

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 9589356 -59

TSS clone C clone - 9589339 -42

TSS clone A clone - 9589328 -31

TSS clone T clone - 9589320 -23

TSS clone C clone - 9589317 -20

TSS clone T clone - 9589312 -15

TSS clone A clone - 9589308 -11

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	9589356	-59
TSS clone	`C`	clone	-	9589339	-42
TSS clone	`A`	clone	-	9589328	-31
TSS clone	`T`	clone	-	9589320	-23
TSS clone	`C`	clone	-	9589317	-20
TSS clone	`T`	clone	-	9589312	-15
TSS clone	`A`	clone	-	9589308	-11

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 CTCTTTCTCTCTCTCT - 9589312 9589327 -15 -30

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	`CTCTTTCTCTCTCTCT`	-	9589312	9589327	-15	-30
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 TGAGCCCATAA - 9589390 9589400 -93 -103

AtREG485 TGAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG477   AGCCCATA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG394    GCCCATAA PPDB Motif GCCCA PLACE Motif

REG CTATTGGGCCTATT - 9589404 9589417 -107 -120

AtREG624 CTATTGGG       PPDB Motif GCCCA PLACE Motif

AtREG355 TATTGGGC      PPDB Motif GCCCA PLACE Motif

AtREG352   ATTGGGCC     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356    TTGGGCCT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358     TGGGCCTA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG362      GGGCCTAT PPDB Motif GCCCA PLACE Motif GGGCC

AtREG424       GGCCTATT PPDB Motif PLACE Motif

REG AAACCGGAA - 9589443 9589451 -146 -154

AtREG521 AAACCGGA PPDB Motif AACCG(G/A) PLACE Motif

AtREG534 AACCGGAA PPDB Motif AACCG(G/A) PLACE Motif

REG TTCGGTTT - 9589474 9589481 -177 -184

AtREG568 TTCGGTTT PPDB Motif AACCG(G/A) PLACE Motif

REG CCGGTTTT - 9589484 9589491 -187 -194

AtREG542 CCGGTTTT PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TGAGCCCATAA`		-	9589390	9589400	-93	-103
	AtREG485	`TGAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG477	`AGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG394	`GCCCATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CTATTGGGCCTATT`		-	9589404	9589417	-107	-120
	AtREG624	`CTATTGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG355	`TATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`TTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG362	`GGGCCTAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG424	`GGCCTATT`		PPDB Motif		PLACE Motif
REG	`AAACCGGAA`		-	9589443	9589451	-146	-154
	AtREG521	`AAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`AACCGGAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TTCGGTTT`		-	9589474	9589481	-177	-184
	AtREG568	`TTCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`CCGGTTTT`		-	9589484	9589491	-187	-194
	AtREG542	`CCGGTTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 4 + 9589553 AT4G17050.1

TSS peak A 4 + 9589645 AT4G17050.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	4	+	9589553	AT4G17050.1
TSS peak	`A`	4	+	9589645	AT4G17050.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 9589571 AT4G17050.1

TSS clone T clone + 9589575 AT4G17050.1

TSS clone A clone + 9589616 AT4G17050.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	9589571	AT4G17050.1
TSS clone	`T`	clone	+	9589575	AT4G17050.1
TSS clone	`A`	clone	+	9589616	AT4G17050.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box TTTATAAACA + 9589613 9589622 AT4G17050.1

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	`TTTATAAACA`	+	9589613	9589622	AT4G17050.1
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 TTATGGGCTCA + 9589390 9589400 AT4G17050.1

AtREG394 TTATGGGC    PPDB Motif GCCCA PLACE Motif

AtREG477 TATGGGCT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG485    TGGGCTCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG AATAGGCCCAATAG + 9589404 9589417 AT4G17050.1

AtREG424 AATAGGCC       PPDB Motif PLACE Motif

AtREG362 ATAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358   TAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356    AGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352     GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355      GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG624       CCCAATAG PPDB Motif GCCCA PLACE Motif

REG TTCCGGTTT + 9589443 9589451 AT4G17050.1

AtREG534 TTCCGGTT PPDB Motif AACCG(G/A) PLACE Motif

AtREG521 TCCGGTTT PPDB Motif AACCG(G/A) PLACE Motif

REG AAACCGAA + 9589474 9589481 AT4G17050.1

AtREG568 AAACCGAA PPDB Motif AACCG(G/A) PLACE Motif

REG AAAACCGG + 9589484 9589491 AT4G17050.1

AtREG542 AAAACCGG PPDB Motif AACCG(G/A) PLACE Motif