PlantPromoterDB promoter information of AT3G42950.1

Summary of Gene (AT3G42950.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G42950 TAIR NCBI
Gene model	AT3G42950.1
Description	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein; FUNCTIONS IN: polygalacturonase activity; INVOLVED IN: carbohydrate metabolic process; LOCATED IN: endomembrane system; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 8 growth stages; CONTAINS InterPro DOMAIN/s: Pectin lyase fold/virulence factor (InterPro:IPR011050), Glycoside hydrolase, family 28 (InterPro:IPR000743), Pectin lyase fold (InterPro:IPR012334), Parallel beta-helix repeat (InterPro:IPR006626); BEST Arabidopsis thaliana protein match is: glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein (TAIR:AT1G19170.1); Has 2496 Blast hits to 2489 proteins in 316 species: Archae - 2; Bacteria - 615; Metazoa - 8; Fungi - 925; Plants - 839; Viruses - 0; Other Eukaryotes - 107 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 15014383-15015582)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G42950.1 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 AT3G42950.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 13 + 15015163 -220

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	13	+	15015163	-220

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone C clone + 15015167 -216

TSS clone T clone + 15015189 -194

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`C`	clone	+	15015167	-216
TSS clone	`T`	clone	+	15015189	-194

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 CTTCTCTC + 15015167 15015174 -216 -209

Y Patch CTTTCTCT + 15015184 15015191 -199 -192

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	`CTTCTCTC`	+	15015167	15015174	-216	-209
Y Patch	`CTTTCTCT`	+	15015184	15015191	-199	-192
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 TCGGTTCGGTTT + 15015014 15015025 -369 -358

AtREG575 TCGGTTCG     PPDB Motif AACCG(G/A) PLACE Motif

AtREG456 CGGTTCGG    PPDB Motif AACCG(G/A) PLACE Motif

AtREG451   GGTTCGGT   PPDB Motif PLACE Motif

AtREG556    GTTCGGTT PPDB Motif AACCG(G/A) PLACE Motif

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

REG ACGGTTTAT + 15015038 15015046 -345 -337

AtREG652 ACGGTTTA PPDB Motif PLACE Motif

AtREG598 CGGTTTAT PPDB Motif AACCG(G/A) PLACE Motif

REG TCGGTTCG + 15015056 15015063 -327 -320

AtREG575 TCGGTTCG PPDB Motif AACCG(G/A) PLACE Motif

REG TTTCCGGTTCA + 15015087 15015097 -296 -286

AtREG644 TTTCCGGT    PPDB Motif AACCG(G/A) PLACE Motif

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

AtREG579   TCCGGTTC PPDB Motif AACCG(G/A) PLACE Motif

AtREG480    CCGGTTCA PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TCGGTTCGGTTT`		+	15015014	15015025	-369	-358
	AtREG575	`TCGGTTCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG456	`CGGTTCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG451	`GGTTCGGT`		PPDB Motif		PLACE Motif
	AtREG556	`GTTCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG568	`TTCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`ACGGTTTAT`		+	15015038	15015046	-345	-337
	AtREG652	`ACGGTTTA`		PPDB Motif		PLACE Motif
	AtREG598	`CGGTTTAT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TCGGTTCG`		+	15015056	15015063	-327	-320
	AtREG575	`TCGGTTCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TTTCCGGTTCA`		+	15015087	15015097	-296	-286
	AtREG644	`TTTCCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`TTCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG579	`TCCGGTTC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG480	`CCGGTTCA`		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