PlantPromoterDB promoter information of AT1G04680

Summary of Gene (AT1G04680)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G04680 TAIR NCBI
Gene model	AT1G04680
Description	pectate lyase family protein; FUNCTIONS IN: lyase activity, pectate lyase activity; INVOLVED IN: biological_process unknown; LOCATED IN: membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Pectin lyase fold/virulence factor (InterPro:IPR011050), AmbAllergen (InterPro:IPR018082), Pectate lyase/Amb allergen (InterPro:IPR002022), Pectin lyase fold (InterPro:IPR012334); BEST Arabidopsis thaliana protein match is: pectate lyase family protein (TAIR:AT4G13710.1); Has 926 Blast hits to 921 proteins in 162 species: Archae - 0; Bacteria - 377; Metazoa - 0; Fungi - 139; Plants - 402; Viruses - 0; Other Eukaryotes - 8 (source: NCBI BLink).

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Overview

Focused view (chromosome 1: 1308530-1307331)

`Genome position from initiation codon` `AT1G04680.1 TSS from cDNA TSS information AT1G04680 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 AT1G04680

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 51 - 1307882 -102

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	51	-	1307882	-102

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 1307882 -102

TSS clone C clone - 1307881 -101

TSS clone C clone - 1307875 -95

TSS clone G clone - 1307873 -93

TSS clone T clone - 1307872 -92

TSS clone C clone - 1307871 -91

TSS clone T clone - 1307870 -90

TSS clone A clone - 1307866 -86

TSS clone T clone - 1307858 -78

TSS clone G clone - 1307835 -55

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	1307882	-102
TSS clone	`C`	clone	-	1307881	-101
TSS clone	`C`	clone	-	1307875	-95
TSS clone	`G`	clone	-	1307873	-93
TSS clone	`T`	clone	-	1307872	-92
TSS clone	`C`	clone	-	1307871	-91
TSS clone	`T`	clone	-	1307870	-90
TSS clone	`A`	clone	-	1307866	-86
TSS clone	`T`	clone	-	1307858	-78
TSS clone	`G`	clone	-	1307835	-55

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 TTCTATAAG - 1307908 1307916 -128 -136

Y Patch CTCTCTCTCTCTCTCTCCTCT - 1307836 1307856 -56 -76

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	`TTCTATAAG`	-	1307908	1307916	-128	-136
Y Patch	`CTCTCTCTCTCTCTCTCCTCT`	-	1307836	1307856	-56	-76
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 GGTGTCGT - 1307950 1307957 -170 -177

AtREG599 GGTGTCGT PPDB Motif PLACE Motif

REG GACGACGTCGT - 1307997 1308007 -217 -227

AtREG526 GACGACGT PPDB Motif ACGT PLACE Motif ACGT

AtREG431 ACGACGTCGT PPDB Motif ACGT PLACE Motif ACGT

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GGTGTCGT`		-	1307950	1307957	-170	-177
	AtREG599	`GGTGTCGT`		PPDB Motif		PLACE Motif
REG	`GACGACGTCGT`		-	1307997	1308007	-217	-227
	AtREG526	`GACGACGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
	AtREG431	`ACGACGTCGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`

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