PlantPromoterDB promoter information of AT3G04790.1

Summary of Gene (AT3G04790.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G04790 TAIR NCBI
Gene model	AT3G04790.1
Description	ribose 5-phosphate isomerase-related; FUNCTIONS IN: ribose-5-phosphate isomerase activity; INVOLVED IN: defense response to bacterium, reductive pentose-phosphate cycle; LOCATED IN: thylakoid, chloroplast thylakoid membrane, chloroplast stroma, chloroplast, chloroplast envelope; EXPRESSED IN: 26 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Ribose 5-phosphate isomerase (InterPro:IPR004788); BEST Arabidopsis thaliana protein match is: ribose-5-phosphate isomerase (TAIR:AT2G01290.1); Has 3164 Blast hits to 3164 proteins in 1122 species: Archae - 153; Bacteria - 1911; Metazoa - 90; Fungi - 101; Plants - 84; Viruses - 0; Other Eukaryotes - 825 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 1312365-1313564)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G04790.1 5'->3' (+) Promoter sequence AT3G04780.1 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 AT3G04790.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 1313295 -70

TSS clone A clone + 1313296 -69

TSS clone peak G clone + 1313318 -47

TSS clone A clone + 1313324 -41

TSS clone T clone + 1313325 -40

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	1313295	-70
TSS clone	`A`	clone	+	1313296	-69
TSS clone peak	`G`	clone	+	1313318	-47
TSS clone	`A`	clone	+	1313324	-41
TSS clone	`T`	clone	+	1313325	-40

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 CCTTCCTCT + 1313279 1313287 -86 -78

Y Patch TTTCTTCTCC + 1313330 1313339 -35 -26

Y Patch TCCTCTCTCTCC + 1313352 1313363 -13 -2

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	`CCTTCCTCT`	+	1313279	1313287	-86	-78
Y Patch	`TTTCTTCTCC`	+	1313330	1313339	-35	-26
Y Patch	`TCCTCTCTCTCC`	+	1313352	1313363	-13	-2
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 AAAACGACATCG + 1313142 1313153 -223 -212

AtREG520 AAAACGAC     PPDB Motif PLACE Motif

AtREG569 AAACGACA    PPDB Motif PLACE Motif

AtREG630     CGACATCG PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AAAACGACATCG`		+	1313142	1313153	-223	-212
	AtREG520	`AAAACGAC`		PPDB Motif		PLACE Motif
	AtREG569	`AAACGACA`		PPDB Motif		PLACE Motif
	AtREG630	`CGACATCG`		PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 4 - 1313081 AT3G04780.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	4	-	1313081	AT3G04780.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone - 1313089 AT3G04780.1

TSS clone A clone - 1313088 AT3G04780.1

TSS clone T clone - 1313084 AT3G04780.1

TSS clone A clone - 1313081 AT3G04780.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	-	1313089	AT3G04780.1
TSS clone	`A`	clone	-	1313088	AT3G04780.1
TSS clone	`T`	clone	-	1313084	AT3G04780.1
TSS clone	`A`	clone	-	1313081	AT3G04780.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box TTATATAAAAA - 1313112 1313122 AT3G04780.1

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	`TTATATAAAAA`	-	1313112	1313122	AT3G04780.1
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 CGATGTCGTTTT - 1313142 1313153 AT3G04780.1

AtREG630 CGATGTCG     PPDB Motif PLACE Motif

AtREG569    TGTCGTTT PPDB Motif PLACE Motif

AtREG520     GTCGTTTT PPDB Motif PLACE Motif

REG TTGACTTT - 1313296 1313303 AT3G04780.1

AtREG632 TTGACTTT PPDB Motif PLACE Motif TTGAC