PlantPromoterDB promoter information of AT1G09340

Summary of Gene (AT1G09340)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G09340 TAIR NCBI
Gene model	AT1G09340
Description	Encodes CHLOROPLAST RNA BINDING (CRB), a putative RNA-binding protein. CRB is important for the proper functioning of the chloroplast. Mutations in CRB also affects the circadian system, altering the expression of both oscillator and output genes.

#

Overview

Focused view (chromosome 1: 3014473-3015672)

`Genome position from initiation codon` `AT1G09340.1 TSS from cDNA TSS information AT1G09340 5'->3' (+) Promoter sequence AT1G09330.1 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 AT1G09340

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 36 + 3015397 -76

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	36	+	3015397	-76

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone + 3015386 -87

TSS clone C clone + 3015398 -75

TSS clone G clone + 3015399 -74

TSS clone A clone + 3015413 -60

TSS clone G clone + 3015443 -30

TSS clone T clone + 3015447 -26

TSS clone A clone + 3015453 -20

TSS clone G clone + 3015456 -17

TSS clone A clone + 3015457 -16

TSS clone C clone + 3015458 -15

TSS clone A clone + 3015461 -12

TSS clone A clone + 3015465 -8

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	3015386	-87
TSS clone	`C`	clone	+	3015398	-75
TSS clone	`G`	clone	+	3015399	-74
TSS clone	`A`	clone	+	3015413	-60
TSS clone	`G`	clone	+	3015443	-30
TSS clone	`T`	clone	+	3015447	-26
TSS clone	`A`	clone	+	3015453	-20
TSS clone	`G`	clone	+	3015456	-17
TSS clone	`A`	clone	+	3015457	-16
TSS clone	`C`	clone	+	3015458	-15
TSS clone	`A`	clone	+	3015461	-12
TSS clone	`A`	clone	+	3015465	-8

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 None None None

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	None	None	None
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 TGGCCCAATAA + 3015144 3015154 -329 -319

AtREG420 TGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352 GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355   GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417    CCCAATAA PPDB Motif GCCCA PLACE Motif

REG GTTAGGCCCAATTA + 3015166 3015179 -307 -294

AtREG535 GTTAGGCC       PPDB Motif PLACE Motif

AtREG360 TTAGGCCC      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

AtREG418      GCCCAATT PPDB Motif GCCCA PLACE Motif

AtREG600       CCCAATTA PPDB Motif GCCCA PLACE Motif

REG TAATTACG + 3015194 3015201 -279 -272

AtREG646 TAATTACG ABA PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TGGCCCAATAA`		+	3015144	3015154	-329	-319
	AtREG420	`TGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GTTAGGCCCAATTA`		+	3015166	3015179	-307	-294
	AtREG535	`GTTAGGCC`		PPDB Motif		PLACE Motif
	AtREG360	`TTAGGCCC`		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`
	AtREG418	`GCCCAATT`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG600	`CCCAATTA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TAATTACG`		+	3015194	3015201	-279	-272
	AtREG646	`TAATTACG`	ABA	PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 5 - 3015038 AT1G09330.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	5	-	3015038	AT1G09330.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone C clone - 3015058 AT1G09330.1

TSS clone C clone - 3015056 AT1G09330.1

TSS clone G clone - 3015019 AT1G09330.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`C`	clone	-	3015058	AT1G09330.1
TSS clone	`C`	clone	-	3015056	AT1G09330.1
TSS clone	`G`	clone	-	3015019	AT1G09330.1

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 TTATTGGGCCA - 3015144 3015154 AT1G09330.1

AtREG417 TTATTGGG    PPDB Motif GCCCA PLACE Motif

AtREG355 TATTGGGC   PPDB Motif GCCCA PLACE Motif

AtREG352   ATTGGGCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG420    TTGGGCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG TAATTGGGCCTAAC - 3015166 3015179 AT1G09330.1

AtREG600 TAATTGGG       PPDB Motif GCCCA PLACE Motif

AtREG418 AATTGGGC      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

AtREG360      GGGCCTAA PPDB Motif GCCCA PLACE Motif GGGCC

AtREG535       GGCCTAAC PPDB Motif PLACE Motif

REG CGTAATTA - 3015194 3015201 AT1G09330.1

AtREG646 CGTAATTA ABA PPDB Motif PLACE Motif