PlantPromoterDB promoter information of AT4G09040.2

Summary of Gene (AT4G09040.2)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G09040 TAIR NCBI
Gene model	AT4G09040.2
Description	RNA recognition motif (RRM)-containing protein; FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast stroma, chloroplast; EXPRESSED IN: leaf; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: 33 kDa ribonucleoprotein, chloroplast, putative / RNA-binding protein cp33, putative (TAIR:AT2G35410.1); Has 13296 Blast hits to 10466 proteins in 519 species: Archae - 12; Bacteria - 987; Metazoa - 6994; Fungi - 1866; Plants - 1955; Viruses - 0; Other Eukaryotes - 1482 (source: NCBI BLink).

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Overview

Focused view (chromosome 4: 5798193-5796994)

`Genome position from initiation codon` `AT4G09040.1 AT4G09060.1 TSS from cDNA TSS information AT4G09040.2 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 AT4G09040.2

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 T clone - 5797339 -146

TSS clone peak A clone - 5797334 -141

TSS clone T clone - 5797333 -140

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	5797339	-146
TSS clone peak	`A`	clone	-	5797334	-141
TSS clone	`T`	clone	-	5797333	-140

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 CTCTTCTTCGTCTTCC - 5797296 5797311 -103 -118

Y Patch TTTCTTCTTCTT - 5797335 5797346 -142 -153

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	`CTCTTCTTCGTCTTCC`	-	5797296	5797311	-103	-118
Y Patch	`TTTCTTCTTCTT`	-	5797335	5797346	-142	-153
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 AACGACGTCGTT - 5797391 5797402 -198 -209

AtREG493 AACGACGTCGTT PPDB Motif ACGT PLACE Motif ACGT

AtREG431 ACGACGTCGT PPDB Motif ACGT PLACE Motif ACGT

REG ACGTCGTTTT - 5797412 5797421 -219 -228

AtREG493 ACGTCGTT   PPDB Motif ACGT PLACE Motif ACGT

AtREG415 CGTCGTTT PPDB Motif PLACE Motif

AtREG520   GTCGTTTT PPDB Motif PLACE Motif

REG TAAACGACGTC - 5797457 5797467 -264 -274

AtREG565 TAAACGAC    PPDB Motif PLACE Motif

AtREG415 AAACGACG   PPDB Motif PLACE Motif

AtREG493   AACGACGT PPDB Motif ACGT PLACE Motif ACGT

AtREG431    ACGACGTC PPDB Motif ACGT PLACE Motif ACGT

REG TGTCGTTTT - 5797481 5797489 -288 -296

AtREG569 TGTCGTTT PPDB Motif PLACE Motif

AtREG520 GTCGTTTT PPDB Motif PLACE Motif

REG AACGACGTCGTT - 5797524 5797535 -331 -342

AtREG493 AACGACGTCGTT 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	`AACGACGTCGTT`		-	5797391	5797402	-198	-209
	AtREG493	`AACGACGTCGTT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
	AtREG431	`ACGACGTCGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
REG	`ACGTCGTTTT`		-	5797412	5797421	-219	-228
	AtREG493	`ACGTCGTT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
	AtREG415	`CGTCGTTT`		PPDB Motif		PLACE Motif
	AtREG520	`GTCGTTTT`		PPDB Motif		PLACE Motif
REG	`TAAACGACGTC`		-	5797457	5797467	-264	-274
	AtREG565	`TAAACGAC`		PPDB Motif		PLACE Motif
	AtREG415	`AAACGACG`		PPDB Motif		PLACE Motif
	AtREG493	`AACGACGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
	AtREG431	`ACGACGTC`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
REG	`TGTCGTTTT`		-	5797481	5797489	-288	-296
	AtREG569	`TGTCGTTT`		PPDB Motif		PLACE Motif
	AtREG520	`GTCGTTTT`		PPDB Motif		PLACE Motif
REG	`AACGACGTCGTT`		-	5797524	5797535	-331	-342
	AtREG493	`AACGACGTCGTT`		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