PlantPromoterDB promoter information of AT3G25520.1

Summary of Gene (AT3G25520.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G25520 TAIR NCBI
Gene model	AT3G25520.1
Description	Encodes ribosomal protein L5 that binds to 5S ribosomal RNA and in involved in its export from the nucleus to the cytoplasm. Identified in a screen for enhancers of as1. as1/pgy double mutants show defects in leaf vascular patterning and adaxial cell fate. Double mutant analysis indicates pgy genes function in the same pathway as REV, KAN1 and KAN2.

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Overview

Focused view (chromosome 3: 9272327-9271128)

`Genome position from initiation codon` `AT3G25530.1 AT3G25530.2 TSS from cDNA TSS information AT3G25520.1 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 AT3G25520.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 222 - 9271374 -47

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	222	-	9271374	-47

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone C clone - 9271390 -63

TSS clone T clone - 9271386 -59

TSS clone G clone - 9271384 -57

TSS clone C clone - 9271383 -56

TSS clone T clone - 9271382 -55

TSS clone T clone - 9271379 -52

TSS clone A clone - 9271374 -47

TSS clone C clone - 9271373 -46

TSS clone C clone - 9271369 -42

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`C`	clone	-	9271390	-63
TSS clone	`T`	clone	-	9271386	-59
TSS clone	`G`	clone	-	9271384	-57
TSS clone	`C`	clone	-	9271383	-56
TSS clone	`T`	clone	-	9271382	-55
TSS clone	`T`	clone	-	9271379	-52
TSS clone	`A`	clone	-	9271374	-47
TSS clone	`C`	clone	-	9271373	-46
TSS clone	`C`	clone	-	9271369	-42

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 CTTCTCTTC - 9271375 9271383 -48 -56

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	`CTTCTCTTC`	-	9271375	9271383	-48	-56
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 TCTAGGGT - 9271426 9271433 -99 -106

AtREG658 TCTAGGGT PPDB Motif ACCCT PLACE Motif

REG TCAGCCCA - 9271444 9271451 -117 -124

AtREG609 TCAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG TAAAGCCCATTAA - 9271458 9271470 -131 -143

AtREG365 TAAAGCCC      PPDB Motif GCCCA PLACE Motif

AtREG376 AAAGCCCA     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378   AAGCCCAT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG372    AGCCCATT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG357     GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396      CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

REG TAAAAGCCCATAGGCCCATTAA - 9271483 9271504 -156 -177

AtREG549 TAAAAGCC               PPDB Motif PLACE Motif

AtREG409 AAAAGCCC              PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA             PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378    AAGCCCAT            PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG477     AGCCCATA           PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG362          ATAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358           TAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354            AGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361             GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357              GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396               CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TCTAGGGT`		-	9271426	9271433	-99	-106
	AtREG658	`TCTAGGGT`		PPDB Motif	`ACCCT`	PLACE Motif
REG	`TCAGCCCA`		-	9271444	9271451	-117	-124
	AtREG609	`TCAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`TAAAGCCCATTAA`		-	9271458	9271470	-131	-143
	AtREG365	`TAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`AAGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG372	`AGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG396	`CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`
REG	`TAAAAGCCCATAGGCCCATTAA`		-	9271483	9271504	-156	-177
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
	AtREG409	`AAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`AAGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG477	`AGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG362	`ATAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG361	`GGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG396	`CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`

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