PlantPromoterDB promoter information of AT5G52470.2

Summary of Gene (AT5G52470.2)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G52470 TAIR NCBI
Gene model	AT5G52470.2
Description	encodes a fibrillarin, a key nucleolar protein in eukaryotes which associates with box C/D small nucleolar RNAs (snoRNAs) directing 2'-O-ribose methylation of the rRNA. This gene also encodes a novel box C/D snoRNA, U60.1f in its fifth intron that accumulates in seedlings and that their targeted residue on the 25 S rRNA is methylated.

#

Overview

Focused view (chromosome 5: 21293290-21294489)

`Genome position from initiation codon` `AT5G52470.1 TSS from cDNA TSS information AT5G52470.2 5'->3' (+) Promoter sequence AT5G52460.1 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 AT5G52470.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 46 + 21294208 -82

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	46	+	21294208	-82

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 21294187 -103

TSS clone A clone + 21294208 -82

TSS clone G clone + 21294209 -81

TSS clone C clone + 21294210 -80

TSS clone C clone + 21294213 -77

TSS clone C clone + 21294236 -54

TSS clone C clone + 21294273 -17

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	21294187	-103
TSS clone	`A`	clone	+	21294208	-82
TSS clone	`G`	clone	+	21294209	-81
TSS clone	`C`	clone	+	21294210	-80
TSS clone	`C`	clone	+	21294213	-77
TSS clone	`C`	clone	+	21294236	-54
TSS clone	`C`	clone	+	21294273	-17

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 AATATATAAACC + 21294174 21294185 -116 -105

Y Patch CATCTCTCTCCT + 21294221 21294232 -69 -58

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	`AATATATAAACC`	+	21294174	21294185	-116	-105
Y Patch	`CATCTCTCTCCT`	+	21294221	21294232	-69	-58
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 TTTGGGCCAAT + 21293982 21293992 -308 -298

AtREG373 TTTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG420 TTGGGCCA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG484   TGGGCCAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG446    GGGCCAAT CK PPDB Motif GCCCA PLACE Motif GGGCC

REG ATCGGCCCATTAT + 21293996 21294008 -294 -282

AtREG555 ATCGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG393 TCGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380   CGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361    GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357     GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG546      CCCATTAT PPDB Motif PLACE Motif

REG GGGCCTATT + 21294111 21294119 -179 -171

AtREG362 GGGCCTAT PPDB Motif GCCCA PLACE Motif GGGCC

AtREG424 GGCCTATT PPDB Motif PLACE Motif

REG TAAAAGCCCTA + 21294156 21294166 -134 -124

AtREG549 TAAAAGCC    PPDB Motif PLACE Motif

AtREG409 AAAAGCCC   PPDB Motif GCCCA PLACE Motif

AtREG651    AAGCCCTA PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTTGGGCCAAT`		+	21293982	21293992	-308	-298
	AtREG373	`TTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG420	`TTGGGCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG484	`TGGGCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG446	`GGGCCAAT`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`ATCGGCCCATTAT`		+	21293996	21294008	-294	-282
	AtREG555	`ATCGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG393	`TCGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`CGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG361	`GGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG546	`CCCATTAT`		PPDB Motif		PLACE Motif
REG	`GGGCCTATT`		+	21294111	21294119	-179	-171
	AtREG362	`GGGCCTAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG424	`GGCCTATT`		PPDB Motif		PLACE Motif
REG	`TAAAAGCCCTA`		+	21294156	21294166	-134	-124
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
	AtREG409	`AAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG651	`AAGCCCTA`		PPDB Motif		PLACE Motif

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