PlantPromoterDB promoter information of AT1G27400.1

Summary of Gene (AT1G27400.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G27400 TAIR NCBI
Gene model	AT1G27400.1
Description	60S ribosomal protein L17 (RPL17A); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic large ribosomal subunit, ribosome, plasma membrane, chloroplast, vacuole; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L22/L17 (InterPro:IPR001063), Ribosomal protein L22/L17, eukaryotic/archaeal (InterPro:IPR005721), Ribosomal protein L22/L17, conserved site (InterPro:IPR018260); BEST Arabidopsis thaliana protein match is: 60S ribosomal protein L17 (RPL17B) (TAIR:AT1G67430.1); Has 1647 Blast hits to 1647 proteins in 483 species: Archae - 235; Bacteria - 361; Metazoa - 438; Fungi - 108; Plants - 104; Viruses - 0; Other Eukaryotes - 401 (source: NCBI BLink).

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Overview

Focused view (chromosome 1: 9514230-9515429)

`Genome position from initiation codon` `TSS from cDNA TSS information AT1G27400.1 5'->3' (+) Promoter sequence AT1G27390.1 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 AT1G27400.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 2 + 9515211 -19

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	2	+	9515211	-19

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 9515139 -91

TSS clone G clone + 9515143 -87

TSS clone A clone + 9515195 -35

TSS clone T clone + 9515196 -34

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	9515139	-91
TSS clone	`G`	clone	+	9515143	-87
TSS clone	`A`	clone	+	9515195	-35
TSS clone	`T`	clone	+	9515196	-34

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 TCCTCTCC + 9515196 9515203 -34 -27

Y Patch TTCTTCTC + 9515212 9515219 -18 -11

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	`TCCTCTCC`	+	9515196	9515203	-34	-27
Y Patch	`TTCTTCTC`	+	9515212	9515219	-18	-11
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 TCTAGGGTTCGGT + 9514936 9514948 -294 -282

AtREG658 TCTAGGGT      PPDB Motif ACCCT PLACE Motif

AtREG451      GGTTCGGT PPDB Motif PLACE Motif

REG TAATTGGGCTTTTT + 9515039 9515052 -191 -178

AtREG600 TAATTGGG       PPDB Motif GCCCA PLACE Motif

AtREG418 AATTGGGC      PPDB Motif GCCCA PLACE Motif

AtREG402   ATTGGGCT     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407    TTGGGCTT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG376     TGGGCTTT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG409      GGGCTTTT PPDB Motif GCCCA PLACE Motif

AtREG589       GGCTTTTT PPDB Motif PLACE Motif

REG GTGGCCCAGAAGGCCCATAT + 9515073 9515092 -157 -138

AtREG445 GTGGCCCA             PPDB Motif GCCCA PLACE Motif GCCAC, GGGCC, TGGGCY

AtREG458 TGGCCCAG            PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG397   GGCCCAGA           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353          AAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354           AGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364            GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG432             GCCCATAT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TCTAGGGTTCGGT`		+	9514936	9514948	-294	-282
	AtREG658	`TCTAGGGT`		PPDB Motif	`ACCCT`	PLACE Motif
	AtREG451	`GGTTCGGT`		PPDB Motif		PLACE Motif
REG	`TAATTGGGCTTTTT`		+	9515039	9515052	-191	-178
	AtREG600	`TAATTGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG418	`AATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG402	`ATTGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`TTGGGCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG376	`TGGGCTTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG409	`GGGCTTTT`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG589	`GGCTTTTT`		PPDB Motif		PLACE Motif
REG	`GTGGCCCAGAAGGCCCATAT`		+	9515073	9515092	-157	-138
	AtREG445	`GTGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GCCAC, GGGCC, TGGGCY`
	AtREG458	`TGGCCCAG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG397	`GGCCCAGA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG432	`GCCCATAT`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 4 - 9514926 AT1G27390.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	4	-	9514926	AT1G27390.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone - 9515001 AT1G27390.1

TSS clone C clone - 9514980 AT1G27390.1

TSS clone A clone - 9514978 AT1G27390.1

TSS clone C clone - 9514925 AT1G27390.1

TSS clone T clone - 9514923 AT1G27390.1

TSS clone G clone - 9514922 AT1G27390.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	-	9515001	AT1G27390.1
TSS clone	`C`	clone	-	9514980	AT1G27390.1
TSS clone	`A`	clone	-	9514978	AT1G27390.1
TSS clone	`C`	clone	-	9514925	AT1G27390.1
TSS clone	`T`	clone	-	9514923	AT1G27390.1
TSS clone	`G`	clone	-	9514922	AT1G27390.1

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 AAAAAGCCCAATTA - 9515039 9515052 AT1G27390.1

AtREG589 AAAAAGCC       PPDB Motif PLACE Motif

AtREG409 AAAAGCCC      PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407    AAGCCCAA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG402     AGCCCAAT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG418      GCCCAATT PPDB Motif GCCCA PLACE Motif

AtREG600       CCCAATTA PPDB Motif GCCCA PLACE Motif

REG ATATGGGCCTTCTGGGCCAC - 9515073 9515092 AT1G27390.1

AtREG432 ATATGGGC             PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC            PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   ATGGGCCT           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353    TGGGCCTT          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG397           TCTGGGCC   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG458            CTGGGCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG445             TGGGCCAC PPDB Motif GCCCA PLACE Motif GCCAC, GGGCC, TGGGCY