PlantPromoterDB promoter information of AT5G02960.1

Summary of Gene (AT5G02960.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G02960 TAIR NCBI
Gene model	AT5G02960.1
Description	40S ribosomal protein S23 (RPS23B); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic small ribosomal subunit, cytosolic ribosome, ribosome; EXPRESSED IN: guard cell, leaf; CONTAINS InterPro DOMAIN/s: Ribosomal protein S23, eukaryotic/archaeal (InterPro:IPR005680), Ribosomal protein S12/S23 (InterPro:IPR006032), Nucleic acid-binding, OB-fold-like (InterPro:IPR016027), Nucleic acid-binding, OB-fold (InterPro:IPR012340); BEST Arabidopsis thaliana protein match is: 40S ribosomal protein S23 (RPS23A) (TAIR:AT3G09680.1); Has 6124 Blast hits to 6121 proteins in 1817 species: Archae - 180; Bacteria - 2807; Metazoa - 329; Fungi - 198; Plants - 755; Viruses - 0; Other Eukaryotes - 1855 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 695396-694197)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G02960.1 5'->3' (-) Promoter sequence AT5G02970.1 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 AT5G02960.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 161 - 694485 -89

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	161	-	694485	-89

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 694485 -89

TSS clone G clone - 694484 -88

TSS clone G clone - 694483 -87

TSS clone G clone - 694482 -86

TSS clone T clone - 694481 -85

TSS clone G clone - 694473 -77

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	694485	-89
TSS clone	`G`	clone	-	694484	-88
TSS clone	`G`	clone	-	694483	-87
TSS clone	`G`	clone	-	694482	-86
TSS clone	`T`	clone	-	694481	-85
TSS clone	`G`	clone	-	694473	-77

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 TGATGGGCCAA - 694553 694563 -157 -167

AtREG635 TGATGGGC    PPDB Motif GCCCA PLACE Motif

AtREG403 GATGGGCC   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG490   ATGGGCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG484    TGGGCCAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG CTTAATGGGCCTAC - 694568 694581 -172 -185

AtREG604 CTTAATGG       PPDB Motif PLACE Motif TTAATGG

AtREG396 TTAATGGG      PPDB Motif GCCCA PLACE Motif TTAATGG

AtREG357   TAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG361    AATGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354     ATGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358      TGGGCCTA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG435       GGGCCTAC PPDB Motif GCCCA PLACE Motif GGGCC

REG TAAAAGCCCAT - 694584 694594 -188 -198

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

REG TAAAAGCCCAAAA - 694632 694644 -236 -248

AtREG549 TAAAAGCC      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

AtREG469     AGCCCAAA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG529      GCCCAAAA PPDB Motif GCCCA PLACE Motif

REG ATCCAACGGTTTAG - 694656 694669 -260 -273

AtREG586 ATCCAACG       PPDB Motif CCAACGG PLACE Motif

AtREG554 TCCAACGG      PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

AtREG652      ACGGTTTA PPDB Motif PLACE Motif

AtREG511       CGGTTTAG PPDB Motif AACCG(G/A) PLACE Motif

REG GCCGGTTC - 694768 694775 -372 -379

AtREG637 GCCGGTTC PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TGATGGGCCAA`		-	694553	694563	-157	-167
	AtREG635	`TGATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG403	`GATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG490	`ATGGGCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG484	`TGGGCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
REG	`CTTAATGGGCCTAC`		-	694568	694581	-172	-185
	AtREG604	`CTTAATGG`		PPDB Motif		PLACE Motif	`TTAATGG`
	AtREG396	`TTAATGGG`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`
	AtREG357	`TAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG435	`GGGCCTAC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`TAAAAGCCCAT`		-	694584	694594	-188	-198
	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`
REG	`TAAAAGCCCAAAA`		-	694632	694644	-236	-248
	AtREG549	`TAAAAGCC`		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`
	AtREG469	`AGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG529	`GCCCAAAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`ATCCAACGGTTTAG`		-	694656	694669	-260	-273
	AtREG586	`ATCCAACG`		PPDB Motif	`CCAACGG`	PLACE Motif
	AtREG554	`TCCAACGG`		PPDB Motif	`CCAACGG`	PLACE Motif	`YAACKG, CNGTTR`
	AtREG652	`ACGGTTTA`		PPDB Motif		PLACE Motif
	AtREG511	`CGGTTTAG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`GCCGGTTC`		-	694768	694775	-372	-379
	AtREG637	`GCCGGTTC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 2 + 694979 AT5G02970.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	2	+	694979	AT5G02970.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone + 694969 AT5G02970.1

TSS clone G clone + 694982 AT5G02970.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	+	694969	AT5G02970.1
TSS clone	`G`	clone	+	694982	AT5G02970.1

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 GAACCGGC + 694768 694775 AT5G02970.1

AtREG637 GAACCGGC PPDB Motif AACCG(G/A) PLACE Motif

REG CTTAACCG + 694849 694856 AT5G02970.1

AtREG605 CTTAACCG PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG ACGTGGAC + 694876 694883 AT5G02970.1

AtREG513 ACGTGGAC ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG