PlantPromoterDB promoter information of AT3G52960.1

Summary of Gene (AT3G52960.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G52960 TAIR NCBI
Gene model	AT3G52960.1
Description	peroxiredoxin type 2, putative; FUNCTIONS IN: oxidoreductase activity, antioxidant activity; INVOLVED IN: defense response to bacterium, peptidyl-cysteine S-nitrosylation; LOCATED IN: thylakoid, chloroplast stroma, chloroplast, plant-type cell wall; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Thioredoxin fold (InterPro:IPR012335), Thioredoxin-like (InterPro:IPR017936), Thioredoxin-like fold (InterPro:IPR012336), Redoxin (InterPro:IPR013740); BEST Arabidopsis thaliana protein match is: TPX1 (thioredoxin-dependent peroxidase 1); antioxidant/ oxidoreductase (TAIR:AT1G65980.1); Has 3329 Blast hits to 3329 proteins in 622 species: Archae - 43; Bacteria - 1005; Metazoa - 160; Fungi - 217; Plants - 175; Viruses - 0; Other Eukaryotes - 1729 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 19638699-19639898)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G52960.1 5'->3' (+) Promoter sequence AT3G52957.1 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 AT3G52960.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 34 + 19639677 -22

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	34	+	19639677	-22

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 19639668 -31

TSS clone A clone + 19639673 -26

TSS clone C clone + 19639674 -25

TSS clone A clone + 19639677 -22

TSS clone A clone + 19639684 -15

TSS clone C clone + 19639685 -14

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	19639668	-31
TSS clone	`A`	clone	+	19639673	-26
TSS clone	`C`	clone	+	19639674	-25
TSS clone	`A`	clone	+	19639677	-22
TSS clone	`A`	clone	+	19639684	-15
TSS clone	`C`	clone	+	19639685	-14

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 TCTTTCTCT + 19639638 19639646 -61 -53

Y Patch CTTCTCTCTCC + 19639706 19639716 7 17

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	`TCTTTCTCT`	+	19639638	19639646	-61	-53
Y Patch	`CTTCTCTCTCC`	+	19639706	19639716	7	17
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 GTAGGCCCATTAAGGCCCAATAACGGCGT + 19639400 19639428 -299 -271

AtREG435 GTAGGCCC                      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

AtREG604       CCATTAAG                PPDB Motif PLACE Motif TTAATGG

AtREG416          TTAAGGCC             PPDB Motif PLACE Motif

AtREG351           TAAGGCCC            PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353            AAGGCCCA           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356             AGGCCCAA          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352              GGCCCAAT         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355               GCCCAATA        PPDB Motif GCCCA PLACE Motif

AtREG417                CCCAATAA       PPDB Motif GCCCA PLACE Motif

AtREG497                      AACGGCGT PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

REG TTTAGGCCCACTA + 19639575 19639587 -124 -112

AtREG430 TTTAGGCC      PPDB Motif PLACE Motif

AtREG360 TTAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358   TAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG482    AGGCCCAC   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG532      GCCCACTA PPDB Motif GCCCA PLACE Motif

REG GTAGGCCCAATAA + 19639610 19639622 -89 -77

AtREG435 GTAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358 TAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356   AGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352    GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355     GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417      CCCAATAA PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GTAGGCCCATTAAGGCCCAATAACGGCGT`		+	19639400	19639428	-299	-271
	AtREG435	`GTAGGCCC`		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`
	AtREG604	`CCATTAAG`		PPDB Motif		PLACE Motif	`TTAATGG`
	AtREG416	`TTAAGGCC`		PPDB Motif		PLACE Motif
	AtREG351	`TAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG497	`AACGGCGT`		PPDB Motif	`AAACG(C/G), CCAACGG`	PLACE Motif
REG	`TTTAGGCCCACTA`		+	19639575	19639587	-124	-112
	AtREG430	`TTTAGGCC`		PPDB Motif		PLACE Motif
	AtREG360	`TTAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG482	`AGGCCCAC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG532	`GCCCACTA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GTAGGCCCAATAA`		+	19639610	19639622	-89	-77
	AtREG435	`GTAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	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