PlantPromoterDB promoter information of AT1G52230

Summary of Gene (AT1G52230)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G52230 TAIR NCBI
Gene model	AT1G52230
Description	PHOTOSYSTEM I SUBUNIT H2 (PSAH2); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: photosynthesis; LOCATED IN: in 6 components; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Photosystem I reaction centre subunit VI (InterPro:IPR004928); BEST Arabidopsis thaliana protein match is: PSAH-1 (photosystem I subunit H-1) (TAIR:AT3G16140.1); Has 72 Blast hits to 72 proteins in 22 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 70; Viruses - 0; Other Eukaryotes - 2 (source: NCBI BLink).

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Overview

Focused view (chromosome 1: 19453902-19455101)

`Genome position from initiation codon` `AT1G52230.1 TSS from cDNA TSS information AT1G52230 5'->3' (+) Promoter sequence AT1G52220.1 AT1G52220.2 AT1G52220.3 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 AT1G52230

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 47 + 19454866 -36

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	47	+	19454866	-36

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 19454843 -59

TSS clone C clone + 19454844 -58

TSS clone A clone + 19454848 -54

TSS clone C clone + 19454854 -48

TSS clone A clone + 19454869 -33

TSS clone A clone + 19454870 -32

TSS clone A clone + 19454874 -28

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	19454843	-59
TSS clone	`C`	clone	+	19454844	-58
TSS clone	`A`	clone	+	19454848	-54
TSS clone	`C`	clone	+	19454854	-48
TSS clone	`A`	clone	+	19454869	-33
TSS clone	`A`	clone	+	19454870	-32
TSS clone	`A`	clone	+	19454874	-28

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 CCACTATA + 19454829 19454836 -73 -66

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	`CCACTATA`	+	19454829	19454836	-73	-66
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 ATCCACGTGGCAT + 19454728 19454740 -174 -162

AtREG547 ATCCACGT      ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG408 TCCACGTG     ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

AtREG367    CACGTGGC   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

AtREG379     ACGTGGCA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG448      CGTGGCAT ABA, DREB1Aox PPDB Motif PLACE Motif GCCAC

REG TCGCCACGTGGCAG + 19454782 19454795 -120 -107

AtREG471 TCGCCACG       ABA PPDB Motif PLACE Motif GCCAC

AtREG371 CGCCACGT      ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG367   GCCACGTGGC   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

AtREG379      ACGTGGCA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG468       CGTGGCAG ABA PPDB Motif PLACE Motif GCCAC

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ATCCACGTGGCAT`		+	19454728	19454740	-174	-162
	AtREG547	`ATCCACGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG408	`TCCACGTG`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`
	AtREG367	`CACGTGGC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC`
	AtREG379	`ACGTGGCA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG448	`CGTGGCAT`	ABA, DREB1Aox	PPDB Motif		PLACE Motif	`GCCAC`
REG	`TCGCCACGTGGCAG`		+	19454782	19454795	-120	-107
	AtREG471	`TCGCCACG`	ABA	PPDB Motif		PLACE Motif	`GCCAC`
	AtREG371	`CGCCACGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG367	`GCCACGTGGC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC`
	AtREG379	`ACGTGGCA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG468	`CGTGGCAG`	ABA	PPDB Motif		PLACE Motif	`GCCAC`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 8 - 19454675 AT1G52220.1, AT1G52220.2, AT1G52220.3

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	8	-	19454675	AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone - 19454674 AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS clone T clone - 19454665 AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS clone A clone - 19454662 AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS clone A clone - 19454658 AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS clone A clone - 19454657 AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS clone T clone - 19454631 AT1G52220.1, AT1G52220.2, AT1G52220.3

TSS clone T clone - 19454628 AT1G52220.1, AT1G52220.2, AT1G52220.3

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	-	19454674	AT1G52220.1, AT1G52220.2, AT1G52220.3
TSS clone	`T`	clone	-	19454665	AT1G52220.1, AT1G52220.2, AT1G52220.3
TSS clone	`A`	clone	-	19454662	AT1G52220.1, AT1G52220.2, AT1G52220.3
TSS clone	`A`	clone	-	19454658	AT1G52220.1, AT1G52220.2, AT1G52220.3
TSS clone	`A`	clone	-	19454657	AT1G52220.1, AT1G52220.2, AT1G52220.3
TSS clone	`T`	clone	-	19454631	AT1G52220.1, AT1G52220.2, AT1G52220.3
TSS clone	`T`	clone	-	19454628	AT1G52220.1, AT1G52220.2, AT1G52220.3

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 ATGCCACGTGGAT - 19454728 19454740 AT1G52220.1, AT1G52220.2, AT1G52220.3

AtREG448 ATGCCACG      ABA, DREB1Aox PPDB Motif PLACE Motif GCCAC

AtREG379 TGCCACGT     ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG367   GCCACGTG    ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

AtREG408     CACGTGGA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

AtREG547      ACGTGGAT ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG CTGCCACGTGGCGA - 19454782 19454795 AT1G52220.1, AT1G52220.2, AT1G52220.3

AtREG468 CTGCCACG       ABA PPDB Motif PLACE Motif GCCAC

AtREG379 TGCCACGT      ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG367   GCCACGTGGC   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

AtREG371      ACGTGGCG ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG471       CGTGGCGA ABA PPDB Motif PLACE Motif GCCAC