PlantPromoterDB promoter information of AT1G08840.1

Summary of Gene (AT1G08840.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G08840 TAIR NCBI
Gene model	AT1G08840.1
Description	embryo defective 2411 (emb2411); FUNCTIONS IN: ATP-dependent DNA helicase activity, DNA binding, ATP binding; INVOLVED IN: embryonic development ending in seed dormancy, DNA replication; LOCATED IN: chloroplast; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA replication factor Dna2 (InterPro:IPR014808); BEST Arabidopsis thaliana protein match is: DNA-binding protein, putative (TAIR:AT2G03270.1); Has 4081 Blast hits to 3639 proteins in 571 species: Archae - 158; Bacteria - 979; Metazoa - 1088; Fungi - 747; Plants - 269; Viruses - 30; Other Eukaryotes - 810 (source: NCBI BLink).

#

Overview

Focused view (chromosome 1: 2839369-2838170)

`Genome position from initiation codon` `TSS from cDNA TSS information AT1G08840.1 5'->3' (-) Promoter sequence AT1G08845.1 AT1G08845.2 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 AT1G08840.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 2 - 2838862 -493

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	2	-	2838862	-493

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

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 TTTCCGGTTTAA - 2838905 2838916 -536 -547

AtREG644 TTTCCGGT     PPDB Motif AACCG(G/A) PLACE Motif

AtREG534 TTCCGGTT    PPDB Motif AACCG(G/A) PLACE Motif

AtREG521   TCCGGTTT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG412    CCGGTTTA PPDB Motif AACCG(G/A) PLACE Motif

AtREG473     CGGTTTAA PPDB Motif AACCG(G/A) PLACE Motif

REG TTGAACCGGAC - 2838919 2838929 -550 -560

AtREG640 TTGAACCG    PPDB Motif AACCG(G/A) PLACE Motif

AtREG480 TGAACCGG   PPDB Motif AACCG(G/A) PLACE Motif

AtREG579   GAACCGGA PPDB Motif AACCG(G/A) PLACE Motif

AtREG573    AACCGGAC PPDB Motif AACCG(G/A) PLACE Motif

REG GACCGACTTA - 2838935 2838944 -566 -575

AtREG638 GACCGACT   DREB1Aox, ABA PPDB Motif CCGAC PLACE Motif CCGAC, RCCGAC

AtREG582   CCGACTTA PPDB Motif CCGAC PLACE Motif CCGAC

REG ACCGGGTT - 2838967 2838974 -598 -605

AtREG516 ACCGGGTT PPDB Motif PLACE Motif

REG ACCGGTTTT - 2838989 2838997 -620 -628

AtREG436 ACCGGTTT PPDB Motif AACCG(G/A) PLACE Motif

AtREG542 CCGGTTTT PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTTCCGGTTTAA`		-	2838905	2838916	-536	-547
	AtREG644	`TTTCCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`TTCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG521	`TCCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG412	`CCGGTTTA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG473	`CGGTTTAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TTGAACCGGAC`		-	2838919	2838929	-550	-560
	AtREG640	`TTGAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG480	`TGAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG579	`GAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG573	`AACCGGAC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`GACCGACTTA`		-	2838935	2838944	-566	-575
	AtREG638	`GACCGACT`	DREB1Aox, ABA	PPDB Motif	`CCGAC`	PLACE Motif	`CCGAC, RCCGAC`
	AtREG582	`CCGACTTA`		PPDB Motif	`CCGAC`	PLACE Motif	`CCGAC`
REG	`ACCGGGTT`		-	2838967	2838974	-598	-605
	AtREG516	`ACCGGGTT`		PPDB Motif		PLACE Motif
REG	`ACCGGTTTT`		-	2838989	2838997	-620	-628
	AtREG436	`ACCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG542	`CCGGTTTT`		PPDB Motif	`AACCG(G/A)`	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

TSS clone peak G clone + 2839144 AT1G08845.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`G`	clone	+	2839144	AT1G08845.1

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 GGTTCGGTT + 2838849 2838857 AT1G08845.1

AtREG451 GGTTCGGT PPDB Motif PLACE Motif

AtREG556 GTTCGGTT PPDB Motif AACCG(G/A) PLACE Motif

REG TTAAACCGGAAA + 2838905 2838916 AT1G08845.1

AtREG473 TTAAACCG     PPDB Motif AACCG(G/A) PLACE Motif

AtREG412 TAAACCGG    PPDB Motif AACCG(G/A) PLACE Motif

AtREG521   AAACCGGA   PPDB Motif AACCG(G/A) PLACE Motif

AtREG534    AACCGGAA PPDB Motif AACCG(G/A) PLACE Motif

AtREG644     ACCGGAAA PPDB Motif AACCG(G/A) PLACE Motif

REG GTCCGGTTCAA + 2838919 2838929 AT1G08845.1

AtREG573 GTCCGGTT    PPDB Motif AACCG(G/A) PLACE Motif

AtREG579 TCCGGTTC   PPDB Motif AACCG(G/A) PLACE Motif

AtREG480   CCGGTTCA PPDB Motif AACCG(G/A) PLACE Motif

AtREG640    CGGTTCAA PPDB Motif AACCG(G/A) PLACE Motif

REG TAAGTCGGTC + 2838935 2838944 AT1G08845.1

AtREG582 TAAGTCGG   PPDB Motif CCGAC PLACE Motif CCGAC

AtREG638   AGTCGGTC DREB1Aox, ABA PPDB Motif CCGAC PLACE Motif CCGAC, RCCGAC

REG AACCCGGT + 2838967 2838974 AT1G08845.1

AtREG516 AACCCGGT PPDB Motif PLACE Motif

REG AAAACCGGT + 2838989 2838997 AT1G08845.1

AtREG542 AAAACCGG PPDB Motif AACCG(G/A) PLACE Motif

AtREG436 AAACCGGT PPDB Motif AACCG(G/A) PLACE Motif