PlantPromoterDB promoter information of AT5G26742.1

Summary of Gene (AT5G26742.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G26742 TAIR NCBI
Gene model	AT5G26742.1
Description	embryo defective 1138 (emb1138); FUNCTIONS IN: in 6 functions; INVOLVED IN: embryonic development ending in seed dormancy; LOCATED IN: chloroplast, membrane; EXPRESSED IN: guard cell, leaf; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), RNA helicase, DEAD-box type, Q motif (InterPro:IPR014014), GUCT (InterPro:IPR012562), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Zinc finger, CCHC-type (InterPro:IPR001878), Helicase, superfamily 1 and 2, ATP-binding (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: PMH2 (putative mitochondrial RNA helicase 2); ATP binding / ATP-dependent helicase/ helicase/ nucleic acid binding (TAIR:AT3G22330.1); Has 41664 Blast hits to 39827 proteins in 1977 species: Archae - 837; Bacteria - 17695; Metazoa - 6892; Fungi - 3987; Plants - 1854; Viruses - 126; Other Eukaryotes - 10273 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 9289871-9288672)

`Genome position from initiation codon` `AT5G26742.2 TSS from cDNA TSS information AT5G26742.1 5'->3' (-) Promoter sequence 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 AT5G26742.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 17 - 9288978 -107

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	17	-	9288978	-107

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 9288984 -113

TSS clone T clone - 9288980 -109

TSS clone G clone - 9288978 -107

TSS clone T clone - 9288977 -106

TSS clone G clone - 9288976 -105

TSS clone A clone - 9288974 -103

TSS clone T clone - 9288960 -89

TSS clone A clone - 9288939 -68

TSS clone A clone - 9288938 -67

TSS clone T clone - 9288936 -65

TSS clone A clone - 9288932 -61

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	9288984	-113
TSS clone	`T`	clone	-	9288980	-109
TSS clone	`G`	clone	-	9288978	-107
TSS clone	`T`	clone	-	9288977	-106
TSS clone	`G`	clone	-	9288976	-105
TSS clone	`A`	clone	-	9288974	-103
TSS clone	`T`	clone	-	9288960	-89
TSS clone	`A`	clone	-	9288939	-68
TSS clone	`A`	clone	-	9288938	-67
TSS clone	`T`	clone	-	9288936	-65
TSS clone	`A`	clone	-	9288932	-61

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 AGCCCAATAACGGCCCACTA - 9289051 9289070 -180 -199

AtREG402 AGCCCAAT             PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG355 GCCCAATA            PPDB Motif GCCCA PLACE Motif

AtREG417   CCCAATAA           PPDB Motif GCCCA PLACE Motif

AtREG377         AACGGCCC     PPDB Motif GCCCA, AAACG(C/G) PLACE Motif GGGCC

AtREG368          ACGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG532             GCCCACTA PPDB Motif GCCCA PLACE Motif

REG TAAAAGCC - 9289094 9289101 -223 -230

AtREG549 TAAAAGCC PPDB Motif PLACE Motif

REG GAAGCCCA - 9289114 9289121 -243 -250

AtREG476 GAAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AGCCCAATAACGGCCCACTA`		-	9289051	9289070	-180	-199
	AtREG402	`AGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG377	`AACGGCCC`		PPDB Motif	`GCCCA, AAACG(C/G)`	PLACE Motif	`GGGCC`
	AtREG368	`ACGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG532	`GCCCACTA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TAAAAGCC`		-	9289094	9289101	-223	-230
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
REG	`GAAGCCCA`		-	9289114	9289121	-243	-250
	AtREG476	`GAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`

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