PlantPromoterDB promoter information of AT4G25672.1

Summary of Gene (AT4G25672.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G25672 TAIR NCBI
Gene model	AT4G25672.1
Description	Upstream open reading frames (uORFs) are small open reading frames found in the 5' UTR of a mature mRNA, and can potentially mediate translational regulation of the largest, or major, ORF (mORF). CPuORF12 represents a conserved upstream opening reading frame relative to major ORF AT4G25670.1

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Overview

Focused view (chromosome 4: 13087227-13086028)

`Genome position from initiation codon` `AT4G25670.1 TSS from cDNA TSS information AT4G25672.1 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 AT4G25672.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak C 4 - 13087052 -825

TSS peak G 4 - 13087045 -818

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`C`	4	-	13087052	-825
TSS peak	`G`	4	-	13087045	-818

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 13087053 -826

TSS clone C clone - 13087052 -825

TSS clone T clone - 13087051 -824

TSS clone T clone - 13087044 -817

TSS clone G clone - 13087041 -814

TSS clone C clone - 13087040 -813

TSS clone T clone - 13087034 -807

TSS clone G clone - 13087021 -794

TSS clone A clone - 13087020 -793

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	13087053	-826
TSS clone	`C`	clone	-	13087052	-825
TSS clone	`T`	clone	-	13087051	-824
TSS clone	`T`	clone	-	13087044	-817
TSS clone	`G`	clone	-	13087041	-814
TSS clone	`C`	clone	-	13087040	-813
TSS clone	`T`	clone	-	13087034	-807
TSS clone	`G`	clone	-	13087021	-794
TSS clone	`A`	clone	-	13087020	-793

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 TTCCTCTCTCTTTCTCTCT - 13086999 13087017 -772 -790

Y Patch CTCTTCTT - 13087033 13087040 -806 -813

Y Patch TCCTCTCTCTCTCGTCTTCTTC - 13087046 13087067 -819 -840

Y Patch TTCCTTCT - 13087072 13087079 -845 -852

Y Patch TCTTTCTCT - 13087093 13087101 -866 -874

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	`TTCCTCTCTCTTTCTCTCT`	-	13086999	13087017	-772	-790
Y Patch	`CTCTTCTT`	-	13087033	13087040	-806	-813
Y Patch	`TCCTCTCTCTCTCGTCTTCTTC`	-	13087046	13087067	-819	-840
Y Patch	`TTCCTTCT`	-	13087072	13087079	-845	-852
Y Patch	`TCTTTCTCT`	-	13087093	13087101	-866	-874
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 CGACACGTGTCC - 13087129 13087140 -902 -913

AtREG478 CGACACGT     ABA, DREB1Aox, Drought PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

AtREG366 GACACGTGTC ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC

AtREG472     ACGTGTCC ABA, DREB1Aox, Drought PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

REG CCCAATTG - 13087176 13087183 -949 -956

AtREG647 CCCAATTG PPDB Motif PLACE Motif

REG GGACCCAC - 13087230 13087237 -1003 -1010

AtREG523 GGACCCAC PPDB Motif GGGACCC PLACE Motif

REG AATAGCCC - 13087244 13087251 -1017 -1024

AtREG584 AATAGCCC PPDB Motif GCCCA PLACE Motif

REG GAACCGGAAA - 13087289 13087298 -1062 -1071

AtREG579 GAACCGGA   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 GAACCGGAA - 13087319 13087327 -1092 -1100

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

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

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CGACACGTGTCC`		-	13087129	13087140	-902	-913
	AtREG478	`CGACACGT`	ABA, DREB1Aox, Drought	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
	AtREG366	`GACACGTGTC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC`
	AtREG472	`ACGTGTCC`	ABA, DREB1Aox, Drought	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
REG	`CCCAATTG`		-	13087176	13087183	-949	-956
	AtREG647	`CCCAATTG`		PPDB Motif		PLACE Motif
REG	`GGACCCAC`		-	13087230	13087237	-1003	-1010
	AtREG523	`GGACCCAC`		PPDB Motif	`GGGACCC`	PLACE Motif
REG	`AATAGCCC`		-	13087244	13087251	-1017	-1024
	AtREG584	`AATAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GAACCGGAAA`		-	13087289	13087298	-1062	-1071
	AtREG579	`GAACCGGA`		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	`GAACCGGAA`		-	13087319	13087327	-1092	-1100
	AtREG579	`GAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`AACCGGAA`		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 T 17 - 13086073 AT4G25670.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`T`	17	-	13086073	AT4G25670.1

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 TAAGGGGT - 13086209 13086216 AT4G25670.1

AtREG636 TAAGGGGT PPDB Motif ACCCCT PLACE Motif

REG AAATGGGC - 13086222 13086229 AT4G25670.1

AtREG386 AAATGGGC PPDB Motif GCCCA PLACE Motif