PlantPromoterDB promoter information of AT3G61860.1

Summary of Gene (AT3G61860.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G61860 TAIR NCBI
Gene model	AT3G61860.1
Description	encodes an arginine/serine-rich splicing factor. transcript is alternatively spliced and is differentially expressed in different tissues (flowers, roots, stems, and leaves) examined.

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Overview

Focused view (chromosome 3: 22903159-22901960)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G61860.1 5'->3' (-) Promoter sequence AT3G61870.1 AT3G61870.2 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 AT3G61860.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 13 - 22902334 -175

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	13	-	22902334	-175

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 22902336 -177

TSS clone G clone - 22902334 -175

TSS clone G clone - 22902332 -173

TSS clone T clone - 22902311 -152

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	22902336	-177
TSS clone	`G`	clone	-	22902334	-175
TSS clone	`G`	clone	-	22902332	-173
TSS clone	`T`	clone	-	22902311	-152

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 TTTCTTCTC - 22902285 22902293 -126 -134

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	`TTTCTTCTC`	-	22902285	22902293	-126	-134
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 AAGGCCCATTAT - 22902412 22902423 -253 -264

AtREG353 AAGGCCCA     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

AtREG546     CCCATTAT PPDB Motif PLACE Motif

REG TGTGGGCCTATT - 22902431 22902442 -272 -283

AtREG612 TGTGGGCC     DREB1Aox PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG482 GTGGGCCT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358   TGGGCCTA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG362    GGGCCTAT PPDB Motif GCCCA PLACE Motif GGGCC

AtREG424     GGCCTATT PPDB Motif PLACE Motif

REG TCCACGTGTCA - 22902577 22902587 -418 -428

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

AtREG382 CCACGTGT   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

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

AtREG389    ACGTGTCA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AAGGCCCATTAT`		-	22902412	22902423	-253	-264
	AtREG353	`AAGGCCCA`		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
	AtREG546	`CCCATTAT`		PPDB Motif		PLACE Motif
REG	`TGTGGGCCTATT`		-	22902431	22902442	-272	-283
	AtREG612	`TGTGGGCC`	DREB1Aox	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG482	`GTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG362	`GGGCCTAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG424	`GGCCTATT`		PPDB Motif		PLACE Motif
REG	`TCCACGTGTCA`		-	22902577	22902587	-418	-428
	AtREG408	`TCCACGTG`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`
	AtREG382	`CCACGTGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACACNNG`
	AtREG366	`CACGTGTC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACGTGKC, ACACNNG, ACGTGTC`
	AtREG389	`ACGTGTCA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 17 + 22902638 AT3G61870.2, AT3G61870.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	17	+	22902638	AT3G61870.2, AT3G61870.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone + 22902639 AT3G61870.2, AT3G61870.1

TSS clone T clone + 22902660 AT3G61870.2, AT3G61870.1

TSS clone T clone + 22902667 AT3G61870.2, AT3G61870.1

TSS clone A clone + 22902689 AT3G61870.2, AT3G61870.1

TSS clone T clone + 22902694 AT3G61870.2, AT3G61870.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	+	22902639	AT3G61870.2, AT3G61870.1
TSS clone	`T`	clone	+	22902660	AT3G61870.2, AT3G61870.1
TSS clone	`T`	clone	+	22902667	AT3G61870.2, AT3G61870.1
TSS clone	`A`	clone	+	22902689	AT3G61870.2, AT3G61870.1
TSS clone	`T`	clone	+	22902694	AT3G61870.2, AT3G61870.1

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 TTTCTTCTTC + 22902653 22902662 AT3G61870.1, AT3G61870.2

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	`TTTCTTCTTC`	+	22902653	22902662	AT3G61870.1, AT3G61870.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG AAAAAGCCC + 22902365 22902373 AT3G61870.1, AT3G61870.2

AtREG589 AAAAAGCC PPDB Motif PLACE Motif

AtREG409 AAAAGCCC PPDB Motif GCCCA PLACE Motif

REG ATAATGGGCCTT + 22902412 22902423 AT3G61870.1, AT3G61870.2

AtREG546 ATAATGGG     PPDB Motif PLACE Motif

AtREG357 TAATGGGC    PPDB Motif GCCCA PLACE Motif

AtREG361   AATGGGCC   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    ATGGGCCT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353     TGGGCCTT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG AATAGGCCCACA + 22902431 22902442 AT3G61870.1, AT3G61870.2

AtREG424 AATAGGCC     PPDB Motif PLACE Motif

AtREG362 ATAGGCCC    PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358   TAGGCCCA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG482    AGGCCCAC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG612     GGCCCACA DREB1Aox PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG TGACACGTGGA + 22902577 22902587 AT3G61870.1, AT3G61870.2

AtREG389 TGACACGT    ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

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

AtREG382   ACACGTGG ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

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