PlantPromoterDB promoter information of AT5G02100.1

Summary of Gene (AT5G02100.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G02100 TAIR NCBI
Gene model	AT5G02100.1
Description	Encodes a protein that binds to beta-sitosterol and localizes to the ER. The WFDE motif in ORP3a appears to be important for a direct interaction with PVA12 [Plant VAMP-Associated protein 12]. Mutation of this motif causes ORP3a to relocalize to the Golgi and cytosol. The interaction between PVA12 and ORP3a does not appear to be sterol-dependent.

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Overview

Focused view (chromosome 5: 412639-413838)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G02100.1 5'->3' (+) Promoter sequence AT5G02090.1 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 AT5G02100.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone peak A clone + 413523 -116

TSS clone peak A clone + 413528 -111

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`A`	clone	+	413523	-116
TSS clone peak	`A`	clone	+	413528	-111

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 ATATAAGA + 413490 413497 -149 -142

Y Patch CGTCTTCTTC + 413557 413566 -82 -73

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	`ATATAAGA`	+	413490	413497	-149	-142
Y Patch	`CGTCTTCTTC`	+	413557	413566	-82	-73
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 CCGTTAAA + 413318 413325 -321 -314

AtREG610 CCGTTAAA PPDB Motif PLACE Motif YAACKG, CNGTTR

REG TTTTGGGCCGTT + 413342 413353 -297 -286

AtREG529 TTTTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG373 TTTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414   TTGGGCCG   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG368    TGGGCCGT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

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

REG ATAAAGCCCAACA + 413356 413368 -283 -271

AtREG601 ATAAAGCC      PPDB Motif PLACE Motif

AtREG365 TAAAGCCC     PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407    AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG574     AGCCCAAC PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG543      GCCCAACA PPDB Motif GCCCA PLACE Motif CAACA

REG ATATTGGGCCTCACGTGGT + 413385 413403 -254 -236

AtREG509 ATATTGGG            PPDB Motif PLACE Motif

AtREG355 TATTGGGC           PPDB Motif GCCCA PLACE Motif

AtREG352   ATTGGGCC          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356    TTGGGCCT         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG447     TGGGCCTC        PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG587      GGGCCTCA       PPDB Motif GCCCA PLACE Motif GGGCC

AtREG544            CACGTGGT ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG ATCCGGTTTGGTTCGGTT + 413450 413467 -189 -172

AtREG561 ATCCGGTT           PPDB Motif AACCG(G/A) PLACE Motif

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

AtREG496   CCGGTTTG         PPDB Motif AACCG(G/A) PLACE Motif

AtREG550    CGGTTTGG        PPDB Motif AACCG(G/A) PLACE Motif

AtREG655         TGGTTCGG   PPDB Motif PLACE Motif

AtREG451          GGTTCGGT PPDB Motif PLACE Motif

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

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CCGTTAAA`		+	413318	413325	-321	-314
	AtREG610	`CCGTTAAA`		PPDB Motif		PLACE Motif	`YAACKG, CNGTTR`
REG	`TTTTGGGCCGTT`		+	413342	413353	-297	-286
	AtREG529	`TTTTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG373	`TTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`TTGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG368	`TGGGCCGT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG377	`GGGCCGTT`		PPDB Motif	`GCCCA, AAACG(C/G)`	PLACE Motif	`GGGCC`
REG	`ATAAAGCCCAACA`		+	413356	413368	-283	-271
	AtREG601	`ATAAAGCC`		PPDB Motif		PLACE Motif
	AtREG365	`TAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG574	`AGCCCAAC`		PPDB Motif	`GCCCA, CCAACGG`	PLACE Motif	`TGGGCY`
	AtREG543	`GCCCAACA`		PPDB Motif	`GCCCA`	PLACE Motif	`CAACA`
REG	`ATATTGGGCCTCACGTGGT`		+	413385	413403	-254	-236
	AtREG509	`ATATTGGG`		PPDB Motif		PLACE Motif
	AtREG355	`TATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`TTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG447	`TGGGCCTC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG587	`GGGCCTCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG544	`CACGTGGT`	ABA, DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
REG	`ATCCGGTTTGGTTCGGTT`		+	413450	413467	-189	-172
	AtREG561	`ATCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG521	`TCCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG496	`CCGGTTTG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG550	`CGGTTTGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG655	`TGGTTCGG`		PPDB Motif		PLACE Motif
	AtREG451	`GGTTCGGT`		PPDB Motif		PLACE Motif
	AtREG556	`GTTCGGTT`		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 G 13 - 412695 AT5G02090.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	13	-	412695	AT5G02090.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone - 412698 AT5G02090.1

TSS clone T clone - 412697 AT5G02090.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	-	412698	AT5G02090.1
TSS clone	`T`	clone	-	412697	AT5G02090.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box CTCTTATA - 412724 412731 AT5G02090.1

Y Patch CCCTCTCTC - 412701 412709 AT5G02090.1

Y Patch CCCTCTTCCCTCT - 412728 412740 AT5G02090.1

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	`CTCTTATA`	-	412724	412731	AT5G02090.1
Y Patch	`CCCTCTCTC`	-	412701	412709	AT5G02090.1
Y Patch	`CCCTCTTCCCTCT`	-	412728	412740	AT5G02090.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG ACGCCACGTCAC - 412749 412760 AT5G02090.1

AtREG508 ACGCCACG     PPDB Motif PLACE Motif GCCAC

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

AtREG388   GCCACGTC   PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG419    CCACGTCA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, TGACGTGG, CCACGTCA

AtREG466     CACGTCAC ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG TACGTGGCAA - 412771 412780 AT5G02090.1

AtREG413 TACGTGGC   PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

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

AtREG452   CGTGGCAA PPDB Motif PLACE Motif GCCAC