PlantPromoterDB promoter information of AT4G38130.2

Summary of Gene (AT4G38130.2)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G38130 TAIR NCBI
Gene model	AT4G38130.2
Description	Encodes a histone deacetylase that enhances AtERF7-mediated transcriptional repression. Binds SIM3 and ERF7. Expressed in the nucleus in most tissues examined and throughout the life of the plant. Involved in jasmonic acid and ethylene dependent pathogen resistance. The sequence in GenBank has 17 AG dinucleotide repeats missing, which is also missing in Ler shotgun sequence from Cereon. Although it is annotated to be in Columbia, the GB sequence is probably not of Columbia origin. Plays a role in embryogenesis as mutants grown at higher temperatures display abnormalities in the organization of the root and shoot. Plant lines expressing an RNAi construct targeted against HDA19 shows some resistance to agrobacterium-mediated root transformation.

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Overview

Focused view (chromosome 4: 17900057-17898858)

`Genome position from initiation codon` `AT4G38130.1 AT4G38140.1 TSS from cDNA TSS information AT4G38130.2 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 AT4G38130.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 26 - 17899480 -423

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	26	-	17899480	-423

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 17899491 -434

TSS clone A clone - 17899489 -432

TSS clone A clone - 17899480 -423

TSS clone C clone - 17899479 -422

TSS clone G clone - 17899477 -420

TSS clone G clone - 17899467 -410

TSS clone A clone - 17899459 -402

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	17899491	-434
TSS clone	`A`	clone	-	17899489	-432
TSS clone	`A`	clone	-	17899480	-423
TSS clone	`C`	clone	-	17899479	-422
TSS clone	`G`	clone	-	17899477	-420
TSS clone	`G`	clone	-	17899467	-410
TSS clone	`A`	clone	-	17899459	-402

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 GTGGGCCTTT - 17899531 17899540 -474 -483

AtREG482 GTGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353 TGGGCCTT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG359   GGGCCTTT PPDB Motif GCCCA PLACE Motif GGGCC

REG GTGGGCCTCA - 17899564 17899573 -507 -516

AtREG482 GTGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG447 TGGGCCTC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG587   GGGCCTCA PPDB Motif GCCCA PLACE Motif GGGCC

REG AATAGGCCTTAT - 17899592 17899603 -535 -546

AtREG424 AATAGGCC     PPDB Motif PLACE Motif

AtREG649 ATAGGCCT    PPDB Motif PLACE Motif

AtREG425     GGCCTTAT PPDB Motif AACCG(G/A) PLACE Motif

REG CCATTAAG - 17899625 17899632 -568 -575

AtREG604 CCATTAAG PPDB Motif PLACE Motif TTAATGG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GTGGGCCTTT`		-	17899531	17899540	-474	-483
	AtREG482	`GTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG353	`TGGGCCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG359	`GGGCCTTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`GTGGGCCTCA`		-	17899564	17899573	-507	-516
	AtREG482	`GTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG447	`TGGGCCTC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG587	`GGGCCTCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`AATAGGCCTTAT`		-	17899592	17899603	-535	-546
	AtREG424	`AATAGGCC`		PPDB Motif		PLACE Motif
	AtREG649	`ATAGGCCT`		PPDB Motif		PLACE Motif
	AtREG425	`GGCCTTAT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`CCATTAAG`		-	17899625	17899632	-568	-575
	AtREG604	`CCATTAAG`		PPDB Motif		PLACE Motif	`TTAATGG`

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