PlantPromoterDB promoter information of AT3G06770.3

Summary of Gene (AT3G06770.3)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G06770 TAIR NCBI
Gene model	AT3G06770.3
Description	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein; FUNCTIONS IN: polygalacturonase activity; INVOLVED IN: response to cyclopentenone, carbohydrate metabolic process; LOCATED IN: endomembrane system; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Pectin lyase fold/virulence factor (InterPro:IPR011050), Glycoside hydrolase, family 28 (InterPro:IPR000743), Pectin lyase fold (InterPro:IPR012334), Parallel beta-helix repeat (InterPro:IPR006626); BEST Arabidopsis thaliana protein match is: glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein (TAIR:AT5G49215.1); Has 1737 Blast hits to 1735 proteins in 255 species: Archae - 2; Bacteria - 483; Metazoa - 5; Fungi - 453; Plants - 700; Viruses - 2; Other Eukaryotes - 92 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 2132916-2131717)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G06770.3 5'->3' (-) Promoter sequence AT3G06760.1 AT3G06760.2 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 AT3G06770.3

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 8 - 2137334 -718

TSS peak G 5 - 2137122 -506

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	8	-	2137334	-718
TSS peak	`G`	5	-	2137122	-506

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 2137129 -513

TSS clone T clone - 2136977 -361

TSS clone G clone - 2136962 -346

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	2137129	-513
TSS clone	`T`	clone	-	2136977	-361
TSS clone	`G`	clone	-	2136962	-346

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 TCTTTCTCTTCTTCTTCTCTCTCTCTCTCTCTCT - 2137123 2137156 -507 -540

Y Patch TCCTTCTCCTTCT - 2137160 2137172 -544 -556

Y Patch CTTTCTTCT - 2137303 2137311 -687 -695

Y Patch TCTTCTTCCTTC - 2137321 2137332 -705 -716

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	`TCTTTCTCTTCTTCTTCTCTCTCTCTCTCTCTCT`	-	2137123	2137156	-507	-540
Y Patch	`TCCTTCTCCTTCT`	-	2137160	2137172	-544	-556
Y Patch	`CTTTCTTCT`	-	2137303	2137311	-687	-695
Y Patch	`TCTTCTTCCTTC`	-	2137321	2137332	-705	-716
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 CCCATTAA - 2137523 2137530 -907 -914

AtREG396 CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CCCATTAA`		-	2137523	2137530	-907	-914
	AtREG396	`CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 4 + 2132780 AT3G06760.1, AT3G06760.2

TSS peak A 4 + 2132808 AT3G06760.1, AT3G06760.2

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	4	+	2132780	AT3G06760.1, AT3G06760.2
TSS peak	`A`	4	+	2132808	AT3G06760.1, AT3G06760.2

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone C clone + 2132837 AT3G06760.1, AT3G06760.2

TSS clone C clone + 2132840 AT3G06760.1, AT3G06760.2

TSS clone T clone + 2132857 AT3G06760.1, AT3G06760.2

TSS clone T clone + 2132895 AT3G06760.1, AT3G06760.2

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`C`	clone	+	2132837	AT3G06760.1, AT3G06760.2
TSS clone	`C`	clone	+	2132840	AT3G06760.1, AT3G06760.2
TSS clone	`T`	clone	+	2132857	AT3G06760.1, AT3G06760.2
TSS clone	`T`	clone	+	2132895	AT3G06760.1, AT3G06760.2

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 TTTCTTCTTCC + 2132827 2132837 AT3G06760.1, AT3G06760.2

Y Patch TTTCTCTCTCTCTC + 2132843 2132856 AT3G06760.1, AT3G06760.2

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	`TTTCTTCTTCC`	+	2132827	2132837	AT3G06760.1, AT3G06760.2
Y Patch	`TTTCTCTCTCTCTC`	+	2132843	2132856	AT3G06760.1, AT3G06760.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TACACGTGTGA + 2132629 2132639 AT3G06760.1, AT3G06760.2

AtREG453 TACACGTG    ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACACNNG

AtREG460   CACGTGTG ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

AtREG588    ACGTGTGA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG CCAAACCGCGTGAAACGAC + 2132683 2132701 AT3G06760.1, AT3G06760.2

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

AtREG441    AACCGCGT         Drought PPDB Motif PLACE Motif

AtREG502      CCGCGTGA       Drought PPDB Motif PLACE Motif

AtREG631       CGCGTGAA      Drought PPDB Motif PLACE Motif

AtREG576            GAAACGAC PPDB Motif PLACE Motif