PlantPromoterDB promoter information of AT3G01270.1

Summary of Gene (AT3G01270.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G01270 TAIR NCBI
Gene model	AT3G01270.1
Description	pectate lyase family protein; FUNCTIONS IN: lyase activity, pectate lyase activity; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Pectin lyase fold/virulence factor (InterPro:IPR011050), Pectate lyase, N-terminal (InterPro:IPR007524), AmbAllergen (InterPro:IPR018082), Pectate lyase/Amb allergen (InterPro:IPR002022), Pectin lyase fold (InterPro:IPR012334); BEST Arabidopsis thaliana protein match is: lyase/ pectate lyase (TAIR:AT5G15110.1); Has 882 Blast hits to 879 proteins in 160 species: Archae - 0; Bacteria - 383; Metazoa - 0; Fungi - 94; Plants - 399; Viruses - 0; Other Eukaryotes - 6 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 85720-84521)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G01270.1 5'->3' (-) Promoter sequence AT3G01280.1 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 AT3G01270.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 8 - 84894 -174

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	8	-	84894	-174

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 84894 -174

TSS clone A clone - 84892 -172

TSS clone A clone - 84891 -171

TSS clone C clone - 84877 -157

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	84894	-174
TSS clone	`A`	clone	-	84892	-172
TSS clone	`A`	clone	-	84891	-171
TSS clone	`C`	clone	-	84877	-157

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 None None None

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	None	None	None

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 8 + 85649 AT3G01280.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	8	+	85649	AT3G01280.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone + 85613 AT3G01280.1

TSS clone T clone + 85616 AT3G01280.1

TSS clone A clone + 85637 AT3G01280.1

TSS clone G clone + 85638 AT3G01280.1

TSS clone T clone + 85664 AT3G01280.1

TSS clone G clone + 85692 AT3G01280.1

TSS clone T clone + 85694 AT3G01280.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	+	85613	AT3G01280.1
TSS clone	`T`	clone	+	85616	AT3G01280.1
TSS clone	`A`	clone	+	85637	AT3G01280.1
TSS clone	`G`	clone	+	85638	AT3G01280.1
TSS clone	`T`	clone	+	85664	AT3G01280.1
TSS clone	`G`	clone	+	85692	AT3G01280.1
TSS clone	`T`	clone	+	85694	AT3G01280.1

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 TCTTTCTCT + 85600 85608 AT3G01280.1

Y Patch TCTCTCTCTCTT + 85651 85662 AT3G01280.1

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	None	None	None
Y Patch	`TCTTTCTCT`	+	85600	85608	AT3G01280.1
Y Patch	`TCTCTCTCTCTT`	+	85651	85662	AT3G01280.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TAAACGACGCCGTTTA + 85445 85460 AT3G01280.1

AtREG565 TAAACGAC         PPDB Motif PLACE Motif

AtREG415 AAACGACG        PPDB Motif PLACE Motif

AtREG439   AACGACGC       PPDB Motif PLACE Motif

AtREG537    ACGACGCC      PPDB Motif PLACE Motif

AtREG540      GACGCCGT    PPDB Motif PLACE Motif

AtREG497       ACGCCGTT   PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

AtREG524        CGCCGTTT PPDB Motif AAACG(C/G) PLACE Motif

AtREG613         GCCGTTTA PPDB Motif AAACG(C/G) PLACE Motif

REG TTGCCACGTA + 85462 85471 AT3G01280.1

AtREG452 TTGCCACG   PPDB Motif PLACE Motif GCCAC

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

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

REG ATCCAACGG + 85556 85564 AT3G01280.1

AtREG586 ATCCAACG PPDB Motif CCAACGG PLACE Motif

AtREG554 TCCAACGG PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR