PlantPromoterDB promoter information of AT1G50000.1

Summary of Gene (AT1G50000.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G50000 TAIR NCBI
Gene model	AT1G50000.1
Description	methyltransferase; FUNCTIONS IN: methyltransferase activity; INVOLVED IN: rRNA processing; LOCATED IN: chloroplast; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: PUA-like (InterPro:IPR015947), Ribosomal RNA small subunit methyltransferase E (InterPro:IPR006700); Has 3924 Blast hits to 3924 proteins in 1156 species: Archae - 0; Bacteria - 2219; Metazoa - 2; Fungi - 0; Plants - 16; Viruses - 0; Other Eukaryotes - 1687 (source: NCBI BLink).

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Overview

Focused view (chromosome 1: 18518244-18517045)

`Genome position from initiation codon` `AT1G50000.2 TSS from cDNA TSS information AT1G50000.1 5'->3' (-) Promoter sequence AT1G50010.1 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 AT1G50000.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 4 - 18517294 -50

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	4	-	18517294	-50

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

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 TTGAACCGGAT - 18517337 18517347 -93 -103

AtREG640 TTGAACCG    PPDB Motif AACCG(G/A) PLACE Motif

AtREG480 TGAACCGG   PPDB Motif AACCG(G/A) PLACE Motif

AtREG579   GAACCGGA PPDB Motif AACCG(G/A) PLACE Motif

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

REG TGAACCGGAA - 18517359 18517368 -115 -124

AtREG480 TGAACCGG   PPDB Motif AACCG(G/A) PLACE Motif

AtREG579 GAACCGGA PPDB Motif AACCG(G/A) PLACE Motif

AtREG534   AACCGGAA PPDB Motif AACCG(G/A) PLACE Motif

REG TAATTGGG - 18517518 18517525 -274 -281

AtREG600 TAATTGGG PPDB Motif GCCCA PLACE Motif

REG TACACGTGTA - 18517532 18517541 -288 -297

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

REG ACGGCACG - 18517547 18517554 -303 -310

AtREG522 ACGGCACG PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTGAACCGGAT`		-	18517337	18517347	-93	-103
	AtREG640	`TTGAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG480	`TGAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG579	`GAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG561	`AACCGGAT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TGAACCGGAA`		-	18517359	18517368	-115	-124
	AtREG480	`TGAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG579	`GAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`AACCGGAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TAATTGGG`		-	18517518	18517525	-274	-281
	AtREG600	`TAATTGGG`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TACACGTGTA`		-	18517532	18517541	-288	-297
	AtREG453	`TACACGTGTA`	ABA, DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACACNNG`
REG	`ACGGCACG`		-	18517547	18517554	-303	-310
	AtREG522	`ACGGCACG`		PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak T 13 + 18517613 AT1G50010.1

TSS peak A 2 + 18517729 AT1G50010.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`T`	13	+	18517613	AT1G50010.1
TSS peak	`A`	2	+	18517729	AT1G50010.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone C clone + 18517611 AT1G50010.1

TSS clone T clone + 18517613 AT1G50010.1

TSS clone A clone + 18517614 AT1G50010.1

TSS clone G clone + 18517615 AT1G50010.1

TSS clone T clone + 18517619 AT1G50010.1

TSS clone A clone + 18517622 AT1G50010.1

TSS clone T clone + 18517641 AT1G50010.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`C`	clone	+	18517611	AT1G50010.1
TSS clone	`T`	clone	+	18517613	AT1G50010.1
TSS clone	`A`	clone	+	18517614	AT1G50010.1
TSS clone	`G`	clone	+	18517615	AT1G50010.1
TSS clone	`T`	clone	+	18517619	AT1G50010.1
TSS clone	`A`	clone	+	18517622	AT1G50010.1
TSS clone	`T`	clone	+	18517641	AT1G50010.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box CGCTTATAAATATA + 18517575 18517588 AT1G50010.1

Y Patch CGTCTTCTTCC + 18517680 18517690 AT1G50010.1

Y Patch CTTTCTTC + 18517717 18517724 AT1G50010.1

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	`CGCTTATAAATATA`	+	18517575	18517588	AT1G50010.1
Y Patch	`CGTCTTCTTCC`	+	18517680	18517690	AT1G50010.1
Y Patch	`CTTTCTTC`	+	18517717	18517724	AT1G50010.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG ATCCGGTTCAA + 18517337 18517347 AT1G50010.1

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

AtREG579 TCCGGTTC   PPDB Motif AACCG(G/A) PLACE Motif

AtREG480   CCGGTTCA PPDB Motif AACCG(G/A) PLACE Motif

AtREG640    CGGTTCAA PPDB Motif AACCG(G/A) PLACE Motif

REG TTCCGGTTCA + 18517359 18517368 AT1G50010.1

AtREG534 TTCCGGTT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG579 TCCGGTTC PPDB Motif AACCG(G/A) PLACE Motif

AtREG480   CCGGTTCA PPDB Motif AACCG(G/A) PLACE Motif

REG CCCAATTA + 18517518 18517525 AT1G50010.1

AtREG600 CCCAATTA PPDB Motif GCCCA PLACE Motif

REG TACACGTGTA + 18517532 18517541 AT1G50010.1

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

REG CGTGCCGT + 18517547 18517554 AT1G50010.1

AtREG522 CGTGCCGT PPDB Motif PLACE Motif