PlantPromoterDB promoter information of AT5G42000.1

Summary of Gene (AT5G42000.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G42000 TAIR NCBI
Gene model	AT5G42000.1
Description	ORMDL family protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: protein folding; LOCATED IN: integral to membrane, endoplasmic reticulum; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: ORMDL (InterPro:IPR007203); BEST Arabidopsis thaliana protein match is: ORMDL family protein (TAIR:AT1G01230.1); Has 398 Blast hits to 398 proteins in 109 species: Archae - 0; Bacteria - 0; Metazoa - 233; Fungi - 101; Plants - 52; Viruses - 0; Other Eukaryotes - 12 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 16796955-16798154)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G42000.1 5'->3' (+) Promoter sequence AT5G41990.1 AT5G41992.1 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 AT5G42000.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 4 + 16799316 -139

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	4	+	16799316	-139

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 CGGGTCGGGTCGGAAAACCGGT + 16799100 16799121 -355 -334

AtREG375 CGGGTCGGGTCGG          PPDB Motif CCGAC PLACE Motif CCGAC

AtREG442 GGGTCGGG              PPDB Motif CCGAC PLACE Motif CCGAC

AtREG405   GGTCGGGT             PPDB Motif CCGAC PLACE Motif CCGAC

AtREG390    GTCGGGTC            PPDB Motif CCGAC, GGGACCC PLACE Motif CCGAC

AtREG383     TCGGGTCG           PPDB Motif PLACE Motif

AtREG542              AAAACCGG PPDB Motif AACCG(G/A) PLACE Motif

AtREG436               AAACCGGT PPDB Motif AACCG(G/A) PLACE Motif

REG TAATGGGCCTCT + 16799130 16799141 -325 -314

AtREG357 TAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG361 AATGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   ATGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG447    TGGGCCTC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG411     GGGCCTCT PPDB Motif GCCCA PLACE Motif GGGCC

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CGGGTCGGGTCGGAAAACCGGT`		+	16799100	16799121	-355	-334
	AtREG375	`CGGGTCGGGTCGG`		PPDB Motif	`CCGAC`	PLACE Motif	`CCGAC`
	AtREG442	`GGGTCGGG`		PPDB Motif	`CCGAC`	PLACE Motif	`CCGAC`
	AtREG405	`GGTCGGGT`		PPDB Motif	`CCGAC`	PLACE Motif	`CCGAC`
	AtREG390	`GTCGGGTC`		PPDB Motif	`CCGAC, GGGACCC`	PLACE Motif	`CCGAC`
	AtREG383	`TCGGGTCG`		PPDB Motif		PLACE Motif
	AtREG542	`AAAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG436	`AAACCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TAATGGGCCTCT`		+	16799130	16799141	-325	-314
	AtREG357	`TAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG447	`TGGGCCTC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG411	`GGGCCTCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 8 - 16798000 AT5G41992.1, AT5G41990.1

TSS peak A 8 - 16797820 AT5G41990.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	8	-	16798000	AT5G41992.1, AT5G41990.1
TSS peak	`A`	8	-	16797820	AT5G41990.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone - 16798026 AT5G41992.1, AT5G41990.1

TSS clone T clone - 16798004 AT5G41992.1, AT5G41990.1

TSS clone T clone - 16797999 AT5G41992.1, AT5G41990.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	-	16798026	AT5G41992.1, AT5G41990.1
TSS clone	`T`	clone	-	16798004	AT5G41992.1, AT5G41990.1
TSS clone	`T`	clone	-	16797999	AT5G41992.1, AT5G41990.1

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 CTTTCTCC - 16798013 16798020 AT5G41990.1, AT5G41992.1

Y Patch TTCTTCCT - 16798028 16798035 AT5G41990.1, AT5G41992.1

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	`CTTTCTCC`	-	16798013	16798020	AT5G41990.1, AT5G41992.1
Y Patch	`TTCTTCCT`	-	16798028	16798035	AT5G41990.1, AT5G41992.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TTGACTTT - 16798071 16798078 AT5G41990.1, AT5G41992.1

AtREG632 TTGACTTT PPDB Motif PLACE Motif TTGAC