PlantPromoterDB promoter information of AT4G23890.1

Summary of Gene (AT4G23890.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G23890 TAIR NCBI
Gene model	AT4G23890.1
Description	unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: chloroplast thylakoid membrane, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; Has 252 Blast hits to 252 proteins in 67 species: Archae - 0; Bacteria - 101; Metazoa - 15; Fungi - 4; Plants - 21; Viruses - 0; Other Eukaryotes - 111 (source: NCBI BLink).

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Overview

Focused view (chromosome 4: 12422345-12421146)

`Genome position from initiation codon` `TSS from cDNA TSS information AT4G23890.1 5'->3' (-) Promoter sequence AT4G23895.1 AT4G23895.2 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 AT4G23890.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 5 - 12421361 -16

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	5	-	12421361	-16

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 12421451 -106

TSS clone T clone - 12421450 -105

TSS clone A clone - 12421442 -97

TSS clone A clone - 12421439 -94

TSS clone G clone - 12421361 -16

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	12421451	-106
TSS clone	`T`	clone	-	12421450	-105
TSS clone	`A`	clone	-	12421442	-97
TSS clone	`A`	clone	-	12421439	-94
TSS clone	`G`	clone	-	12421361	-16

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 TCTTCTTC - 12421393 12421400 -48 -55

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	`TCTTCTTC`	-	12421393	12421400	-48	-55
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 TTAACCGGTTCA - 12421506 12421517 -161 -172

AtREG501 TTAACCGG     PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG503 TAACCGGT    PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG528    ACCGGTTC PPDB Motif AACCG(G/A) PLACE Motif

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

REG ACCGGTTA - 12421522 12421529 -177 -184

AtREG503 ACCGGTTA PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG CAAAGCCCAAAT - 12421565 12421576 -220 -231

AtREG559 CAAAGCCC     PPDB Motif GCCCA PLACE Motif

AtREG376 AAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407   AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG469    AGCCCAAA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG421     GCCCAAAT PPDB Motif GCCCA PLACE Motif

REG CTAGGCCCATAT - 12421618 12421629 -273 -284

AtREG475 CTAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358 TAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   AGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364    GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG432     GCCCATAT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTAACCGGTTCA`		-	12421506	12421517	-161	-172
	AtREG501	`TTAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG503	`TAACCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG528	`ACCGGTTC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG480	`CCGGTTCA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`ACCGGTTA`		-	12421522	12421529	-177	-184
	AtREG503	`ACCGGTTA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
REG	`CAAAGCCCAAAT`		-	12421565	12421576	-220	-231
	AtREG559	`CAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG469	`AGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG421	`GCCCAAAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CTAGGCCCATAT`		-	12421618	12421629	-273	-284
	AtREG475	`CTAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG432	`GCCCATAT`		PPDB Motif	`GCCCA`	PLACE Motif

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

TSS clone G clone + 12422105 AT4G23895.1, AT4G23895.2

TSS clone peak A clone + 12422106 AT4G23895.1, AT4G23895.2

TSS clone G clone + 12422111 AT4G23895.1, AT4G23895.2

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	+	12422105	AT4G23895.1, AT4G23895.2
TSS clone peak	`A`	clone	+	12422106	AT4G23895.1, AT4G23895.2
TSS clone	`G`	clone	+	12422111	AT4G23895.1, AT4G23895.2

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 TCTTCTTCCT + 12422092 12422101 AT4G23895.1, AT4G23895.2

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	`TCTTCTTCCT`	+	12422092	12422101	AT4G23895.1, AT4G23895.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG None None None