PlantPromoterDB promoter information of AT3G09490.1

Summary of Gene (AT3G09490.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G09490 TAIR NCBI
Gene model	AT3G09490.1
Description	chloroplast lumen common family protein; FUNCTIONS IN: binding; INVOLVED IN: photosynthesis, light reaction; LOCATED IN: chloroplast thylakoid lumen; EXPRESSED IN: 15 plant structures; EXPRESSED DURING: 9 growth stages; CONTAINS InterPro DOMAIN/s: Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide region (InterPro:IPR013026); BEST Arabidopsis thaliana protein match is: chloroplast lumen common family protein (TAIR:AT2G37400.1); Has 637 Blast hits to 548 proteins in 146 species: Archae - 92; Bacteria - 301; Metazoa - 8; Fungi - 0; Plants - 41; Viruses - 0; Other Eukaryotes - 195 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 2914636-2915835)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G09490.1 5'->3' (+) Promoter sequence AT3G09480.1 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 AT3G09490.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 5 + 2915598 -38

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	5	+	2915598	-38

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone + 2915559 -77

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	2915559	-77

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 CTCTTCTT + 2915560 2915567 -76 -69

Y Patch TTCTTCTCTTTC + 2915580 2915591 -56 -45

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	`CTCTTCTT`	+	2915560	2915567	-76	-69
Y Patch	`TTCTTCTCTTTC`	+	2915580	2915591	-56	-45
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 CTACGTGGCGT + 2915404 2915414 -232 -222

AtREG495 CTACGTGG    PPDB Motif ACGT PLACE Motif ACGT, ACGTG

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

AtREG371   ACGTGGCG ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG508    CGTGGCGT PPDB Motif PLACE Motif GCCAC

REG CACGTGCG + 2915418 2915425 -218 -211

AtREG541 CACGTGCG PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

REG AACCGAAC + 2915463 2915470 -173 -166

AtREG556 AACCGAAC PPDB Motif AACCG(G/A) PLACE Motif

REG TGGGCTCA + 2915477 2915484 -159 -152

AtREG485 TGGGCTCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG CTAATGGGCCTTGGCCTTTT + 2915486 2915505 -150 -131

AtREG558 CTAATGGG             PPDB Motif GCCCA PLACE Motif

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

AtREG353     TGGGCCTT         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG398      GGGCCTTG        PPDB Motif GCCCA PLACE Motif GGGCC

AtREG459             GGCCTTTT PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CTACGTGGCGT`		+	2915404	2915414	-232	-222
	AtREG495	`CTACGTGG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG413	`TACGTGGC`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG371	`ACGTGGCG`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG508	`CGTGGCGT`		PPDB Motif		PLACE Motif	`GCCAC`
REG	`CACGTGCG`		+	2915418	2915425	-218	-211
	AtREG541	`CACGTGCG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`
REG	`AACCGAAC`		+	2915463	2915470	-173	-166
	AtREG556	`AACCGAAC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TGGGCTCA`		+	2915477	2915484	-159	-152
	AtREG485	`TGGGCTCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`CTAATGGGCCTTGGCCTTTT`		+	2915486	2915505	-150	-131
	AtREG558	`CTAATGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	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`
	AtREG353	`TGGGCCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG398	`GGGCCTTG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG459	`GGCCTTTT`		PPDB Motif		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 peak T clone - 2915320 AT3G09470.1, AT3G09470.2, AT3G09480.1

TSS clone peak C clone - 2915312 AT3G09470.1, AT3G09470.2, AT3G09480.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`T`	clone	-	2915320	AT3G09470.1, AT3G09470.2, AT3G09480.1
TSS clone peak	`C`	clone	-	2915312	AT3G09470.1, AT3G09470.2, AT3G09480.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box CCTCTATATATATCT - 2915344 2915358 AT3G09470.1, AT3G09470.2, AT3G09480.1

Y Patch None None None

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	`CCTCTATATATATCT`	-	2915344	2915358	AT3G09470.1, AT3G09470.2, AT3G09480.1
Y Patch	None	None	None
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG ATTGGCCCAGCCCAACA - 2914634 2914650 AT3G09470.1, AT3G09470.2

AtREG446 ATTGGCCC          CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG484 TTGGCCCA         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG458   TGGCCCAG        PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG454     GCCCAGCC      PPDB Motif GCCCA PLACE Motif

AtREG574         AGCCCAAC PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG543          GCCCAACA PPDB Motif GCCCA PLACE Motif CAACA

REG ACGCCACGTAG - 2915404 2915414 AT3G09470.1, AT3G09470.2, AT3G09480.1

AtREG508 ACGCCACG    PPDB Motif PLACE Motif GCCAC

AtREG371 CGCCACGT   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

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

AtREG495    CCACGTAG PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG CGCACGTG - 2915418 2915425 AT3G09470.1, AT3G09470.2, AT3G09480.1

AtREG541 CGCACGTG PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

REG GTTCGGTT - 2915463 2915470 AT3G09470.1, AT3G09470.2, AT3G09480.1

AtREG556 GTTCGGTT PPDB Motif AACCG(G/A) PLACE Motif

REG TGAGCCCA - 2915477 2915484 AT3G09470.1, AT3G09470.2, AT3G09480.1

AtREG485 TGAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG AAAAGGCCAAGGCCCATTAG - 2915486 2915505 AT3G09470.1, AT3G09470.2, AT3G09480.1

AtREG459 AAAAGGCC             PPDB Motif PLACE Motif

AtREG398        CAAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353         AAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354          AGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361           GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357            GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG558             CCCATTAG PPDB Motif GCCCA PLACE Motif

REG CCCAATAA - 2915611 2915618 AT3G09470.1, AT3G09470.2, AT3G09480.1

AtREG417 CCCAATAA PPDB Motif GCCCA PLACE Motif