PlantPromoterDB promoter information of AT3G12280.1

Summary of Gene (AT3G12280.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G12280 TAIR NCBI
Gene model	AT3G12280.1
Description	Encodes a retinoblastoma homologue RETINOBLASTOMA-RELATED protein (RBR or RBR1). RBR controls nuclear proliferation in the female gametophyte. Also required for correct differentiation of male gametophytic cell types. Regulates stem cell maintenance in Arabidopsis roots. Involved in the determination of cell cycle arrest in G1 phase after sucrose starvation. RBR1 is also involved in regulation of imprinted genes. Together with MSI1 it represses the expression of MET1. This in turn activates expression of the imprinted genes FIS2 and FWA.

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Overview

Focused view (chromosome 3: 3919433-3918234)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G12280.1 5'->3' (-) Promoter sequence 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 AT3G12280.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 3919133 -700

TSS clone peak T clone - 3919096 -663

TSS clone G clone - 3919080 -647

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	3919133	-700
TSS clone peak	`T`	clone	-	3919096	-663
TSS clone	`G`	clone	-	3919080	-647

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 CGCGCGAG - 3919137 3919144 -704 -711

AtREG512 CGCGCGAG PPDB Motif ACGCGC PLACE Motif

REG TACGTGTCG - 3919217 3919225 -784 -792

AtREG557 TACGTGTC ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

AtREG478 ACGTGTCG ABA, DREB1Aox, Drought PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

REG CAGCGTTT - 3919274 3919281 -841 -848

AtREG626 CAGCGTTT PPDB Motif AAACG(C/G) PLACE Motif

REG ATGGCCCA - 3919326 3919333 -893 -900

AtREG437 ATGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG TGGGCCCAAT - 3919384 3919393 -951 -960

AtREG422 TGGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392 GGGCCCAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352 GGCCCAAT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG AAACGGCA - 3919406 3919413 -973 -980

AtREG500 AAACGGCA PPDB Motif AAACG(C/G) PLACE Motif

REG CCGCGTGA - 3919424 3919431 -991 -998

AtREG502 CCGCGTGA Drought PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CGCGCGAG`		-	3919137	3919144	-704	-711
	AtREG512	`CGCGCGAG`		PPDB Motif	`ACGCGC`	PLACE Motif
REG	`TACGTGTCG`		-	3919217	3919225	-784	-792
	AtREG557	`TACGTGTC`	ABA, DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
	AtREG478	`ACGTGTCG`	ABA, DREB1Aox, Drought	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
REG	`CAGCGTTT`		-	3919274	3919281	-841	-848
	AtREG626	`CAGCGTTT`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
REG	`ATGGCCCA`		-	3919326	3919333	-893	-900
	AtREG437	`ATGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
REG	`TGGGCCCAAT`		-	3919384	3919393	-951	-960
	AtREG422	`TGGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG392	`GGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
REG	`AAACGGCA`		-	3919406	3919413	-973	-980
	AtREG500	`AAACGGCA`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
REG	`CCGCGTGA`		-	3919424	3919431	-991	-998
	AtREG502	`CCGCGTGA`	Drought	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

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

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 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	None	None	None
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 AAACGCTG + 3919274 3919281 AT3G12290.1

AtREG626 AAACGCTG PPDB Motif AAACG(C/G) PLACE Motif

REG TGGGCCAT + 3919326 3919333 AT3G12290.1

AtREG437 TGGGCCAT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG ATTGGGCCCA + 3919384 3919393 AT3G12290.1

AtREG352 ATTGGGCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392 TTGGGCCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG422 TGGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG TGCCGTTT + 3919406 3919413 AT3G12290.1

AtREG500 TGCCGTTT PPDB Motif AAACG(C/G) PLACE Motif

REG TCACGCGG + 3919424 3919431 AT3G12290.1

AtREG502 TCACGCGG Drought PPDB Motif PLACE Motif