PlantPromoterDB promoter information of AT3G51880.2

Summary of Gene (AT3G51880.2)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G51880 TAIR NCBI
Gene model	AT3G51880.2
Description	Encodes a protein belonging to the subgroup of HMGB (high mobility group B) proteins that have a distinctive DNA-binding motif, the HMG-box domain. The motif confers non-sequence specific interaction with linear DNA and structure-specific binding to distorted DNA sites. The HMGB proteins are involved in the assembly of nucleoprotein complexes. Can be phosphorylated by CK2alpha. In interphase cells, HMGB1 is found throughout the nucleus, whereas in mitotic cells it is not chromatin-associated.

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Overview

Focused view (chromosome 3: 19249491-19248292)

`Genome position from initiation codon` `AT3G51880.1 AT3G51880.3 AT3G51890.1 TSS from cDNA TSS information AT3G51880.2 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 AT3G51880.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 17 - 19249051 -560

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	17	-	19249051	-560

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 19249095 -604

TSS clone T clone - 19249068 -577

TSS clone T clone - 19249066 -575

TSS clone G clone - 19249050 -559

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	19249095	-604
TSS clone	`T`	clone	-	19249068	-577
TSS clone	`T`	clone	-	19249066	-575
TSS clone	`G`	clone	-	19249050	-559

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 CTCTCTCTCT - 19249027 19249036 -536 -545

Y Patch TCTCTTTCTCTTTTCCTCCTCCTTC - 19249052 19249076 -561 -585

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	`CTCTCTCTCT`	-	19249027	19249036	-536	-545
Y Patch	`TCTCTTTCTCTTTTCCTCCTCCTTC`	-	19249052	19249076	-561	-585
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 CTTAACCGG - 19249119 19249127 -628 -636

AtREG605 CTTAACCG PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

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

REG CGTTTTGA - 19249224 19249231 -733 -740

AtREG653 CGTTTTGA PPDB Motif AAACG(C/G) PLACE Motif

REG GTCACGTG - 19249277 19249284 -786 -793

AtREG583 GTCACGTG PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

REG TCAGGCCCATATA - 19249297 19249309 -806 -818

AtREG374 TCAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG370 CAGGCCCA     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

AtREG620      CCCATATA PPDB Motif GCCCA PLACE Motif

REG GCCCAACA - 19249325 19249332 -834 -841

AtREG543 GCCCAACA PPDB Motif GCCCA PLACE Motif CAACA

REG TGGCCCATAA - 19249336 19249345 -845 -854

AtREG490 TGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364 GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG394   GCCCATAA PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CTTAACCGG`		-	19249119	19249127	-628	-636
	AtREG605	`CTTAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG501	`TTAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
REG	`CGTTTTGA`		-	19249224	19249231	-733	-740
	AtREG653	`CGTTTTGA`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
REG	`GTCACGTG`		-	19249277	19249284	-786	-793
	AtREG583	`GTCACGTG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`
REG	`TCAGGCCCATATA`		-	19249297	19249309	-806	-818
	AtREG374	`TCAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG370	`CAGGCCCA`		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
	AtREG620	`CCCATATA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GCCCAACA`		-	19249325	19249332	-834	-841
	AtREG543	`GCCCAACA`		PPDB Motif	`GCCCA`	PLACE Motif	`CAACA`
REG	`TGGCCCATAA`		-	19249336	19249345	-845	-854
	AtREG490	`TGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG394	`GCCCATAA`		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

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 None None None