PlantPromoterDB promoter information of AT1G54050

Summary of Gene (AT1G54050)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G54050 TAIR NCBI
Gene model	AT1G54050
Description	17.4 kDa class III heat shock protein (HSP17.4-CIII); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to high light intensity, response to hydrogen peroxide, response to heat; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Heat shock protein Hsp20 (InterPro:IPR002068), HSP20-like chaperone (InterPro:IPR008978); BEST Arabidopsis thaliana protein match is: AT-HSP17.6A (ARABIDOPSIS THALIANA HEAT SHOCK PROTEIN 17.6A); unfolded protein binding (TAIR:AT5G12030.1); Has 2777 Blast hits to 2777 proteins in 704 species: Archae - 100; Bacteria - 1361; Metazoa - 1; Fungi - 104; Plants - 843; Viruses - 0; Other Eukaryotes - 368 (source: NCBI BLink).

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Overview

Focused view (chromosome 1: 20181122-20179923)

`Genome position from initiation codon` `AT1G54050.1 TSS from cDNA TSS information AT1G54050 5'->3' (-) Promoter sequence AT1G54060.1 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 AT1G54050

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 4 - 20180298 -176

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	4	-	20180298	-176

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone C clone - 20180281 -159

TSS clone C clone - 20180280 -158

TSS clone A clone - 20180279 -157

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`C`	clone	-	20180281	-159
TSS clone	`C`	clone	-	20180280	-158
TSS clone	`A`	clone	-	20180279	-157

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 ATGACGTGGAA - 20180393 20180403 -271 -281

AtREG483 ATGACGTG    PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG419 TGACGTGG   PPDB Motif ACGT PLACE Motif ACGT, ACGTG, TGACGTGG, CCACGTCA

AtREG627    ACGTGGAA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG ATAAGGCCCAATAA - 20180415 20180428 -293 -306

AtREG425 ATAAGGCC       PPDB Motif AACCG(G/A) PLACE Motif

AtREG351 TAAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353   AAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356    AGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352     GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355      GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417       CCCAATAA PPDB Motif GCCCA PLACE Motif

REG TAAACGGCCTATA - 20180437 20180449 -315 -327

AtREG613 TAAACGGC      PPDB Motif AAACG(C/G) PLACE Motif

AtREG487      GGCCTATA PPDB Motif PLACE Motif

REG CAAGGCCCAATAA - 20180511 20180523 -389 -401

AtREG398 CAAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353 AAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356   AGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352    GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355     GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417      CCCAATAA PPDB Motif GCCCA PLACE Motif

REG CTAATGGGCTAAGGCC - 20180536 20180551 -414 -429

AtREG558 CTAATGGG         PPDB Motif GCCCA PLACE Motif

AtREG357 TAATGGGC        PPDB Motif GCCCA PLACE Motif

AtREG372   AATGGGCT       PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG581    ATGGGCTA      PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG571     TGGGCTAA     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG577         CTAAGGCC PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ATGACGTGGAA`		-	20180393	20180403	-271	-281
	AtREG483	`ATGACGTG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG419	`TGACGTGG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, TGACGTGG, CCACGTCA`
	AtREG627	`ACGTGGAA`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
REG	`ATAAGGCCCAATAA`		-	20180415	20180428	-293	-306
	AtREG425	`ATAAGGCC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG351	`TAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TAAACGGCCTATA`		-	20180437	20180449	-315	-327
	AtREG613	`TAAACGGC`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG487	`GGCCTATA`		PPDB Motif		PLACE Motif
REG	`CAAGGCCCAATAA`		-	20180511	20180523	-389	-401
	AtREG398	`CAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CTAATGGGCTAAGGCC`		-	20180536	20180551	-414	-429
	AtREG558	`CTAATGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG357	`TAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG372	`AATGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG581	`ATGGGCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG571	`TGGGCTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG577	`CTAAGGCC`		PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 8 + 20180900 AT1G54060.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	8	+	20180900	AT1G54060.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 20180887 AT1G54060.1

TSS clone C clone + 20180895 AT1G54060.1

TSS clone G clone + 20180897 AT1G54060.1

TSS clone G clone + 20180900 AT1G54060.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	20180887	AT1G54060.1
TSS clone	`C`	clone	+	20180895	AT1G54060.1
TSS clone	`G`	clone	+	20180897	AT1G54060.1
TSS clone	`G`	clone	+	20180900	AT1G54060.1

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 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 CGTCATTT + 20180831 20180838 AT1G54060.1

AtREG657 CGTCATTT PPDB Motif PLACE Motif

REG TCGGGTCA + 20180849 20180856 AT1G54060.1

AtREG617 TCGGGTCA PPDB Motif PLACE Motif