PlantPromoterDB promoter information of AT5G18620.2

Summary of Gene (AT5G18620.2)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G18620 TAIR NCBI
Gene model	AT5G18620.2
Description	CHROMATIN REMODELING FACTOR17 (CHR17); FUNCTIONS IN: in 7 functions; INVOLVED IN: ATP-dependent chromatin remodeling, chromatin remodeling; LOCATED IN: nucleus, chromatin remodeling complex; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: ATPase, nucleosome remodelling ISWI, HAND domain (InterPro:IPR015194), SANT, eukarya (InterPro:IPR017884), SNF2-related (InterPro:IPR000330), SANT, DNA-binding (InterPro:IPR001005), Myb, DNA-binding (InterPro:IPR014778), Homeodomain-like (InterPro:IPR009057), SLIDE (InterPro:IPR015195), DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1 and 2, ATP-binding (InterPro:IPR014021); BEST Arabidopsis thaliana protein match is: CHR11 (CHROMATIN-REMODELING PROTEIN 11); ATP binding / DNA binding / DNA-dependent ATPase/ helicase/ hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid binding / nucleosome binding (TAIR:AT3G06400.1); Has 19924 Blast hits to 15142 proteins in 1291 species: Archae - 93; Bacteria - 3277; Metazoa - 6471; Fungi - 3450; Plants - 1004; Viruses - 457; Other Eukaryotes - 5172 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 6203058-6201859)

`Genome position from initiation codon` `AT5G18620.1 TSS from cDNA TSS information AT5G18620.2 5'->3' (-) Promoter sequence AT5G18630.1 AT5G18630.2 AT5G18630.3 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 AT5G18620.2

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 peak T clone - 6202166 -108

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`T`	clone	-	6202166	-108

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 ACGTGGCAC - 6202240 6202248 -182 -190

AtREG379 ACGTGGCA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG444 CGTGGCAC PPDB Motif PLACE Motif GCCAC

REG GCCCATGGGCCTTTAAAGCCC - 6202319 6202339 -261 -281

AtREG591 CCCATGGG             PPDB Motif GCCCA, CCATGG PLACE Motif

AtREG507 GCCCATGGGC            PPDB Motif GCCCA, CCATGG PLACE Motif

AtREG504    CATGGGCC           PPDB Motif GCCCA, CCATGG PLACE Motif GGGCC, TGGGCY

AtREG354     ATGGGCCT          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353      TGGGCCTT         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG359       GGGCCTTT        PPDB Motif GCCCA PLACE Motif GGGCC

AtREG467        GGCCTTTA       PPDB Motif PLACE Motif

AtREG639         GCCTTTAA      PPDB Motif AAACG(C/G) PLACE Motif

AtREG545             TTAAAGCC PPDB Motif PLACE Motif

AtREG365              TAAAGCCC PPDB Motif GCCCA PLACE Motif

REG TTGACTTT - 6202365 6202372 -307 -314

AtREG632 TTGACTTT PPDB Motif PLACE Motif TTGAC

REG ATAAGGCC - 6202404 6202411 -346 -353

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

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ACGTGGCAC`		-	6202240	6202248	-182	-190
	AtREG379	`ACGTGGCA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG444	`CGTGGCAC`		PPDB Motif		PLACE Motif	`GCCAC`
REG	`GCCCATGGGCCTTTAAAGCCC`		-	6202319	6202339	-261	-281
	AtREG591	`CCCATGGG`		PPDB Motif	`GCCCA, CCATGG`	PLACE Motif
	AtREG507	`GCCCATGGGC`		PPDB Motif	`GCCCA, CCATGG`	PLACE Motif
	AtREG504	`CATGGGCC`		PPDB Motif	`GCCCA, CCATGG`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG353	`TGGGCCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG359	`GGGCCTTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG467	`GGCCTTTA`		PPDB Motif		PLACE Motif
	AtREG639	`GCCTTTAA`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG545	`TTAAAGCC`		PPDB Motif		PLACE Motif
	AtREG365	`TAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TTGACTTT`		-	6202365	6202372	-307	-314
	AtREG632	`TTGACTTT`		PPDB Motif		PLACE Motif	`TTGAC`
REG	`ATAAGGCC`		-	6202404	6202411	-346	-353
	AtREG425	`ATAAGGCC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 5 + 6202612 AT5G18630.3, AT5G18630.2, AT5G18630.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	5	+	6202612	AT5G18630.3, AT5G18630.2, AT5G18630.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone + 6202641 AT5G18630.3, AT5G18630.2, AT5G18630.1

TSS clone T clone + 6202654 AT5G18630.3, AT5G18630.2, AT5G18630.1

TSS clone G clone + 6202680 AT5G18630.3, AT5G18630.2, AT5G18630.1

TSS clone G clone + 6202681 AT5G18630.3, AT5G18630.2, AT5G18630.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	+	6202641	AT5G18630.3, AT5G18630.2, AT5G18630.1
TSS clone	`T`	clone	+	6202654	AT5G18630.3, AT5G18630.2, AT5G18630.1
TSS clone	`G`	clone	+	6202680	AT5G18630.3, AT5G18630.2, AT5G18630.1
TSS clone	`G`	clone	+	6202681	AT5G18630.3, AT5G18630.2, AT5G18630.1

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 TTTCTTCT + 6202601 6202608 AT5G18630.1, AT5G18630.2, AT5G18630.3

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	`TTTCTTCT`	+	6202601	6202608	AT5G18630.1, AT5G18630.2, AT5G18630.3
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG GGGCTTTAAAGGCCCATGGGC + 6202319 6202339 AT5G18630.1, AT5G18630.2, AT5G18630.3

AtREG365 GGGCTTTA              PPDB Motif GCCCA PLACE Motif

AtREG545 GGCTTTAA             PPDB Motif PLACE Motif

AtREG639      TTAAAGGC         PPDB Motif AAACG(C/G) PLACE Motif

AtREG467       TAAAGGCC        PPDB Motif PLACE Motif

AtREG359        AAAGGCCC       PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353         AAGGCCCA      PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354          AGGCCCAT     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG504           GGCCCATG    PPDB Motif GCCCA, CCATGG PLACE Motif GGGCC, TGGGCY

AtREG591             CCCATGGG PPDB Motif GCCCA, CCATGG PLACE Motif

AtREG507            GCCCATGGGC PPDB Motif GCCCA, CCATGG PLACE Motif

REG AAAGTCAA + 6202365 6202372 AT5G18630.1, AT5G18630.2, AT5G18630.3

AtREG632 AAAGTCAA PPDB Motif PLACE Motif TTGAC

REG GGCCTTAT + 6202404 6202411 AT5G18630.1, AT5G18630.2, AT5G18630.3

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

REG AATACCCTT + 6202489 6202497 AT5G18630.1, AT5G18630.2, AT5G18630.3

AtREG567 AATACCCT PPDB Motif ACCCT PLACE Motif

AtREG623 ATACCCTT PPDB Motif ACCCT PLACE Motif