PlantPromoterDB promoter information of AT4G05420.1

Summary of Gene (AT4G05420.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G05420 TAIR NCBI
Gene model	AT4G05420.1
Description	Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis.

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Overview

Focused view (chromosome 4: 2745288-2746487)

`Genome position from initiation codon` `AT4G05420.2 TSS from cDNA TSS information AT4G05420.1 5'->3' (+) Promoter sequence AT4G05410.1 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 AT4G05420.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 5 + 2746138 -150

TSS peak G 2 + 2746284 -4

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	5	+	2746138	-150
TSS peak	`G`	2	+	2746284	-4

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone + 2746122 -166

TSS clone A clone + 2746166 -122

TSS clone T clone + 2746167 -121

TSS clone G clone + 2746236 -52

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	2746122	-166
TSS clone	`A`	clone	+	2746166	-122
TSS clone	`T`	clone	+	2746167	-121
TSS clone	`G`	clone	+	2746236	-52

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 CTTTCTTCTTCCT + 2746124 2746136 -164 -152

Y Patch TTCTCTCTCT + 2746167 2746176 -121 -112

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	`CTTTCTTCTTCCT`	+	2746124	2746136	-164	-152
Y Patch	`TTCTCTCTCT`	+	2746167	2746176	-121	-112
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 GTAAACCGAA + 2745884 2745893 -404 -395

AtREG519 GTAAACCG   PPDB Motif AACCG(G/A) PLACE Motif

AtREG514 TAAACCGA PPDB Motif AACCG(G/A) PLACE Motif

AtREG568   AAACCGAA PPDB Motif AACCG(G/A) PLACE Motif

REG TTCCGGTTTAA + 2745985 2745995 -303 -293

AtREG534 TTCCGGTT    PPDB Motif AACCG(G/A) PLACE Motif

AtREG521 TCCGGTTT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG412   CCGGTTTA PPDB Motif AACCG(G/A) PLACE Motif

AtREG473    CGGTTTAA PPDB Motif AACCG(G/A) PLACE Motif

REG GTTCGGTTTAG + 2746009 2746019 -279 -269

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

AtREG568 TTCGGTTT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG514   TCGGTTTA PPDB Motif AACCG(G/A) PLACE Motif

AtREG511    CGGTTTAG PPDB Motif AACCG(G/A) PLACE Motif

REG ACCGAACCGGAC + 2746053 2746064 -235 -224

AtREG451 ACCGAACC     PPDB Motif PLACE Motif

AtREG456 CCGAACCG    PPDB Motif AACCG(G/A) PLACE Motif

AtREG423   CGAACCGG   PPDB Motif AACCG(G/A) PLACE Motif

AtREG579    GAACCGGA PPDB Motif AACCG(G/A) PLACE Motif

AtREG573     AACCGGAC PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GTAAACCGAA`		+	2745884	2745893	-404	-395
	AtREG519	`GTAAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG514	`TAAACCGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG568	`AAACCGAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TTCCGGTTTAA`		+	2745985	2745995	-303	-293
	AtREG534	`TTCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG521	`TCCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG412	`CCGGTTTA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG473	`CGGTTTAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`GTTCGGTTTAG`		+	2746009	2746019	-279	-269
	AtREG556	`GTTCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG568	`TTCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG514	`TCGGTTTA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG511	`CGGTTTAG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`ACCGAACCGGAC`		+	2746053	2746064	-235	-224
	AtREG451	`ACCGAACC`		PPDB Motif		PLACE Motif
	AtREG456	`CCGAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG423	`CGAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG579	`GAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG573	`AACCGGAC`		PPDB Motif	`AACCG(G/A)`	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 A clone - 2745627 AT4G05410.1

TSS clone peak A clone - 2745626 AT4G05410.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`A`	clone	-	2745627	AT4G05410.1
TSS clone peak	`A`	clone	-	2745626	AT4G05410.1

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 CTTCTTCC - 2745605 2745612 AT4G05410.1

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	`CTTCTTCC`	-	2745605	2745612	AT4G05410.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG AACCCGGT - 2745693 2745700 AT4G05410.1

AtREG516 AACCCGGT PPDB Motif PLACE Motif

REG ATGGGCTTG - 2745714 2745722 AT4G05410.1

AtREG378 ATGGGCTT PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG525 TGGGCTTG PPDB Motif GCCCA PLACE Motif TGGGCY

REG TTAATGGGCTCA - 2745743 2745754 AT4G05410.1

AtREG396 TTAATGGG     PPDB Motif GCCCA PLACE Motif TTAATGG

AtREG357 TAATGGGC    PPDB Motif GCCCA PLACE Motif

AtREG372   AATGGGCT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG485     TGGGCTCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG TTAAAGGCCCAAG - 2745780 2745792 AT4G05410.1

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

AtREG356     AGGCCCAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG505      GGCCCAAG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG GTCCGGTTA - 2745810 2745818 AT4G05410.1

AtREG573 GTCCGGTT PPDB Motif AACCG(G/A) PLACE Motif

AtREG621 TCCGGTTA PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG TTCGGTTTAC - 2745884 2745893 AT4G05410.1

AtREG568 TTCGGTTT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG514 TCGGTTTA PPDB Motif AACCG(G/A) PLACE Motif

AtREG519   CGGTTTAC PPDB Motif AACCG(G/A) PLACE Motif