PlantPromoterDB promoter information of AT3G02540.1

Summary of Gene (AT3G02540.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G02540 TAIR NCBI
Gene model	AT3G02540.1
Description	PUTATIVE DNA REPAIR PROTEIN RAD23-3 (RAD23-3); FUNCTIONS IN: damaged DNA binding; INVOLVED IN: protein modification process, proteasomal ubiquitin-dependent protein catabolic process, nucleotide-excision repair; LOCATED IN: nucleus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Heat shock chaperonin-binding (InterPro:IPR006636), Ubiquitin-associated/translation elongation factor EF1B, N-terminal (InterPro:IPR000449), UV excision repair protein Rad23 (InterPro:IPR004806), Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (InterPro:IPR015940), Ubiquitin (InterPro:IPR000626), UV excision repair protein Rad23, C-terminal (InterPro:IPR014761), XPC-binding domain (InterPro:IPR015360), UBA-like (InterPro:IPR009060); BEST Arabidopsis thaliana protein match is: DNA repair protein RAD23, putative (TAIR:AT5G38470.1); Has 36702 Blast hits to 20290 proteins in 1352 species: Archae - 153; Bacteria - 8192; Metazoa - 9251; Fungi - 4074; Plants - 5824; Viruses - 1459; Other Eukaryotes - 7749 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 537151-535952)

`Genome position from initiation codon` `AT3G02540.2 AT3G02550.1 TSS from cDNA TSS information AT3G02540.1 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 AT3G02540.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 4 - 537003 -852

TSS peak A 8 - 536280 -129

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	4	-	537003	-852
TSS peak	`A`	8	-	536280	-129

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 536305 -154

TSS clone A clone - 536302 -151

TSS clone G clone - 536286 -135

TSS clone A clone - 536280 -129

TSS clone G clone - 536270 -119

TSS clone C clone - 536267 -116

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	536305	-154
TSS clone	`A`	clone	-	536302	-151
TSS clone	`G`	clone	-	536286	-135
TSS clone	`A`	clone	-	536280	-129
TSS clone	`G`	clone	-	536270	-119
TSS clone	`C`	clone	-	536267	-116

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 CTCTCTTTC - 536242 536250 -91 -99

Y Patch CCTTCTTC - 536260 536267 -109 -116

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	`CTCTCTTTC`	-	536242	536250	-91	-99
Y Patch	`CCTTCTTC`	-	536260	536267	-109	-116
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 ACCACGTGGCAT - 536386 536397 -235 -246

AtREG544 ACCACGTG     ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG367   CACGTGGC   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

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

AtREG448     CGTGGCAT ABA, DREB1Aox PPDB Motif PLACE Motif GCCAC

REG TTTTGGGCCTAT - 536430 536441 -279 -290

AtREG529 TTTTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG373 TTTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356   TTGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358    TGGGCCTA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG362     GGGCCTAT PPDB Motif GCCCA PLACE Motif GGGCC

REG TTATGGGCCTAT - 536465 536476 -314 -325

AtREG394 TTATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   ATGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358    TGGGCCTA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG362     GGGCCTAT PPDB Motif GCCCA PLACE Motif GGGCC

REG ACGCTGCG - 537188 537195 -1037 -1044

AtREG369 ACGCTGCG PPDB Motif PLACE Motif

REG GAACCGGTC - 537212 537220 -1061 -1069

AtREG528 GAACCGGT PPDB Motif AACCG(G/A) PLACE Motif

AtREG552 AACCGGTC PPDB Motif AACCG(G/A) PLACE Motif

REG GACGCCGT - 537240 537247 -1089 -1096

AtREG540 GACGCCGT PPDB Motif PLACE Motif

REG TGGTTCGGT - 537285 537293 -1134 -1142

AtREG655 TGGTTCGG PPDB Motif PLACE Motif

AtREG451 GGTTCGGT PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ACCACGTGGCAT`		-	536386	536397	-235	-246
	AtREG544	`ACCACGTG`	ABA, DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG367	`CACGTGGC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC`
	AtREG379	`ACGTGGCA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG448	`CGTGGCAT`	ABA, DREB1Aox	PPDB Motif		PLACE Motif	`GCCAC`
REG	`TTTTGGGCCTAT`		-	536430	536441	-279	-290
	AtREG529	`TTTTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG373	`TTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`TTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG362	`GGGCCTAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`TTATGGGCCTAT`		-	536465	536476	-314	-325
	AtREG394	`TTATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG364	`TATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG362	`GGGCCTAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`ACGCTGCG`		-	537188	537195	-1037	-1044
	AtREG369	`ACGCTGCG`		PPDB Motif		PLACE Motif
REG	`GAACCGGTC`		-	537212	537220	-1061	-1069
	AtREG528	`GAACCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG552	`AACCGGTC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`GACGCCGT`		-	537240	537247	-1089	-1096
	AtREG540	`GACGCCGT`		PPDB Motif		PLACE Motif
REG	`TGGTTCGGT`		-	537285	537293	-1134	-1142
	AtREG655	`TGGTTCGG`		PPDB Motif		PLACE Motif
	AtREG451	`GGTTCGGT`		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 None None None