PlantPromoterDB promoter information of AT5G25460.1

Summary of Gene (AT5G25460.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G25460 TAIR NCBI
Gene model	AT5G25460.1
Description	unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: plant-type cell wall; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF642 (InterPro:IPR006946); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G11420.1); Has 182 Blast hits to 159 proteins in 12 species: Archae - 0; Bacteria - 2; Metazoa - 0; Fungi - 0; Plants - 180; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 8856230-8857429)

`Genome position from initiation codon` `AT5G25450.1 TSS from cDNA TSS information AT5G25460.1 5'->3' (+) Promoter sequence AT5G25440.1 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 AT5G25460.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 102 + 8863394 -36

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	102	+	8863394	-36

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 8863363 -67

TSS clone A clone + 8863391 -39

TSS clone A clone + 8863394 -36

TSS clone C clone + 8863395 -35

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	8863363	-67
TSS clone	`A`	clone	+	8863391	-39
TSS clone	`A`	clone	+	8863394	-36
TSS clone	`C`	clone	+	8863395	-35

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 CCCTTATAA + 8863357 8863365 -73 -65

Y Patch CTCTCTTT + 8863379 8863386 -51 -44

Y Patch TTCTCTCTTCC + 8863413 8863423 -17 -7

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	`CCCTTATAA`	+	8863357	8863365	-73	-65
Y Patch	`CTCTCTTT`	+	8863379	8863386	-51	-44
Y Patch	`TTCTCTCTTCC`	+	8863413	8863423	-17	-7
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 CCCAATTG + 8863103 8863110 -327 -320

AtREG647 CCCAATTG PPDB Motif PLACE Motif

REG CCCACGTGGG + 8863276 8863285 -154 -145

AtREG464 CCCACGTGGG ABA, Auxin, JA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CCCAATTG`		+	8863103	8863110	-327	-320
	AtREG647	`CCCAATTG`		PPDB Motif		PLACE Motif
REG	`CCCACGTGGG`		+	8863276	8863285	-154	-145
	AtREG464	`CCCACGTGGG`	ABA, Auxin, JA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 4 + 8857000 AT5G25450.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	4	+	8857000	AT5G25450.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone - 8856758 AT5G25440.1

TSS clone peak G clone - 8856750 AT5G25440.1

TSS clone T clone - 8856747 AT5G25440.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	-	8856758	AT5G25440.1
TSS clone peak	`G`	clone	-	8856750	AT5G25440.1
TSS clone	`T`	clone	-	8856747	AT5G25440.1

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 TCCTCTCTTCTTC - 8856762 8856774 AT5G25440.1

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	`TCCTCTCTTCTTC`	-	8856762	8856774	AT5G25440.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TTGACTTT - 8856800 8856807 AT5G25440.1

AtREG632 TTGACTTT PPDB Motif PLACE Motif TTGAC

REG AAACGCGTTTT - 8856810 8856820 AT5G25440.1

AtREG633 AAACGCGTTT PPDB Motif AAACG(C/G) PLACE Motif

AtREG566    CGCGTTTT PPDB Motif AAACG(C/G) PLACE Motif

REG TAAAACGCGT - 8856836 8856845 AT5G25440.1

AtREG564 TAAAACGC   PPDB Motif AAACG(C/G) PLACE Motif

AtREG566 AAAACGCG PPDB Motif AAACG(C/G) PLACE Motif

AtREG633   AAACGCGT PPDB Motif AAACG(C/G) PLACE Motif

REG AAAACGGCGTCGT - 8856859 8856871 AT5G25440.1

AtREG531 AAAACGGC      PPDB Motif AAACG(C/G) PLACE Motif

AtREG524 AAACGGCG     PPDB Motif AAACG(C/G) PLACE Motif

AtREG497   AACGGCGT    PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

AtREG540    ACGGCGTC   PPDB Motif PLACE Motif

AtREG537      GGCGTCGT PPDB Motif PLACE Motif

REG AAACGGCGT - 8856890 8856898 AT5G25440.1

AtREG524 AAACGGCG PPDB Motif AAACG(C/G) PLACE Motif

AtREG497 AACGGCGT PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

REG GAAACGACGCC - 8857038 8857048 AT5G25440.1

AtREG576 GAAACGAC    PPDB Motif PLACE Motif

AtREG415 AAACGACG   PPDB Motif PLACE Motif

AtREG439   AACGACGC PPDB Motif PLACE Motif

AtREG537    ACGACGCC PPDB Motif PLACE Motif

REG AAAGTCAA + 8856800 8856807 AT5G25450.1

AtREG632 AAAGTCAA PPDB Motif PLACE Motif TTGAC

REG AAAACGCGTTT + 8856810 8856820 AT5G25450.1

AtREG566 AAAACGCG    PPDB Motif AAACG(C/G) PLACE Motif

AtREG633 AAACGCGTTT PPDB Motif AAACG(C/G) PLACE Motif

REG ACGCGTTTTA + 8856836 8856845 AT5G25450.1

AtREG633 ACGCGTTT   PPDB Motif AAACG(C/G) PLACE Motif

AtREG566 CGCGTTTT PPDB Motif AAACG(C/G) PLACE Motif

AtREG564   GCGTTTTA PPDB Motif AAACG(C/G) PLACE Motif

REG ACGACGCCGTTTT + 8856859 8856871 AT5G25450.1

AtREG537 ACGACGCC      PPDB Motif PLACE Motif

AtREG540   GACGCCGT    PPDB Motif PLACE Motif

AtREG497    ACGCCGTT   PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

AtREG524     CGCCGTTT PPDB Motif AAACG(C/G) PLACE Motif

AtREG531      GCCGTTTT PPDB Motif AAACG(C/G) PLACE Motif

REG ACGCCGTTT + 8856890 8856898 AT5G25450.1

AtREG497 ACGCCGTT PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

AtREG524 CGCCGTTT PPDB Motif AAACG(C/G) PLACE Motif