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: 8869280-8870479)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G25460.1 5'->3' (+) Promoter sequence AT5G25475.1 AT5G25475.2 AT5G25475.3 AT5G25480.1 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 G 5 - 8869786 AT5G25475.2, AT5G25475.1, AT5G25475.3

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	5	-	8869786	AT5G25475.2, AT5G25475.1, AT5G25475.3

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone - 8869821 AT5G25475.2, AT5G25475.1, AT5G25475.3

TSS clone T clone - 8869820 AT5G25475.2, AT5G25475.1, AT5G25475.3

TSS clone T clone - 8869818 AT5G25475.2, AT5G25475.1, AT5G25475.3

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	-	8869821	AT5G25475.2, AT5G25475.1, AT5G25475.3
TSS clone	`T`	clone	-	8869820	AT5G25475.2, AT5G25475.1, AT5G25475.3
TSS clone	`T`	clone	-	8869818	AT5G25475.2, AT5G25475.1, AT5G25475.3

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 TCTCTCTCTCTCTCTC - 8869805 8869820 AT5G25475.1, AT5G25475.2, AT5G25475.3

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	`TCTCTCTCTCTCTCTC`	-	8869805	8869820	AT5G25475.1, AT5G25475.2, AT5G25475.3
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TAAATGGGCCTTATTCGGCCCGTTA - 8869893 8869917 AT5G25475.1, AT5G25475.2, AT5G25475.3

AtREG443 TAAATGGG                  PPDB Motif GCCCA PLACE Motif

AtREG386 AAATGGGC                 PPDB Motif GCCCA PLACE Motif

AtREG361   AATGGGCC                PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    ATGGGCCT               PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353     TGGGCCTT              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG351      GGGCCTTA             PPDB Motif GCCCA PLACE Motif GGGCC

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

AtREG427              TTCGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG401                 GGCCCGTT PPDB Motif AAACG(C/G), ACGGGC, CCAACGG PLACE Motif GGGCC

AtREG399                  GCCCGTTA PPDB Motif ACGGGC PLACE Motif YAACKG, CNGTTR

REG TTATGGGCCA - 8869924 8869933 AT5G25475.1, AT5G25475.2, AT5G25475.3

AtREG394 TTATGGGC   PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG490   ATGGGCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY