PlantPromoterDB promoter information of AT5G27460.1

Summary of Gene (AT5G27460.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G27460 TAIR NCBI
Gene model	AT5G27460.1
Description	pentatricopeptide (PPR) repeat-containing protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 7 growth stages; CONTAINS InterPro DOMAIN/s: Pentatricopeptide repeat (InterPro:IPR002885); BEST Arabidopsis thaliana protein match is: pentatricopeptide (PPR) repeat-containing protein (TAIR:AT1G02150.1); Has 3781 Blast hits to 2103 proteins in 60 species: Archae - 0; Bacteria - 4; Metazoa - 0; Fungi - 13; Plants - 3697; Viruses - 0; Other Eukaryotes - 67 (source: NCBI BLink).

#

Overview

Focused view (chromosome 5: 9695815-9694616)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G27460.1 5'->3' (-) Promoter sequence AT5G27470.1 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 AT5G27460.1

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 G clone - 9694840 -25

TSS clone peak A clone - 9694823 -8

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	9694840	-25
TSS clone peak	`A`	clone	-	9694823	-8

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 TCTCTTCTCT - 9694866 9694875 -51 -60

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	`TCTCTTCTCT`	-	9694866	9694875	-51	-60
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 TACGGCCCAAAT - 9694888 9694899 -73 -84

AtREG499 TACGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG368 ACGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414   CGGCCCAA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG373    GGCCCAAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG421     GCCCAAAT PPDB Motif GCCCA PLACE Motif

REG ATATGGGCCGGGTAAGCCCAACT - 9694908 9694930 -93 -115

AtREG432 ATATGGGC                PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC               PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380   ATGGGCCG              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG457    TGGGCCGG             CK PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG404     GGGCCGGG            CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG426             TAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407              AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG574               AGCCCAAC PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG607                GCCCAACT PPDB Motif GCCCA PLACE Motif

REG GGGCTTAT - 9694939 9694946 -124 -131

AtREG462 GGGCTTAT PPDB Motif GCCCA PLACE Motif

REG ACGACGTC - 9694959 9694966 -144 -151

AtREG431 ACGACGTC PPDB Motif ACGT PLACE Motif ACGT

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TACGGCCCAAAT`		-	9694888	9694899	-73	-84
	AtREG499	`TACGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG368	`ACGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`CGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG373	`GGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG421	`GCCCAAAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`ATATGGGCCGGGTAAGCCCAACT`		-	9694908	9694930	-93	-115
	AtREG432	`ATATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG364	`TATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`ATGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG457	`TGGGCCGG`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG404	`GGGCCGGG`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG426	`TAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG574	`AGCCCAAC`		PPDB Motif	`GCCCA, CCAACGG`	PLACE Motif	`TGGGCY`
	AtREG607	`GCCCAACT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GGGCTTAT`		-	9694939	9694946	-124	-131
	AtREG462	`GGGCTTAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`ACGACGTC`		-	9694959	9694966	-144	-151
	AtREG431	`ACGACGTC`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 8 + 9695027 AT5G27470.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	8	+	9695027	AT5G27470.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone + 9695008 AT5G27470.1

TSS clone C clone + 9695019 AT5G27470.1

TSS clone T clone + 9695028 AT5G27470.1

TSS clone G clone + 9695036 AT5G27470.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	+	9695008	AT5G27470.1
TSS clone	`C`	clone	+	9695019	AT5G27470.1
TSS clone	`T`	clone	+	9695028	AT5G27470.1
TSS clone	`G`	clone	+	9695036	AT5G27470.1

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 CTTCCTTCTTCTTCCTC + 9694991 9695007 AT5G27470.1

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	`CTTCCTTCTTCTTCCTC`	+	9694991	9695007	AT5G27470.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TGGTTCGGT + 9694841 9694849 AT5G27470.1

AtREG655 TGGTTCGG PPDB Motif PLACE Motif

AtREG451 GGTTCGGT PPDB Motif PLACE Motif

REG ATTTGGGCCGTA + 9694888 9694899 AT5G27470.1

AtREG421 ATTTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG373 TTTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414   TTGGGCCG   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG368    TGGGCCGT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG499     GGGCCGTA PPDB Motif GCCCA PLACE Motif GGGCC

REG AGTTGGGCTTACCCGGCCCATAT + 9694908 9694930 AT5G27470.1

AtREG607 AGTTGGGC                PPDB Motif GCCCA PLACE Motif

AtREG574 GTTGGGCT               PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG407   TTGGGCTT              PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG426    TGGGCTTA             PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG404            CCCGGCCC     CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG457             CCGGCCCA    CK PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380              CGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364               GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG432                GCCCATAT PPDB Motif GCCCA PLACE Motif

REG ATAAGCCC + 9694939 9694946 AT5G27470.1

AtREG462 ATAAGCCC PPDB Motif GCCCA PLACE Motif

REG GACGTCGT + 9694959 9694966 AT5G27470.1

AtREG431 GACGTCGT PPDB Motif ACGT PLACE Motif ACGT