PlantPromoterDB promoter information of AT4G01570.1

Summary of Gene (AT4G01570.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G01570 TAIR NCBI
Gene model	AT4G01570.1
Description	pentatricopeptide (PPR) repeat-containing protein; INVOLVED IN: biological_process unknown; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Pentatricopeptide repeat (InterPro:IPR002885); BEST Arabidopsis thaliana protein match is: pentatricopeptide (PPR) repeat-containing protein (TAIR:AT1G62910.1); Has 25223 Blast hits to 5430 proteins in 165 species: Archae - 8; Bacteria - 10; Metazoa - 231; Fungi - 283; Plants - 23698; Viruses - 0; Other Eukaryotes - 993 (source: NCBI BLink).

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Overview

Focused view (chromosome 4: 678487-679686)

`Genome position from initiation codon` `TSS from cDNA TSS information AT4G01570.1 5'->3' (+) Promoter sequence AT4G01560.1 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 AT4G01570.1

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 peak A clone + 679472 -15

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`A`	clone	+	679472	-15

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 None None None

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	None	None	None
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 AAAACGGCA + 679210 679218 -277 -269

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

AtREG500 AAACGGCA PPDB Motif AAACG(C/G) PLACE Motif

REG AAATGGGCCTAT + 679285 679296 -202 -191

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

AtREG358    TGGGCCTA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG362     GGGCCTAT PPDB Motif GCCCA PLACE Motif GGGCC

REG CTTGGGCCCATCT + 679298 679310 -189 -177

AtREG505 CTTGGGCC      PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392 TTGGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG422   TGGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG391    GGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG403     GGCCCATC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG572      GCCCATCT PPDB Motif GCCCA PLACE Motif

REG ATAGGCCTAT + 679317 679326 -170 -161

AtREG649 ATAGGCCTAT PPDB Motif PLACE Motif

REG TTAAACCGT + 679345 679353 -142 -134

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

AtREG652 TAAACCGT PPDB Motif PLACE Motif

REG TAACGGGC + 679370 679377 -117 -110

AtREG399 TAACGGGC PPDB Motif ACGGGC PLACE Motif YAACKG, CNGTTR

REG TCTGGGCCTTG + 679383 679393 -104 -94

AtREG397 TCTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG410 CTGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353   TGGGCCTT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG398    GGGCCTTG PPDB Motif GCCCA PLACE Motif GGGCC

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AAAACGGCA`		+	679210	679218	-277	-269
	AtREG531	`AAAACGGC`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG500	`AAACGGCA`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
REG	`AAATGGGCCTAT`		+	679285	679296	-202	-191
	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`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG362	`GGGCCTAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`CTTGGGCCCATCT`		+	679298	679310	-189	-177
	AtREG505	`CTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG392	`TTGGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG422	`TGGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG391	`GGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG403	`GGCCCATC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG572	`GCCCATCT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`ATAGGCCTAT`		+	679317	679326	-170	-161
	AtREG649	`ATAGGCCTAT`		PPDB Motif		PLACE Motif
REG	`TTAAACCGT`		+	679345	679353	-142	-134
	AtREG473	`TTAAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG652	`TAAACCGT`		PPDB Motif		PLACE Motif
REG	`TAACGGGC`		+	679370	679377	-117	-110
	AtREG399	`TAACGGGC`		PPDB Motif	`ACGGGC`	PLACE Motif	`YAACKG, CNGTTR`
REG	`TCTGGGCCTTG`		+	679383	679393	-104	-94
	AtREG397	`TCTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG410	`CTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG353	`TGGGCCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG398	`GGGCCTTG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 4 - 679229 AT4G01560.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	4	-	679229	AT4G01560.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone - 679237 AT4G01560.1

TSS clone C clone - 679233 AT4G01560.1

TSS clone T clone - 679218 AT4G01560.1

TSS clone A clone - 679208 AT4G01560.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	-	679237	AT4G01560.1
TSS clone	`C`	clone	-	679233	AT4G01560.1
TSS clone	`T`	clone	-	679218	AT4G01560.1
TSS clone	`A`	clone	-	679208	AT4G01560.1

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 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 ATAGGCCCATTT - 679285 679296 AT4G01560.1

AtREG362 ATAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358 TAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   AGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361    GGCCCATT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG386     GCCCATTT PPDB Motif GCCCA PLACE Motif

REG AGATGGGCCCAAG - 679298 679310 AT4G01560.1

AtREG572 AGATGGGC      PPDB Motif GCCCA PLACE Motif

AtREG403 GATGGGCC     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG391   ATGGGCCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG422    TGGGCCCA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392     GGGCCCAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG505      GGCCCAAG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG ATAGGCCTAT - 679317 679326 AT4G01560.1

AtREG649 ATAGGCCTAT PPDB Motif PLACE Motif

REG ACGGTTTAA - 679345 679353 AT4G01560.1

AtREG652 ACGGTTTA PPDB Motif PLACE Motif

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

REG GCCCGTTA - 679370 679377 AT4G01560.1

AtREG399 GCCCGTTA PPDB Motif ACGGGC PLACE Motif YAACKG, CNGTTR

REG CAAGGCCCAGA - 679383 679393 AT4G01560.1

AtREG398 CAAGGCCC    PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353 AAGGCCCA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG410   AGGCCCAG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG397    GGCCCAGA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG ACGGCGTCGTTTA - 679432 679444 AT4G01560.1

AtREG540 ACGGCGTC      PPDB Motif PLACE Motif

AtREG537   GGCGTCGT    PPDB Motif PLACE Motif

AtREG439    GCGTCGTT   PPDB Motif PLACE Motif

AtREG415     CGTCGTTT PPDB Motif PLACE Motif

AtREG565      GTCGTTTA PPDB Motif PLACE Motif