PlantPromoterDB promoter information of AT3G02560.2

Summary of Gene (AT3G02560.2)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G02560 TAIR NCBI
Gene model	AT3G02560.2
Description	40S ribosomal protein S7 (RPS7B); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic small ribosomal subunit, cytosolic ribosome, chloroplast, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 16 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein S7e (InterPro:IPR000554); BEST Arabidopsis thaliana protein match is: 40S ribosomal protein S7 (RPS7C) (TAIR:AT5G16130.1); Has 555 Blast hits to 555 proteins in 220 species: Archae - 0; Bacteria - 0; Metazoa - 251; Fungi - 93; Plants - 111; Viruses - 0; Other Eukaryotes - 100 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 541341-542540)

`Genome position from initiation codon` `AT3G02560.1 TSS from cDNA TSS information AT3G02560.2 5'->3' (+) Promoter sequence AT3G02555.1 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 AT3G02560.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 5 + 541747 -594

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	5	+	541747	-594

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 541750 -591

TSS clone G clone + 541752 -589

TSS clone C clone + 541753 -588

TSS clone C clone + 541754 -587

TSS clone T clone + 541755 -586

TSS clone C clone + 541757 -584

TSS clone T clone + 541759 -582

TSS clone C clone + 541766 -575

TSS clone A clone + 541786 -555

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	541750	-591
TSS clone	`G`	clone	+	541752	-589
TSS clone	`C`	clone	+	541753	-588
TSS clone	`C`	clone	+	541754	-587
TSS clone	`T`	clone	+	541755	-586
TSS clone	`C`	clone	+	541757	-584
TSS clone	`T`	clone	+	541759	-582
TSS clone	`C`	clone	+	541766	-575
TSS clone	`A`	clone	+	541786	-555

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 TTAATGGGCTA + 541608 541618 -733 -723

AtREG396 TTAATGGG    PPDB Motif GCCCA PLACE Motif TTAATGG

AtREG357 TAATGGGC   PPDB Motif GCCCA PLACE Motif

AtREG372   AATGGGCT PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG581    ATGGGCTA PPDB Motif GCCCA PLACE Motif TGGGCY

REG CATTGGGCCCATTG + 541636 541649 -705 -692

AtREG461 CATTGGGC       PPDB Motif GCCCA PLACE Motif

AtREG352 ATTGGGCC      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

AtREG361      GGCCCATT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG551       GCCCATTG PPDB Motif GCCCA PLACE Motif

REG TTTAACGGCCCATTT + 541652 541666 -689 -675

AtREG610 TTTAACGG        PPDB Motif PLACE Motif YAACKG, CNGTTR

AtREG377    AACGGCCC     PPDB Motif GCCCA, AAACG(C/G) PLACE Motif GGGCC

AtREG368     ACGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380      CGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361       GGCCCATT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG386        GCCCATTT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTAATGGGCTA`		+	541608	541618	-733	-723
	AtREG396	`TTAATGGG`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`
	AtREG357	`TAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG372	`AATGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG581	`ATGGGCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`CATTGGGCCCATTG`		+	541636	541649	-705	-692
	AtREG461	`CATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		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`
	AtREG361	`GGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG551	`GCCCATTG`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TTTAACGGCCCATTT`		+	541652	541666	-689	-675
	AtREG610	`TTTAACGG`		PPDB Motif		PLACE Motif	`YAACKG, CNGTTR`
	AtREG377	`AACGGCCC`		PPDB Motif	`GCCCA, AAACG(C/G)`	PLACE Motif	`GGGCC`
	AtREG368	`ACGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`CGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG361	`GGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG386	`GCCCATTT`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 8 - 541842 AT3G02555.1

TSS peak G 4 - 541512 AT3G02555.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	8	-	541842	AT3G02555.1
TSS peak	`G`	4	-	541512	AT3G02555.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone C clone - 541486 AT3G02555.1

TSS clone T clone - 541485 AT3G02555.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`C`	clone	-	541486	AT3G02555.1
TSS clone	`T`	clone	-	541485	AT3G02555.1

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 TTTCTTCTTCTCTTTC - 541474 541489 AT3G02555.1

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	`TTTCTTCTTCTCTTTC`	-	541474	541489	AT3G02555.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TAGCCCATTAA - 541608 541618 AT3G02555.1

AtREG581 TAGCCCAT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG372 AGCCCATT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG357   GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396    CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

REG CAATGGGCCCAATG - 541636 541649 AT3G02555.1

AtREG551 CAATGGGC       PPDB Motif GCCCA PLACE Motif

AtREG361 AATGGGCC      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

AtREG352      GGCCCAAT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG461       GCCCAATG PPDB Motif GCCCA PLACE Motif

REG AAATGGGCCGTTAAA - 541652 541666 AT3G02555.1

AtREG386 AAATGGGC        PPDB Motif GCCCA PLACE Motif

AtREG361 AATGGGCC       PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380   ATGGGCCG      PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG368    TGGGCCGT     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG377     GGGCCGTT    PPDB Motif GCCCA, AAACG(C/G) PLACE Motif GGGCC

AtREG610        CCGTTAAA PPDB Motif PLACE Motif YAACKG, CNGTTR