PlantPromoterDB promoter information of AT4G34670.1

Summary of Gene (AT4G34670.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G34670 TAIR NCBI
Gene model	AT4G34670.1
Description	40S ribosomal protein S3A (RPS3aB); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: in 6 components; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein S3Ae, conserved site (InterPro:IPR018281), Ribosomal protein S3Ae (InterPro:IPR001593); BEST Arabidopsis thaliana protein match is: 40S ribosomal protein S3A (RPS3aA) (TAIR:AT3G04840.1); Has 941 Blast hits to 936 proteins in 297 species: Archae - 150; Bacteria - 1; Metazoa - 370; Fungi - 111; Plants - 126; Viruses - 0; Other Eukaryotes - 183 (source: NCBI BLink).

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Overview

Focused view (chromosome 4: 16547724-16548923)

`Genome position from initiation codon` `TSS from cDNA TSS information AT4G34670.1 5'->3' (+) Promoter sequence AT4G34660.1 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 AT4G34670.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 47 + 16548655 -69

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	47	+	16548655	-69

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 16548647 -77

TSS clone T clone + 16548649 -75

TSS clone A clone + 16548651 -73

TSS clone C clone + 16548652 -72

TSS clone T clone + 16548653 -71

TSS clone G clone + 16548655 -69

TSS clone T clone + 16548656 -68

TSS clone T clone + 16548657 -67

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	16548647	-77
TSS clone	`T`	clone	+	16548649	-75
TSS clone	`A`	clone	+	16548651	-73
TSS clone	`C`	clone	+	16548652	-72
TSS clone	`T`	clone	+	16548653	-71
TSS clone	`G`	clone	+	16548655	-69
TSS clone	`T`	clone	+	16548656	-68
TSS clone	`T`	clone	+	16548657	-67

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 CATATATAAATG + 16548611 16548622 -113 -102

Y Patch CTTTCTCTC + 16548642 16548650 -82 -74

Y Patch CTTCTTCTTCTTCCTC + 16548665 16548680 -59 -44

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	`CATATATAAATG`	+	16548611	16548622	-113	-102
Y Patch	`CTTTCTCTC`	+	16548642	16548650	-82	-74
Y Patch	`CTTCTTCTTCTTCCTC`	+	16548665	16548680	-59	-44
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 ATATTGGGCTC + 16548509 16548519 -215 -205

AtREG509 ATATTGGG    PPDB Motif PLACE Motif

AtREG355 TATTGGGC   PPDB Motif GCCCA PLACE Motif

AtREG402   ATTGGGCT PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG533    TTGGGCTC PPDB Motif GCCCA PLACE Motif TGGGCY

REG AATAGCCCATTGGGCTTG + 16548525 16548542 -199 -182

AtREG584 AATAGCCC           PPDB Motif GCCCA PLACE Motif

AtREG581   TAGCCCAT         PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG372    AGCCCATT        PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG551     GCCCATTG       PPDB Motif GCCCA PLACE Motif

AtREG461        CATTGGGC    PPDB Motif GCCCA PLACE Motif

AtREG402         ATTGGGCT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407          TTGGGCTT PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG525           TGGGCTTG PPDB Motif GCCCA PLACE Motif TGGGCY

REG ACCCTAGA + 16548603 16548610 -121 -114

AtREG658 ACCCTAGA PPDB Motif ACCCT PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ATATTGGGCTC`		+	16548509	16548519	-215	-205
	AtREG509	`ATATTGGG`		PPDB Motif		PLACE Motif
	AtREG355	`TATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG402	`ATTGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG533	`TTGGGCTC`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`AATAGCCCATTGGGCTTG`		+	16548525	16548542	-199	-182
	AtREG584	`AATAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG581	`TAGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG372	`AGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG551	`GCCCATTG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG461	`CATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG402	`ATTGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`TTGGGCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG525	`TGGGCTTG`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`ACCCTAGA`		+	16548603	16548610	-121	-114
	AtREG658	`ACCCTAGA`		PPDB Motif	`ACCCT`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 10 - 16548462 AT4G34660.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	10	-	16548462	AT4G34660.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone - 16548439 AT4G34660.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	-	16548439	AT4G34660.1

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 GAGCCCAATAT - 16548509 16548519 AT4G34660.1

AtREG533 GAGCCCAA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG402 AGCCCAAT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG355   GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG509    CCCAATAT PPDB Motif PLACE Motif

REG CAAGCCCAATGGGCTATT - 16548525 16548542 AT4G34660.1

AtREG525 CAAGCCCA           PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407 AAGCCCAA          PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG402   AGCCCAAT         PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG461    GCCCAATG        PPDB Motif GCCCA PLACE Motif

AtREG551       CAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG372        AATGGGCT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG581         ATGGGCTA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG584           GGGCTATT PPDB Motif GCCCA PLACE Motif

REG TCTAGGGT - 16548603 16548610 AT4G34660.1

AtREG658 TCTAGGGT PPDB Motif ACCCT PLACE Motif

REG AAGCCCTA - 16548637 16548644 AT4G34660.1

AtREG651 AAGCCCTA PPDB Motif PLACE Motif