PlantPromoterDB promoter information of AT5G04800.3

Summary of Gene (AT5G04800.3)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G04800 TAIR NCBI
Gene model	AT5G04800.3
Description	40S ribosomal protein S17 (RPS17D); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: ribosome, intracellular; EXPRESSED IN: male gametophyte, pollen tube; EXPRESSED DURING: L mature pollen stage, M germinated pollen stage; CONTAINS InterPro DOMAIN/s: Ribosomal protein S17e (InterPro:IPR001210), Ribosomal protein S17e, conserved site (InterPro:IPR018273); BEST Arabidopsis thaliana protein match is: 40S ribosomal protein S17 (RPS17A) (TAIR:AT2G04390.1); Has 727 Blast hits to 727 proteins in 257 species: Archae - 117; Bacteria - 0; Metazoa - 270; Fungi - 98; Plants - 83; Viruses - 0; Other Eukaryotes - 159 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 1388217-1389416)

`Genome position from initiation codon` `AT5G04800.1 AT5G04800.2 AT5G04800.4 TSS from cDNA TSS information AT5G04800.3 5'->3' (+) Promoter sequence AT5G04790.1 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 AT5G04800.3

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 31 + 1388488 -729

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	31	+	1388488	-729

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone + 1388485 -732

TSS clone T clone + 1388486 -731

TSS clone G clone + 1388488 -729

TSS clone C clone + 1388489 -728

TSS clone C clone + 1388490 -727

TSS clone G clone + 1388491 -726

TSS clone C clone + 1388492 -725

TSS clone G clone + 1388496 -721

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	1388485	-732
TSS clone	`T`	clone	+	1388486	-731
TSS clone	`G`	clone	+	1388488	-729
TSS clone	`C`	clone	+	1388489	-728
TSS clone	`C`	clone	+	1388490	-727
TSS clone	`G`	clone	+	1388491	-726
TSS clone	`C`	clone	+	1388492	-725
TSS clone	`G`	clone	+	1388496	-721

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 TTTATATAGA + 1388457 1388466 -760 -751

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	`TTTATATAGA`	+	1388457	1388466	-760	-751
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 AATAGGCCCAACA + 1388403 1388415 -814 -802

AtREG424 AATAGGCC      PPDB Motif PLACE Motif

AtREG362 ATAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358   TAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356    AGGCCCAA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG449     GGCCCAAC PPDB Motif GCCCA, CCAACGG PLACE Motif GGGCC, TGGGCY

AtREG543      GCCCAACA PPDB Motif GCCCA PLACE Motif CAACA

REG TAGGGCCCATTAA + 1388431 1388443 -786 -774

AtREG387 TAGGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG400 AGGGCCCA     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

AtREG357     GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396      CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AATAGGCCCAACA`		+	1388403	1388415	-814	-802
	AtREG424	`AATAGGCC`		PPDB Motif		PLACE Motif
	AtREG362	`ATAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG449	`GGCCCAAC`		PPDB Motif	`GCCCA, CCAACGG`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG543	`GCCCAACA`		PPDB Motif	`GCCCA`	PLACE Motif	`CAACA`
REG	`TAGGGCCCATTAA`		+	1388431	1388443	-786	-774
	AtREG387	`TAGGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG400	`AGGGCCCA`		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`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG396	`CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone peak A clone + 1389308 AT5G04810.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`A`	clone	+	1389308	AT5G04810.1

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 None None None