PlantPromoterDB promoter information of AT5G39740

Summary of Gene (AT5G39740)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G39740 TAIR NCBI
Gene model	AT5G39740
Description	60S ribosomal protein L5 (RPL5B); FUNCTIONS IN: structural constituent of ribosome, 5S rRNA binding; INVOLVED IN: translation, ribosome biogenesis; LOCATED IN: in 6 components; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L5, eukaryotic (InterPro:IPR005485), Ribosomal protein L18/L5 (InterPro:IPR005484); BEST Arabidopsis thaliana protein match is: ATL5 (A. THALIANA RIBOSOMAL PROTEIN L5); 5S rRNA binding / structural constituent of ribosome (TAIR:AT3G25520.1); Has 941 Blast hits to 940 proteins in 333 species: Archae - 245; Bacteria - 6; Metazoa - 326; Fungi - 108; Plants - 79; Viruses - 0; Other Eukaryotes - 177 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 15902365-15903564)

`Genome position from initiation codon` `AT5G39730.1 AT5G39740.1 TSS from cDNA TSS information AT5G39740 5'->3' (+) Promoter sequence 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 AT5G39740

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 31 + 15903323 -42

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	31	+	15903323	-42

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 15903297 -68

TSS clone G clone + 15903323 -42

TSS clone C clone + 15903324 -41

TSS clone G clone + 15903325 -40

TSS clone C clone + 15903326 -39

TSS clone C clone + 15903327 -38

TSS clone T clone + 15903328 -37

TSS clone C clone + 15903329 -36

TSS clone T clone + 15903330 -35

TSS clone C clone + 15903333 -32

TSS clone T clone + 15903336 -29

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	15903297	-68
TSS clone	`G`	clone	+	15903323	-42
TSS clone	`C`	clone	+	15903324	-41
TSS clone	`G`	clone	+	15903325	-40
TSS clone	`C`	clone	+	15903326	-39
TSS clone	`C`	clone	+	15903327	-38
TSS clone	`T`	clone	+	15903328	-37
TSS clone	`C`	clone	+	15903329	-36
TSS clone	`T`	clone	+	15903330	-35
TSS clone	`C`	clone	+	15903333	-32
TSS clone	`T`	clone	+	15903336	-29

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 TTAAAGGCCCAAATATAAAGCCCATTAGGCCTATA + 15903163 15903197 -202 -168

AtREG639 TTAAAGGC                            PPDB Motif AAACG(C/G) PLACE Motif

AtREG467 TAAAGGCC                           PPDB Motif PLACE Motif

AtREG359   AAAGGCCC                          PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353    AAGGCCCA                         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356     AGGCCCAA                        PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG373      GGCCCAAA                       PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG421       GCCCAAAT                      PPDB Motif GCCCA PLACE Motif

AtREG601               ATAAAGCC              PPDB Motif PLACE Motif

AtREG365                TAAAGCCC             PPDB Motif GCCCA PLACE Motif

AtREG376                 AAAGCCCA            PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378                  AAGCCCAT           PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG372                   AGCCCATT          PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG357                    GCCCATTA         PPDB Motif GCCCA PLACE Motif

AtREG558                     CCCATTAG        PPDB Motif GCCCA PLACE Motif

AtREG506                        ATTAGGCC     PPDB Motif PLACE Motif

AtREG649                           AGGCCTAT PPDB Motif PLACE Motif

AtREG487                            GGCCTATA PPDB Motif PLACE Motif

REG GACCGTTG + 15903216 15903223 -149 -142

AtREG553 GACCGTTG Auxin PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG TAAGCCCAC + 15903233 15903241 -132 -124

AtREG426 TAAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG518 AAGCCCAC PPDB Motif GCCCA PLACE Motif TGGGCY

REG GAGCCCAA + 15903266 15903273 -99 -92

AtREG533 GAGCCCAA PPDB Motif GCCCA PLACE Motif TGGGCY

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTAAAGGCCCAAATATAAAGCCCATTAGGCCTATA`		+	15903163	15903197	-202	-168
	AtREG639	`TTAAAGGC`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG467	`TAAAGGCC`		PPDB Motif		PLACE Motif
	AtREG359	`AAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`AGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG373	`GGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG421	`GCCCAAAT`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG601	`ATAAAGCC`		PPDB Motif		PLACE Motif
	AtREG365	`TAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`AAGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG372	`AGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG558	`CCCATTAG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG506	`ATTAGGCC`		PPDB Motif		PLACE Motif
	AtREG649	`AGGCCTAT`		PPDB Motif		PLACE Motif
	AtREG487	`GGCCTATA`		PPDB Motif		PLACE Motif
REG	`GACCGTTG`		+	15903216	15903223	-149	-142
	AtREG553	`GACCGTTG`	Auxin	PPDB Motif	`CCAACGG`	PLACE Motif	`YAACKG, CNGTTR`
REG	`TAAGCCCAC`		+	15903233	15903241	-132	-124
	AtREG426	`TAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG518	`AAGCCCAC`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`GAGCCCAA`		+	15903266	15903273	-99	-92
	AtREG533	`GAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`

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

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

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