PlantPromoterDB promoter information of AT3G54210.1

Summary of Gene (AT3G54210.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G54210 TAIR NCBI
Gene model	AT3G54210.1
Description	ribosomal protein L17 family protein; FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: ribosome, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L17 (InterPro:IPR000456); BEST Arabidopsis thaliana protein match is: ribosomal protein L17 family protein (TAIR:AT5G09770.1); Has 5385 Blast hits to 5385 proteins in 1530 species: Archae - 0; Bacteria - 3017; Metazoa - 102; Fungi - 83; Plants - 73; Viruses - 0; Other Eukaryotes - 2110 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 20069385-20068186)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G54210.1 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 AT3G54210.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 26 - 20068431 -46

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	26	-	20068431	-46

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 20068434 -49

TSS clone C clone - 20068433 -48

TSS clone A clone - 20068431 -46

TSS clone T clone - 20068430 -45

TSS clone C clone - 20068410 -25

TSS clone G clone - 20068406 -21

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	20068434	-49
TSS clone	`C`	clone	-	20068433	-48
TSS clone	`A`	clone	-	20068431	-46
TSS clone	`T`	clone	-	20068430	-45
TSS clone	`C`	clone	-	20068410	-25
TSS clone	`G`	clone	-	20068406	-21

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 CTCTTCCTCT - 20068443 20068452 -58 -67

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	`CTCTTCCTCT`	-	20068443	20068452	-58	-67
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 TATAGGCCCATTAAGGCCCATCA - 20068476 20068498 -91 -113

AtREG487 TATAGGCC                PPDB Motif PLACE Motif

AtREG362 ATAGGCCC               PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358   TAGGCCCA              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    AGGCCCAT  AGGCCCAT   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

AtREG604        CCATTAAG         PPDB Motif PLACE Motif TTAATGG

AtREG416           TTAAGGCC      PPDB Motif PLACE Motif

AtREG351            TAAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353             AAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG403               GGCCCATC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG635                GCCCATCA PPDB Motif GCCCA PLACE Motif

REG AGCCCAAAT - 20068568 20068576 -183 -191

AtREG469 AGCCCAAA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG421 GCCCAAAT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TATAGGCCCATTAAGGCCCATCA`		-	20068476	20068498	-91	-113
	AtREG487	`TATAGGCC`		PPDB Motif		PLACE Motif
	AtREG362	`ATAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT AGGCCCAT`		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`
	AtREG604	`CCATTAAG`		PPDB Motif		PLACE Motif	`TTAATGG`
	AtREG416	`TTAAGGCC`		PPDB Motif		PLACE Motif
	AtREG351	`TAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG403	`GGCCCATC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG635	`GCCCATCA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`AGCCCAAAT`		-	20068568	20068576	-183	-191
	AtREG469	`AGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG421	`GCCCAAAT`		PPDB Motif	`GCCCA`	PLACE Motif

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