PlantPromoterDB promoter information of AT3G24830.1

Summary of Gene (AT3G24830.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G24830 TAIR NCBI
Gene model	AT3G24830.1
Description	60S ribosomal protein L13A (RPL13aB); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic ribosome, cytosolic large ribosomal subunit, large ribosomal subunit, membrane; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L13 (InterPro:IPR005822), Ribosomal protein L13, eukaryotic/archaeal (InterPro:IPR005755); BEST Arabidopsis thaliana protein match is: 60S ribosomal protein L13A (RPL13aA) (TAIR:AT3G07110.1); Has 1473 Blast hits to 1473 proteins in 438 species: Archae - 212; Bacteria - 283; Metazoa - 292; Fungi - 127; Plants - 164; Viruses - 0; Other Eukaryotes - 395 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 9063613-9064812)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G24830.1 5'->3' (+) Promoter sequence AT3G24820.1 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 AT3G24830.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 13 + 9064572 -41

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	13	+	9064572	-41

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone + 9064561 -52

TSS clone A clone + 9064562 -51

TSS clone A clone + 9064564 -49

TSS clone T clone + 9064565 -48

TSS clone C clone + 9064566 -47

TSS clone T clone + 9064567 -46

TSS clone G clone + 9064572 -41

TSS clone A clone + 9064573 -40

TSS clone A clone + 9064576 -37

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	9064561	-52
TSS clone	`A`	clone	+	9064562	-51
TSS clone	`A`	clone	+	9064564	-49
TSS clone	`T`	clone	+	9064565	-48
TSS clone	`C`	clone	+	9064566	-47
TSS clone	`T`	clone	+	9064567	-46
TSS clone	`G`	clone	+	9064572	-41
TSS clone	`A`	clone	+	9064573	-40
TSS clone	`A`	clone	+	9064576	-37

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 TCATATATAAAG + 9064530 9064541 -83 -72

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	`TCATATATAAAG`	+	9064530	9064541	-83	-72
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 AAATGGGCCTGG + 9064427 9064438 -186 -175

AtREG386 AAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG361 AATGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   ATGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG370    TGGGCCTG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG619     GGGCCTGG PPDB Motif GCCCA PLACE Motif GGGCC

REG TACTGGGCTACTGGGCCTTAT + 9064450 9064470 -163 -143

AtREG434 TACTGGGCTACTGGGC      PPDB Motif GCCCA PLACE Motif

AtREG384          ACTGGGCC     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG410           CTGGGCCT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353            TGGGCCTT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG351             GGGCCTTA PPDB Motif GCCCA PLACE Motif GGGCC

AtREG425              GGCCTTAT PPDB Motif AACCG(G/A) PLACE Motif

REG AAAAGGCCCAATAA + 9064480 9064493 -133 -120

AtREG459 AAAAGGCC       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

AtREG352     GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355      GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG417       CCCAATAA PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`AAATGGGCCTGG`		+	9064427	9064438	-186	-175
	AtREG386	`AAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG370	`TGGGCCTG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG619	`GGGCCTGG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`TACTGGGCTACTGGGCCTTAT`		+	9064450	9064470	-163	-143
	AtREG434	`TACTGGGCTACTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG384	`ACTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG410	`CTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG353	`TGGGCCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG351	`GGGCCTTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG425	`GGCCTTAT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`AAAAGGCCCAATAA`		+	9064480	9064493	-133	-120
	AtREG459	`AAAAGGCC`		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`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 5 - 9064378 AT3G24820.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	5	-	9064378	AT3G24820.1

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 TTCTTCTTCTTCTTC - 9064379 9064393 AT3G24820.1

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	`TTCTTCTTCTTCTTC`	-	9064379	9064393	AT3G24820.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG CCAGGCCCATTT - 9064427 9064438 AT3G24820.1

AtREG619 CCAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG370 CAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   AGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361    GGCCCATT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG386     GCCCATTT PPDB Motif GCCCA PLACE Motif

REG ATAAGGCCCAGTAGCCCAGTA - 9064450 9064470 AT3G24820.1

AtREG425 ATAAGGCC              PPDB Motif AACCG(G/A) PLACE Motif

AtREG351 TAAGGCCC             PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353   AAGGCCCA            PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG410    AGGCCCAG           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG384     GGCCCAGT          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG434      GCCCAGTAGCCCAGTA PPDB Motif GCCCA PLACE Motif

REG TTATTGGGCCTTTT - 9064480 9064493 AT3G24820.1

AtREG417 TTATTGGG       PPDB Motif GCCCA PLACE Motif

AtREG355 TATTGGGC      PPDB Motif GCCCA PLACE Motif

AtREG352   ATTGGGCC     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356    TTGGGCCT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353     TGGGCCTT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG359      GGGCCTTT PPDB Motif GCCCA PLACE Motif GGGCC

AtREG459       GGCCTTTT PPDB Motif PLACE Motif

REG AACGACACG - 9064643 9064651 AT3G24820.1

AtREG527 AACGACAC DREB1Aox PPDB Motif PLACE Motif

AtREG428 ACGACACG ABA, DREB1Aox, Ethylene, Drought PPDB Motif PLACE Motif

REG GTGACGTG - 9064659 9064666 AT3G24820.1

AtREG466 GTGACGTG ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG