PlantPromoterDB promoter information of AT3G53740.4

Summary of Gene (AT3G53740.4)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G53740 TAIR NCBI
Gene model	AT3G53740.4
Description	60S ribosomal protein L36 (RPL36B); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic ribosome, cytosolic large ribosomal subunit, ribosome, plasma membrane, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L36e (InterPro:IPR000509); BEST Arabidopsis thaliana protein match is: 60S ribosomal protein L36 (RPL36A) (TAIR:AT2G37600.2); Has 586 Blast hits to 586 proteins in 196 species: Archae - 0; Bacteria - 0; Metazoa - 295; Fungi - 95; Plants - 95; Viruses - 0; Other Eukaryotes - 101 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 19915813-19914614)

`Genome position from initiation codon` `AT3G53740.1 AT3G53740.2 AT3G53740.3 TSS from cDNA TSS information AT3G53740.4 5'->3' (-) Promoter sequence AT3G53750.1 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 AT3G53740.4

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 8 - 19914992 -179

TSS peak G 8 - 19914977 -164

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	8	-	19914992	-179
TSS peak	`G`	8	-	19914977	-164

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 19914992 -179

TSS clone T clone - 19914991 -178

TSS clone C clone - 19914989 -176

TSS clone T clone - 19914988 -175

TSS clone T clone - 19914980 -167

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	19914992	-179
TSS clone	`T`	clone	-	19914991	-178
TSS clone	`C`	clone	-	19914989	-176
TSS clone	`T`	clone	-	19914988	-175
TSS clone	`T`	clone	-	19914980	-167

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 GTATATATACA - 19915014 19915024 -201 -211

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	`GTATATATACA`	-	19915014	19915024	-201	-211
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 ATAAGGCCCAATAAAAGCCCAAAC - 19915055 19915078 -242 -265

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

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

AtREG549            TAAAAGCC      PPDB Motif PLACE Motif

AtREG409             AAAAGCCC     PPDB Motif GCCCA PLACE Motif

AtREG376              AAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407               AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG469                AGCCCAAA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG474                 GCCCAAAC PPDB Motif GCCCA PLACE Motif

REG CGGTTAAG - 19915164 19915171 -351 -358

AtREG605 CGGTTAAG PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG AAATGACG - 19915217 19915224 -404 -411

AtREG657 AAATGACG PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ATAAGGCCCAATAAAAGCCCAAAC`		-	19915055	19915078	-242	-265
	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`
	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
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
	AtREG409	`AAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG469	`AGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG474	`GCCCAAAC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CGGTTAAG`		-	19915164	19915171	-351	-358
	AtREG605	`CGGTTAAG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
REG	`AAATGACG`		-	19915217	19915224	-404	-411
	AtREG657	`AAATGACG`		PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 8 + 19915321 AT3G53750.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	8	+	19915321	AT3G53750.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 19915318 AT3G53750.1

TSS clone T clone + 19915322 AT3G53750.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	19915318	AT3G53750.1
TSS clone	`T`	clone	+	19915322	AT3G53750.1

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 TCTCCTTC + 19915354 19915361 AT3G53750.1

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	`TCTCCTTC`	+	19915354	19915361	AT3G53750.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG GTTTGGGCTTTTATTGGGCCTTAT + 19915055 19915078 AT3G53750.1

AtREG474 GTTTGGGC                 PPDB Motif GCCCA PLACE Motif

AtREG469 TTTGGGCT                PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407   TTGGGCTT               PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG376    TGGGCTTT              PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG409     GGGCTTTT             PPDB Motif GCCCA PLACE Motif

AtREG549      GGCTTTTA            PPDB Motif PLACE Motif

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

AtREG351                GGGCCTTA PPDB Motif GCCCA PLACE Motif GGGCC

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

REG CTTAACCG + 19915164 19915171 AT3G53750.1

AtREG605 CTTAACCG PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG CGTCATTT + 19915217 19915224 AT3G53750.1

AtREG657 CGTCATTT PPDB Motif PLACE Motif