PlantPromoterDB promoter information of AT3G02190.1

Summary of Gene (AT3G02190.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G02190 TAIR NCBI
Gene model	AT3G02190.1
Description	60S ribosomal protein L39 (RPL39B); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation; LOCATED IN: cytosolic large ribosomal subunit, ribosome; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L39e (InterPro:IPR000077); BEST Arabidopsis thaliana protein match is: 60S ribosomal protein L39 (RPL39C) (TAIR:AT4G31985.1); Has 607 Blast hits to 607 proteins in 229 species: Archae - 157; Bacteria - 0; Metazoa - 212; Fungi - 79; Plants - 70; Viruses - 0; Other Eukaryotes - 89 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 407342-406143)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G02190.1 5'->3' (-) Promoter sequence AT3G02200.1 AT3G02200.2 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 AT3G02190.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone peak G clone - 406396 -54

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`G`	clone	-	406396	-54

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 CCCTTATAAAAA - 406427 406438 -85 -96

Y Patch TTCTTCCTC - 406413 406421 -71 -79

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	`CCCTTATAAAAA`	-	406427	406438	-85	-96
Y Patch	`TTCTTCCTC`	-	406413	406421	-71	-79
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 TCCAACGGTC - 406461 406470 -119 -128

AtREG554 TCCAACGG   PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

AtREG553   CAACGGTC Auxin PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG TCTGACGG - 406491 406498 -149 -156

AtREG622 TCTGACGG PPDB Motif PLACE Motif

REG ACGGTTTAC - 406502 406510 -160 -168

AtREG652 ACGGTTTA PPDB Motif PLACE Motif

AtREG519 CGGTTTAC PPDB Motif AACCG(G/A) PLACE Motif

REG TAACCGGAA - 406532 406540 -190 -198

AtREG621 TAACCGGA PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG534 AACCGGAA PPDB Motif AACCG(G/A) PLACE Motif

REG TTTCCGGTTAAA - 406543 406554 -201 -212

AtREG644 TTTCCGGT     PPDB Motif AACCG(G/A) PLACE Motif

AtREG534 TTCCGGTT    PPDB Motif AACCG(G/A) PLACE Motif

AtREG621   TCCGGTTA   PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG501    CCGGTTAA PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG645     CGGTTAAA PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG TCCGGTTT - 406676 406683 -334 -341

AtREG521 TCCGGTTT PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TCCAACGGTC`		-	406461	406470	-119	-128
	AtREG554	`TCCAACGG`		PPDB Motif	`CCAACGG`	PLACE Motif	`YAACKG, CNGTTR`
	AtREG553	`CAACGGTC`	Auxin	PPDB Motif	`CCAACGG`	PLACE Motif	`YAACKG, CNGTTR`
REG	`TCTGACGG`		-	406491	406498	-149	-156
	AtREG622	`TCTGACGG`		PPDB Motif		PLACE Motif
REG	`ACGGTTTAC`		-	406502	406510	-160	-168
	AtREG652	`ACGGTTTA`		PPDB Motif		PLACE Motif
	AtREG519	`CGGTTTAC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TAACCGGAA`		-	406532	406540	-190	-198
	AtREG621	`TAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG534	`AACCGGAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TTTCCGGTTAAA`		-	406543	406554	-201	-212
	AtREG644	`TTTCCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`TTCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG621	`TCCGGTTA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG501	`CCGGTTAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG645	`CGGTTAAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
REG	`TCCGGTTT`		-	406676	406683	-334	-341
	AtREG521	`TCCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 17 + 406602 AT3G02200.1, AT3G02200.2

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	17	+	406602	AT3G02200.1, AT3G02200.2

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 406596 AT3G02200.1, AT3G02200.2

TSS clone T clone + 406598 AT3G02200.1, AT3G02200.2

TSS clone G clone + 406602 AT3G02200.1, AT3G02200.2

TSS clone T clone + 406603 AT3G02200.1, AT3G02200.2

TSS clone T clone + 406605 AT3G02200.1, AT3G02200.2

TSS clone T clone + 406607 AT3G02200.1, AT3G02200.2

TSS clone C clone + 406609 AT3G02200.1, AT3G02200.2

TSS clone G clone + 406619 AT3G02200.1, AT3G02200.2

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	406596	AT3G02200.1, AT3G02200.2
TSS clone	`T`	clone	+	406598	AT3G02200.1, AT3G02200.2
TSS clone	`G`	clone	+	406602	AT3G02200.1, AT3G02200.2
TSS clone	`T`	clone	+	406603	AT3G02200.1, AT3G02200.2
TSS clone	`T`	clone	+	406605	AT3G02200.1, AT3G02200.2
TSS clone	`T`	clone	+	406607	AT3G02200.1, AT3G02200.2
TSS clone	`C`	clone	+	406609	AT3G02200.1, AT3G02200.2
TSS clone	`G`	clone	+	406619	AT3G02200.1, AT3G02200.2

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box ATATAGAG + 406563 406570 AT3G02200.1, AT3G02200.2

Y Patch TTTCTTCTCTCTCTCTT + 406585 406601 AT3G02200.1, AT3G02200.2

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	`ATATAGAG`	+	406563	406570	AT3G02200.1, AT3G02200.2
Y Patch	`TTTCTTCTCTCTCTCTT`	+	406585	406601	AT3G02200.1, AT3G02200.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG CAGCGTTT + 406378 406385 AT3G02200.1, AT3G02200.2

AtREG626 CAGCGTTT PPDB Motif AAACG(C/G) PLACE Motif

REG GACCGTTGGA + 406461 406470 AT3G02200.1, AT3G02200.2

AtREG553 GACCGTTG   Auxin PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

AtREG554   CCGTTGGA PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG CCGTCAGA + 406491 406498 AT3G02200.1, AT3G02200.2

AtREG622 CCGTCAGA PPDB Motif PLACE Motif

REG GTAAACCGT + 406502 406510 AT3G02200.1, AT3G02200.2

AtREG519 GTAAACCG PPDB Motif AACCG(G/A) PLACE Motif

AtREG652 TAAACCGT PPDB Motif PLACE Motif

REG TTCCGGTTA + 406532 406540 AT3G02200.1, AT3G02200.2

AtREG534 TTCCGGTT PPDB Motif AACCG(G/A) PLACE Motif

AtREG621 TCCGGTTA PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

REG TTTAACCGGAAA + 406543 406554 AT3G02200.1, AT3G02200.2

AtREG645 TTTAACCG     PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG501 TTAACCGG    PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG621   TAACCGGA   PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

AtREG534    AACCGGAA PPDB Motif AACCG(G/A) PLACE Motif

AtREG644     ACCGGAAA PPDB Motif AACCG(G/A) PLACE Motif