PlantPromoterDB promoter information of AT2G39390.1

Summary of Gene (AT2G39390.1)

Organism	Arabidopsis thaliana
Chromosome	2
Locus	AT2G39390 TAIR NCBI
Gene model	AT2G39390.1
Description	60S ribosomal protein L35 (RPL35B); FUNCTIONS IN: structural constituent of ribosome; INVOLVED IN: translation, ribosome biogenesis; LOCATED IN: cytosolic ribosome, cytosolic large ribosomal subunit, ribosome; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Ribosomal protein L29 (InterPro:IPR001854), Ribosomal protein L29, conserved site (InterPro:IPR018254); BEST Arabidopsis thaliana protein match is: 60S ribosomal protein L35 (RPL35D) (TAIR:AT5G02610.1); Has 796 Blast hits to 796 proteins in 298 species: Archae - 108; Bacteria - 128; Metazoa - 237; Fungi - 93; Plants - 90; Viruses - 0; Other Eukaryotes - 140 (source: NCBI BLink).

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Overview

Focused view (chromosome 2: 16452762-16451563)

`Genome position from initiation codon` `TSS from cDNA TSS information AT2G39390.1 5'->3' (-) Promoter sequence AT2G39400.1 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 AT2G39390.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 26 - 16451831 -69

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	26	-	16451831	-69

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone C clone - 16451835 -73

TSS clone T clone - 16451832 -70

TSS clone G clone - 16451830 -68

TSS clone A clone - 16451814 -52

TSS clone T clone - 16451813 -51

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`C`	clone	-	16451835	-73
TSS clone	`T`	clone	-	16451832	-70
TSS clone	`G`	clone	-	16451830	-68
TSS clone	`A`	clone	-	16451814	-52
TSS clone	`T`	clone	-	16451813	-51

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 CGTCTTCTTCTTC - 16451842 16451854 -80 -92

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	`CGTCTTCTTCTTC`	-	16451842	16451854	-80	-92
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 CAAAGCCCAAAT - 16451886 16451897 -124 -135

AtREG559 CAAAGCCC     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

AtREG421     GCCCAAAT PPDB Motif GCCCA PLACE Motif

REG TCAGCCCATTAG - 16451925 16451936 -163 -174

AtREG609 TCAGCCCA     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

REG TGGCCCATAA - 16451947 16451956 -185 -194

AtREG490 TGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364 GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG394   GCCCATAA PPDB Motif GCCCA PLACE Motif

REG CGGCGCGTGT - 16452051 16452060 -289 -298

AtREG538 CGGCGCGT   PPDB Motif ACGCGC PLACE Motif

AtREG486 GGCGCGTG PPDB Motif ACGCGC PLACE Motif

AtREG385   GCGCGTGT PPDB Motif ACGCGC PLACE Motif ACACNNG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CAAAGCCCAAAT`		-	16451886	16451897	-124	-135
	AtREG559	`CAAAGCCC`		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`
	AtREG421	`GCCCAAAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TCAGCCCATTAG`		-	16451925	16451936	-163	-174
	AtREG609	`TCAGCCCA`		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
REG	`TGGCCCATAA`		-	16451947	16451956	-185	-194
	AtREG490	`TGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG394	`GCCCATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CGGCGCGTGT`		-	16452051	16452060	-289	-298
	AtREG538	`CGGCGCGT`		PPDB Motif	`ACGCGC`	PLACE Motif
	AtREG486	`GGCGCGTG`		PPDB Motif	`ACGCGC`	PLACE Motif
	AtREG385	`GCGCGTGT`		PPDB Motif	`ACGCGC`	PLACE Motif	`ACACNNG`

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

TSS clone G clone + 16452643 AT2G39400.1

TSS clone peak C clone + 16452644 AT2G39400.1

TSS clone A clone + 16452652 AT2G39400.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	+	16452643	AT2G39400.1
TSS clone peak	`C`	clone	+	16452644	AT2G39400.1
TSS clone	`A`	clone	+	16452652	AT2G39400.1

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 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