PlantPromoterDB promoter information of AT1G28060.1

Summary of Gene (AT1G28060.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G28060 TAIR NCBI
Gene model	AT1G28060.1
Description	small nuclear ribonucleoprotein family protein / snRNP family protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Pre-mRNA-splicing factor 3 (InterPro:IPR013881); BEST Arabidopsis thaliana protein match is: RNA splicing factor-related (TAIR:AT3G55930.1); Has 21413 Blast hits to 11192 proteins in 554 species: Archae - 18; Bacteria - 874; Metazoa - 11490; Fungi - 2755; Plants - 1540; Viruses - 94; Other Eukaryotes - 4642 (source: NCBI BLink).

#

Overview

Focused view (chromosome 1: 9778167-9779366)

`Genome position from initiation codon` `TSS from cDNA TSS information AT1G28060.1 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 AT1G28060.1

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 + 9779138 -29

TSS clone peak T clone + 9779140 -27

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`G`	clone	+	9779138	-29
TSS clone peak	`T`	clone	+	9779140	-27

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 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	None	None	None
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 TAAAAGCCCATTAG + 9778866 9778879 -301 -288

AtREG549 TAAAAGCC       PPDB Motif PLACE Motif

AtREG409 AAAAGCCC      PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378    AAGCCCAT    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 AAATGGGCTTCAGCCCATAA + 9778917 9778936 -250 -231

AtREG386 AAATGGGC             PPDB Motif GCCCA PLACE Motif

AtREG372 AATGGGCT            PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378   ATGGGCTT           PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG476    TGGGCTTC          PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG609          TCAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG477            AGCCCATA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG394             GCCCATAA PPDB Motif GCCCA PLACE Motif

REG GTCGTTTT + 9779052 9779059 -115 -108

AtREG520 GTCGTTTT PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TAAAAGCCCATTAG`		+	9778866	9778879	-301	-288
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
	AtREG409	`AAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`AAGCCCAT`		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	`AAATGGGCTTCAGCCCATAA`		+	9778917	9778936	-250	-231
	AtREG386	`AAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG372	`AATGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`ATGGGCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG476	`TGGGCTTC`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG609	`TCAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG477	`AGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG394	`GCCCATAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GTCGTTTT`		+	9779052	9779059	-115	-108
	AtREG520	`GTCGTTTT`		PPDB Motif		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