Schema for EPDnew Promoters - D. melanogaster Curated Promoter Database (EPDnew)

Database: dm6 Primary Table: EPDnew Data last updated: 2018-01-08
Big Bed File: /gbdb/dm6/bbi/Dmel_EPDnew.bb
Item Count: 16,972
Format description: Browser extensible data, with extended fields for type of promoter

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731769	Start position in chromosome
`chromEnd`	15731829	End position in chromosome
`name`	CycE_2	Short Name of item
`score`	900	Score from 0-1000
`strand`	-	+ or -
`thickStart`	15731769	Start of transcribed region
`thickEnd`	15731780	The 10bp downstream of the initiation site
`promoterType`	region	Type of initiation site
`motifs`	Inr	Motifs associated with the initiation site

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	promoterType	motifs
chr2L	15731769	15731829	CycE_2	900	-	15731769	15731780	region	Inr
chr2L	15746598	15746658	CG1E_1	900	-	15746598	15746609	region	GC,Inr
chr2L	15748112	15748172	CycE_1	900	-	15748112	15748123	region	Inr
chr2L	15751060	15751120	l(2)35Di_1	900	-	15751060	15751071	region	TATA
chr2L	15752244	15752304	CG4152_1	900	+	15752293	15752304	region	Inr
chr2L	15762397	15762457	Gli_2	900	-	15762397	15762408	region	Inr
chr2L	15762744	15762804	Gli_1	900	-	15762744	15762755	region	Inr
chr2L	15764181	15764241	CG3793_1	900	+	15764230	15764241	region	NA
chr2L	15768290	15768350	wek_1	900	-	15768290	15768301	region	NA
chr2L	15771125	15771185	Ku80_1	900	-	15771125	15771136	region	NA

EPDnew Promoters (EPDnew) Track Description


	Description This track shows the D. melanogaster promoter elements that have been annotated by the Eukaryotic Promoter Database (EPDnew). EPDnew defines four types of transcription initiation sites (see the EPD User Manual for details): Single initiation site: >90% of all reported transcripts initiate within 10 bp Multiple initiation sites: >75% of all reported transcripts initiate within 20 bp Initiation region: >75% of all reported transcripts initiate within 100 bp Undefined: Undefined transcription initiation pattern Methods The protocol used to create version 005 of the D. melanogaster curated promoter database is available through the TSS assembly pipeline for Dm_EPDnew_005 page on the EPD web site. References The D. melanogaster EPDnew dataset is available for download through the EPDnew FTP site. Dreos R, Ambrosini G, Périer RC, Bucher P. The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. Nucleic Acids Res. 2015 Jan;43(Database issue):D92-6.

Description

Methods

References