Schema for CORE Promoters - Promoters Annotated by the CORE Database

Database: dm6 Primary Table: coreHoskins Data last updated: 2018-02-19
Big Bed File: /gbdb/dm6/bbi/coreHoskins.bb
Item Count: 13,964
Format description: CORE annotations for CAGE-defined TSSs from Hoskins et al.

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15731730	Start position in chromosome
`chromEnd`	15731831	End position in chromosome
`name`	CycE_1	Short Name of item
`score`	0	Score from 0-1000
`strand`	-	+ or -
`thickStart`	15731730	Start of where display should be thick (start codon)
`thickEnd`	15731831	End of where display should be thick (stop codon)
`reserved`	0,68,27	Used as itemRgb as of 2004-11-22
`peakShape`	Broad	Peak shape
`BREu`	no	BREu motifs
`TATA`	no	TATA Box motifs
`BREd`	no	BREd motifs
`dInr`	-1,0.9401;	Inr motifs
`DPE`	-1,0.0175;	DPE motifs
`MTE`	no	MTE motifs
`Bridge`	no	BREu motifs
`dTCT`	no	TCT motifs

Sample Rows

chrom	chromStart	chromEnd	name	strand	thickStart	thickEnd	reserved	peakShape	BREu	TATA	BREd	dInr	DPE	MTE	Bridge	dTCT
chr2L	15731730	15731831	CycE_1	-	15731730	15731831	0,68,27	Broad	no	no	no	-1,0.9401;	-1,0.0175;	no	no	no
chr2L	15740821	15740922	CycE_2	-	15740821	15740922	77,77,77	Unclassified	no	no	no	3,0.0702;	no	no	no	no
chr2L	15746558	15746659	CycE_3	-	15746558	15746659	64,0,75	Peaked	no	no	no	-2,0.0172;	-2,0.0160;	no	-2,0.0134;	no
chr2L	15748072	15748173	CycE_4	-	15748072	15748173	0,68,27	Broad	no	no	no	1,0.0446;	no	no	no	no
chr2L	15750977	15751078	l(2)35Di_1	-	15750977	15751078	0,68,27	Broad	no	no	no	-6,0.0116;	no	no	no	no
chr2L	15752243	15752344	l(2)35Df_1	+	15752243	15752344	0,68,27	Broad	no	no	no	no	no	no	no	no
chr2L	15760523	15760624	Gli_1	-	15760523	15760624	77,77,77	Unclassified	no	no	no	no	no	no	no	no
chr2L	15762357	15762458	Gli_2	-	15762357	15762458	77,77,77	Unclassified	no	no	-21,0.9317;	-2,1.0000;	no	no	-2,0.0237;	no
chr2L	15762705	15762806	Gli_3	-	15762705	15762806	64,0,75	Peaked	no	no	no	-1,0.9401;	-1,0.1397;	-1,0.0142;	-1,0.0308;	no
chr2L	15764209	15764310	CG3793_1	+	15764209	15764310	0,68,27	Broad	no	no	no	no	no	no	no	no

CORE Promoters (CORE) Track Description

Description

These tracks show the Drosophila promoter annotations from the CORE database. The TSS annotations in the CORE database were based on CAGE data (Hoskins RA et al., 2011) or RNA-Seq data (Nechaev S et al., 2010). The core promoter motifs associated with each TSS were identified by the ElemeNT program.

For the CAGE TSSs track, the color of the feature corresponds to the shape of the promoter:

Promoter Shape	Color
Peaked
Broad
Unclassified

References

Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T. ElemeNT: a computational tool for detecting core promoter elements. Transcription. 2015;6(3):41-50.

Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb;21(2):182-92.

Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science. 2010 Jan 15;327(5963):335-8.