Schema for DGRP TE Insertions (TEMP) - Transposon Insertions in DGRP Lines Identified by TEMP

Database: dm6 Primary Table: dgrp_temp_te Row Count: 25,690 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5755	`int(10) unsigned`	range
`chromEnd`	5794	`int(10) unsigned`	range
`name`	FBgn0001210_hobo	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	5755	`int(10) unsigned`	range
`thickEnd`	5794	`int(10) unsigned`	range
`itemRgb`	8388608	`int(10) unsigned`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb
585	chr2L	5755	5794	FBgn0001210_hobo	1	+	5755	5794	128,0,0
585	chr2L	7996	8015	FBgn0000155_roo	1	-	7996	8015	0,0,200
585	chr2L	9102	9120	FBgn0000155_roo	2	+	9102	9120	0,0,200
585	chr2L	18386	18550	FBgn0003055_P-element	1	+	18386	18550	128,0,0
585	chr2L	19111	19125	FBgn0001283_jockey	1	+	19111	19125	0,0,128
585	chr2L	28395	28399	FBgn0005673_1360	2	-	28395	28399	128,0,0
585	chr2L	43029	43041	FBgn0003122_pogo	1	+	43029	43041	128,0,0
585	chr2L	45174	45178	FBgn0005673_1360	1	+	45174	45178	128,0,0
585	chr2L	45819	45830	FBgn0000155_roo	1	-	45819	45830	0,0,200
585	chr2L	46233	46248	FBgn0000155_roo	1	-	46233	46248	0,0,200

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

DGRP TE Insertions (TEMP) (dgrp_temp_te) Track Description

Description

This track shows the locations of transposon insertions in 53 of the Drosophila melanogaster Genetic Reference Panel (DGRP) lines that were predicted by the Transposable Element Movement in Population (TEMP) program. The dataset for each strain was obtained from the Dr. Zhiping Weng's (Zlab) web site.

These datasets were filtered so that only the insertions that were supported by reads at both sides of the insertion (1p1) were kept. The filtered datasets were then combined into a single file. The score field corresponds to the number of DGRP lines which have the transposon insertion. The color of the feature corresponds to its repeat class:

Repeat Class	Description	Color
TIR	Terminal Inverted Repeats (DNA Transposons)
LINE	Long Interspersed Nuclear Elements (Retrotransposons)
LTR	Long Terminal Repeats (Retrotransposons)
DINE	Drosophila Interspersed Nuclear Elements
Foldback	Foldback Elements

References

Zhuang J, Wang J, Theurkauf W, Weng Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res. 2014 Jun;42(11):6826-38.

Manee MM, Jackson J, Bergman CM. Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila. Genome Biol Evol. 2018 Jun 1;10(6):1533-1545.