Schema for Combined Splice Junctions (Cell Lines) - Combined Splice Junctions for Multiple Cell Lines

Database: dm6 Primary Table: modENCODE_cells_junctions Row Count: 168,655 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5972	`int(10) unsigned`	range
`chromEnd`	6312	`int(10) unsigned`	range
`name`	JUNC00000010	`varchar(255)`	values
`score`	87	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	5972	`int(10) unsigned`	range
`thickEnd`	6312	`int(10) unsigned`	range
`itemRgb`	2263842	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	98,65	`longblob`
`chromStarts`	0,275	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	chr2L	5972	6312	JUNC00000010	87	+	5972	6312	34,139,34	2	98,65	0,275
585	chr2L	5973	7586	JUNC00000011	11	+	5973	7586	51,102,255	2	97,13	0,1600
585	chr2L	6195	7665	JUNC00000012	132	+	6195	7665	192,96,154	2	92,92	0,1378
585	chr2L	6247	7644	JUNC00000013	5	+	6247	7644	0,0,0	2	65,71	0,1326
585	chr2L	6728	7661	JUNC00000014	7	+	6728	7661	0,0,0	2	80,88	0,845
585	chr2L	7655	8076	JUNC00000016	15	-	7655	8076	51,102,255	2	99,97	0,324
585	chr2L	7811	8077	JUNC00000017	4	+	7811	8077	0,0,0	2	99,98	0,168
585	chr2L	8021	8286	JUNC00000018	283	+	8021	8286	192,96,154	2	95,94	0,171
585	chr2L	8039	8251	JUNC00000019	4	+	8039	8251	0,0,0	2	77,23	0,189
585	chr2L	10812	18396	JUNC00000090	4	-	10812	18396	0,0,0	2	99,66	0,7518

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

Combined Splice Junctions (Cell Lines) (modENCODE_cells_junctions) Track Description

Description

This track shows the exon junctions extracted from spliced RNA-Seq reads of D. melanogaster cell lines. The RNA-Seq reads were obtained from the ENCODE data portal at UCSC on August 2019, and then mapped against the D. melanogaster dm6 genome assembly using HISAT2.

The splice junctions in each sample were identified by the regtools junctions extract subprogram. The splice junction predictions from the different samples are filtered and merged together into a single set of predictions. The predictions are color-coded based on the number of reads supporting the junction:

Color	Number of reads
	> 1000
	500-999
	100-499
	50-99
	10-49
	< 10

References

Cherbas L, et al. The transcriptional diversity of 25 Drosophila cell lines.. Genome Res. 2011 Feb;21(2):301-14.

Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015 Apr;12(4):357-60.