Schema for Combined Splice Junctions (Development) - Combined Splice Junctions for Multiple Developmental Stages

Database: dm6 Primary Table: modENCODE_dev_junctions Row Count: 364,775 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5819	`int(10) unsigned`	range
`chromEnd`	5972	`int(10) unsigned`	range
`name`	JUNC00000008	`varchar(255)`	values
`score`	3	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	5819	`int(10) unsigned`	range
`thickEnd`	5972	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	50,50	`longblob`
`chromStarts`	0,103	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	chr2L	5819	5972	JUNC00000008	3	-	5819	5972	0,0,0	2	50,50	0,103
585	chr2L	7284	9808	JUNC00000020	4	-	7284	9808	0,0,0	2	44,55	0,2469
585	chr2L	7429	7667	JUNC00000021	7	+	7429	7667	0,0,0	2	22,94	0,144
585	chr2L	7445	7658	JUNC00000022	79	+	7445	7658	34,139,34	2	44,85	0,128
585	chr2L	7834	7990	JUNC00000026	4	+	7834	7990	0,0,0	2	76,11	0,145
585	chr2L	8018	8256	JUNC00000029	1193	+	8018	8256	200,45,24	2	98,64	0,174
585	chr2L	8018	8317	JUNC00000030	129	+	8018	8317	192,96,154	2	98,89	0,210
585	chr2L	8490	8766	JUNC00000034	15	+	8490	8766	51,102,255	2	99,99	0,177
585	chr2L	8768	9193	JUNC00000039	4	-	8768	9193	0,0,0	2	58,70	0,355
585	chr2L	10110	11872	JUNC00000062	9	-	10110	11872	0,0,0	2	99,94	0,1668

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

Combined Splice Junctions (Development) (modENCODE_dev_junctions) Track Description

Description

This track shows the exon junctions extracted from spliced RNA-Seq reads of multiple developmental stages of D. melanogaster. 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

Brown JB, et al. Diversity and dynamics of the Drosophila transcriptome. Nature. 2014 Aug 28;512(7515):393-9.

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