Schema for Combined Splice Junctions (Tissues) - Combined Splice Junctions for Multiple Tissues

Database: dm6 Primary Table: modENCODE_tissues_junctions Row Count: 249,329 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	7450	`int(10) unsigned`	range
`chromEnd`	7670	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	55	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	7450	`int(10) unsigned`	range
`thickEnd`	7670	`int(10) unsigned`	range
`itemRgb`	2263842	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	39,97	`longblob`
`chromStarts`	0,123	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	chr2L	7450	7670	JUNC00000001	55	+	7450	7670	34,139,34	2	39,97	0,123
585	chr2L	7829	7999	JUNC00000003	5	+	7829	7999	0,0,0	2	81,20	0,150
585	chr2L	8018	8286	JUNC00000005	774	+	8018	8286	100,50,0	2	98,94	0,174
585	chr2L	8018	8319	JUNC00000006	68	+	8018	8319	34,139,34	2	98,91	0,210
585	chr2L	8021	8366	JUNC00000007	8	+	8021	8366	0,0,0	2	95,99	0,246
585	chr2L	8490	8766	JUNC00000008	29	+	8490	8766	51,102,255	2	99,99	0,177
585	chr2L	10433	11221	JUNC00000039	4	-	10433	11221	0,0,0	2	99,58	0,730
585	chr2L	10435	10581	JUNC00000040	3	-	10435	10581	0,0,0	2	98,27	0,119
585	chr2L	10437	10836	JUNC00000042	5	-	10437	10836	0,0,0	2	98,33	0,366
585	chr2L	10784	11032	JUNC00000070	12	-	10784	11032	51,102,255	2	65,99	0,149

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

Combined Splice Junctions (Tissues) (modENCODE_tissues_junctions) Track Description

Description

This track shows the exon junctions extracted from spliced RNA-Seq reads of multiple tissues 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.