Schema for Splice Junctions - Splice Junctions Predicted by regtools using D. mojavensis RNA-Seq

Database: DmojCAF1 Primary Table: regtools_junctions Row Count: 116,982 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1004	`varchar(255)`	values
`chromStart`	1	`int(10) unsigned`	range
`chromEnd`	254	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	211	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	1	`int(10) unsigned`	range
`thickEnd`	254	`int(10) unsigned`	range
`itemRgb`	12607642	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	86,100	`longblob`
`chromStarts`	0,153	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	scaffold_1004	1	254	JUNC00000001	211	+	1	254	192,96,154	2	86,100	0,153
585	scaffold_1004	5	254	JUNC00000002	88	+	5	254	34,139,34	2	57,100	0,149
585	scaffold_1004	28	150	JUNC00000003	1	+	28	150	0,0,0	2	38,63	0,59
585	scaffold_1004	321	552	JUNC00000004	6	+	321	552	0,0,0	2	78,89	0,142
585	scaffold_1006	258	499	JUNC00000005	24	+	258	499	51,102,255	2	99,84	0,157
585	scaffold_1006	281	445	JUNC00000006	1	+	281	445	0,0,0	2	71,30	0,134
585	scaffold_1006	317	479	JUNC00000007	1	+	317	479	0,0,0	2	40,61	0,101
585	scaffold_1006	503	729	JUNC00000008	5	+	503	729	0,0,0	2	67,64	0,162
585	scaffold_1006	503	761	JUNC00000009	30	+	503	761	51,102,255	2	80,96	0,162
585	scaffold_1007	310	566	JUNC00000010	41	+	310	566	51,102,255	2	100,81	0,175

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

Splice Junctions (regtools_junctions) Track Description

Description

This track shows the exon junctions extracted from spliced RNA-Seq reads that have been aligned to the genome. The splice junctions were identified by the regtools junctions extract subprogram. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the accession number SRP006203.

The splice junction predictions from the different libraries 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

Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23.