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

Database: DyakCAF1 Primary Table: regtools_junctions Row Count: 112,483 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	2367	`int(10) unsigned`	range
`chromEnd`	3037	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	3	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	2367	`int(10) unsigned`	range
`thickEnd`	3037	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	40,61	`longblob`
`chromStarts`	0,609	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	chr2L	2367	3037	JUNC00000001	3	-	2367	3037	0,0,0	2	40,61	0,609
585	chr2L	2572	3110	JUNC00000002	1	-	2572	3110	0,0,0	2	23,78	0,460
585	chr2L	2827	3047	JUNC00000003	4	-	2827	3047	0,0,0	2	24,71	0,149
585	chr2L	6086	9347	JUNC00000004	3	-	6086	9347	0,0,0	2	39,68	0,3193
585	chr2L	8673	8930	JUNC00000005	204	-	8673	8930	192,96,154	2	100,94	0,163
585	chr2L	8845	9375	JUNC00000006	261	-	8845	9375	192,96,154	2	100,96	0,434
585	chr2L	8971	9378	JUNC00000007	49	-	8971	9378	51,102,255	2	97,99	0,308
585	chr2L	9622	9857	JUNC00000008	582	-	9622	9857	100,50,0	2	100,73	0,162
585	chr2L	10328	10785	JUNC00000009	364	-	10328	10785	192,96,154	2	99,92	0,365
585	chr2L	10699	10954	JUNC00000010	362	-	10699	10954	192,96,154	2	100,98	0,157

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.