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

Database: DgriCAF1 Primary Table: regtools_junctions Row Count: 61,201 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10016	`varchar(255)`	values
`chromStart`	103	`int(10) unsigned`	range
`chromEnd`	289	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	293	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	103	`int(10) unsigned`	range
`thickEnd`	289	`int(10) unsigned`	range
`itemRgb`	12607642	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	75,49	`longblob`
`chromStarts`	0,137	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	scaffold_10016	103	289	JUNC00000001	293	+	103	289	192,96,154	2	75,49	0,137
585	scaffold_10024	976	1104	JUNC00000002	9	+	976	1104	0,0,0	2	58,18	0,110
585	scaffold_10027	350	560	JUNC00000003	69	+	350	560	34,139,34	2	71,75	0,135
585	scaffold_10027	497	662	JUNC00000004	19	+	497	662	51,102,255	2	63,37	0,128
585	scaffold_10027	651	857	JUNC00000005	59	+	651	857	34,139,34	2	74,51	0,155
585	scaffold_10027	825	1181	JUNC00000006	25	+	825	1181	51,102,255	2	69,17	0,339
585	scaffold_10030	5635	6763	JUNC00000007	7	+	5635	6763	0,0,0	2	63,13	0,1115
585	scaffold_10030	7088	7249	JUNC00000008	7	+	7088	7249	0,0,0	2	35,41	0,120
585	scaffold_10030	7325	8446	JUNC00000009	47	+	7325	8446	51,102,255	2	62,67	0,1054
585	scaffold_10030	7363	8893	JUNC00000010	1	+	7363	8893	0,0,0	2	24,52	0,1478

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 SRP073087.

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

The RNA-Seq data were produced as part of the BioProject PRJNA317989: Expression profiling Hawaiian Drosophila species, tissues, and sexes.