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

Database: DmirGB2 Primary Table: regtools_junctions Row Count: 87,591 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CM001516	`varchar(255)`	values
`chromStart`	1991	`int(10) unsigned`	range
`chromEnd`	4588	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	17	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	1991	`int(10) unsigned`	range
`thickEnd`	4588	`int(10) unsigned`	range
`itemRgb`	3368703	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	96,41	`longblob`
`chromStarts`	0,2556	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	CM001516	1991	4588	JUNC00000001	17	-	1991	4588	51,102,255	2	96,41	0,2556
585	CM001516	3708	3964	JUNC00000002	3	?	3708	3964	0,0,0	2	37,81	0,175
585	CM001516	6137	7071	JUNC00000003	1	+	6137	7071	0,0,0	2	22,79	0,855
585	CM001516	6189	6450	JUNC00000004	19	-	6189	6450	51,102,255	2	87,66	0,195
585	CM001516	6189	7280	JUNC00000005	20	-	6189	7280	51,102,255	2	87,64	0,1027
585	CM001516	6241	11643	JUNC00000006	12	-	6241	11643	51,102,255	2	35,70	0,5332
585	CM001516	7078	11643	JUNC00000007	3	-	7078	11643	0,0,0	2	30,70	0,4495
585	CM001516	15217	15475	JUNC00000008	26	+	15217	15475	51,102,255	2	98,94	0,164
585	CM001516	15688	15902	JUNC00000009	23	+	15688	15902	51,102,255	2	71,92	0,122
585	CM001516	16058	16318	JUNC00000010	58	+	16058	16318	34,139,34	2	100,100	0,160

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 SRP009365.

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

Zhou Q, Bachtrog D. Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science. 2012 Jul 20;337(6092):341-5.