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

Database: DserGB1 Primary Table: regtools_junctions Row Count: 107,587 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	MTTC01000008	`varchar(255)`	values
`chromStart`	1332	`int(10) unsigned`	range
`chromEnd`	9445	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	1332	`int(10) unsigned`	range
`thickEnd`	9445	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	43,32	`longblob`
`chromStarts`	0,8081	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	MTTC01000008	1332	9445	JUNC00000001	1	-	1332	9445	0,0,0	2	43,32	0,8081
585	MTTC01000008	4822	7016	JUNC00000002	1	-	4822	7016	0,0,0	2	55,20	0,2174
585	MTTC01000008	5065	7260	JUNC00000003	1	-	5065	7260	0,0,0	2	34,42	0,2153
585	MTTC01000009	19251	19417	JUNC00000004	2	+	19251	19417	0,0,0	2	75,25	0,141
585	MTTC01000009	19281	19411	JUNC00000005	5	+	19281	19411	0,0,0	2	45,30	0,100
585	MTTC01000009	21063	21236	JUNC00000006	5	+	21063	21236	0,0,0	2	59,53	0,120
585	MTTC01000009	25295	25469	JUNC00000007	1	+	25295	25469	0,0,0	2	50,24	0,150
585	MTTC01000009	28201	28336	JUNC00000008	3	-	28201	28336	0,0,0	2	58,17	0,118
585	MTTC01000009	28647	90867	JUNC00000009	210	-	28647	90867	192,96,154	2	75,75	0,62145
585	MTTC01000009	28648	35626	JUNC00000010	23	-	28648	35626	51,102,255	2	74,58	0,6920

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 SRP096263.

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

Allen SL, Delaney EK, Kopp A, Chenoweth SF. Single-Molecule Sequencing of the Drosophila serrata Genome. G3 (Bethesda). 2017 Mar 10;7(3):781-788.