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

Database: DsecCAF1 Primary Table: regtools_junctions Row Count: 60,334 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	super_0	`varchar(255)`	values
`chromStart`	3022	`int(10) unsigned`	range
`chromEnd`	3236	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	13	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	3022	`int(10) unsigned`	range
`thickEnd`	3236	`int(10) unsigned`	range
`itemRgb`	3368703	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	67,90	`longblob`
`chromStarts`	0,124	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	super_0	3022	3236	JUNC00000001	13	-	3022	3236	51,102,255	2	67,90	0,124
585	super_0	5717	5921	JUNC00000002	3	-	5717	5921	0,0,0	2	24,68	0,136
585	super_0	8985	10256	JUNC00000003	1	-	8985	10256	0,0,0	2	28,60	0,1211
585	super_0	12185	12413	JUNC00000004	13	-	12185	12413	51,102,255	2	76,90	0,138
585	super_0	12639	12843	JUNC00000005	7	-	12639	12843	0,0,0	2	91,36	0,168
585	super_0	13030	14284	JUNC00000006	12	-	13030	14284	51,102,255	2	54,78	0,1176
585	super_0	14016	14274	JUNC00000007	1	-	14016	14274	0,0,0	2	22,68	0,190
585	super_0	15072	15540	JUNC00000008	22	-	15072	15540	51,102,255	2	62,76	0,392
585	super_0	15575	15910	JUNC00000009	91	-	15575	15910	34,139,34	2	93,99	0,236
585	super_0	16487	16730	JUNC00000010	43	-	16487	16730	51,102,255	2	85,93	0,150

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 BioProject accession numbers PRJNA205470 (adult females; McManus CJ et al., 2014) and PRJNA414017 (adult males; Ma S et al., 2018).

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

Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN. Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity. Aging Cell. 2018 Apr 19:e12740.

McManus CJ, Coolon JD, Eipper-Mains J, Wittkopp PJ, Graveley BR. Evolution of splicing regulatory networks in Drosophila. Genome Res. 2014 May;24(5):786-96.