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

Database: DereCAF1 Primary Table: regtools_junctions Row Count: 38,403 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1108	`varchar(255)`	values
`chromStart`	122	`int(10) unsigned`	range
`chromEnd`	1035	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	17	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	122	`int(10) unsigned`	range
`thickEnd`	1035	`int(10) unsigned`	range
`itemRgb`	3368703	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	50,32	`longblob`
`chromStarts`	0,881	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	scaffold_1108	122	1035	JUNC00000001	17	-	122	1035	51,102,255	2	50,32	0,881
585	scaffold_1211	504	903	JUNC00000002	5317	+	504	903	200,45,24	2	50,8	0,391
585	scaffold_1216	112	810	JUNC00000003	18	-	112	810	51,102,255	2	48,38	0,660
585	scaffold_1230	336	467	JUNC00000004	7	-	336	467	0,0,0	2	31,44	0,87
585	scaffold_1234	335	628	JUNC00000005	27	+	335	628	51,102,255	2	47,43	0,250
585	scaffold_1246	600	924	JUNC00000006	3	+	600	924	0,0,0	2	16,35	0,289
585	scaffold_1247	137	644	JUNC00000007	1	+	137	644	0,0,0	2	33,18	0,489
585	scaffold_1247	160	487	JUNC00000008	453	+	160	487	192,96,154	2	50,50	0,277
585	scaffold_1247	160	942	JUNC00000009	15	+	160	942	51,102,255	2	50,50	0,732
585	scaffold_1247	325	653	JUNC00000010	87	-	325	653	34,139,34	2	50,50	0,278

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 PRJNA264407 (ovarian follicle cells; Chirn GW 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.

Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS Genet. 2015 Nov 20;11(11):e1005652.