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

Database: DpseGB3 Primary Table: regtools_junctions Row Count: 105,941 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	5361	`int(10) unsigned`	range
`chromEnd`	30223	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	1	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	5361	`int(10) unsigned`	range
`thickEnd`	30223	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	17,32	`longblob`
`chromStarts`	0,24830	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	CH379058	5361	30223	JUNC00000001	1	-	5361	30223	0,0,0	2	17,32	0,24830
585	CH379058	10189	48567	JUNC00000002	23	+	10189	48567	51,102,255	2	47,26	0,38352
585	CH379058	10197	64971	JUNC00000003	2	+	10197	64971	0,0,0	2	39,61	0,54713
585	CH379058	22530	22787	JUNC00000004	358	-	22530	22787	192,96,154	2	99,96	0,161
585	CH379058	22550	22789	JUNC00000005	27	-	22550	22789	51,102,255	2	99,98	0,141
585	CH379058	22581	23712	JUNC00000006	2	-	22581	23712	0,0,0	2	48,72	0,1059
585	CH379058	30336	48567	JUNC00000007	6	+	30336	48567	0,0,0	2	79,26	0,18205
585	CH379058	45317	45489	JUNC00000008	1	+	45317	45489	0,0,0	2	49,52	0,120
585	CH379058	45495	45760	JUNC00000009	52	+	45495	45760	34,139,34	2	100,100	0,165
585	CH379058	45673	45930	JUNC00000010	156	+	45673	45930	192,96,154	2	97,91	0,166

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 SRP006203.

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

Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23.