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

Database: DbusGB1 Primary Table: regtools_junctions Row Count: 125,562 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CP012523	`varchar(255)`	values
`chromStart`	37732	`int(10) unsigned`	range
`chromEnd`	38934	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	68	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	37732	`int(10) unsigned`	range
`thickEnd`	38934	`int(10) unsigned`	range
`itemRgb`	2263842	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	98,89	`longblob`
`chromStarts`	0,1113	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	CP012523	37732	38934	JUNC00000001	68	-	37732	38934	34,139,34	2	98,89	0,1113
585	CP012523	40037	42431	JUNC00000002	52	-	40037	42431	34,139,34	2	97,97	0,2297
585	CP012523	42633	42856	JUNC00000003	58	-	42633	42856	34,139,34	2	74,86	0,137
585	CP012523	43083	43795	JUNC00000004	23	-	43083	43795	51,102,255	2	98,73	0,639
585	CP012523	56939	58397	JUNC00000005	2	-	56939	58397	0,0,0	2	38,39	0,1419
585	CP012523	89931	90057	JUNC00000006	2	-	89931	90057	0,0,0	2	26,16	0,110
585	CP012523	89936	90486	JUNC00000007	4	-	89936	90486	0,0,0	2	21,73	0,477
585	CP012523	90442	90669	JUNC00000008	66	?	90442	90669	34,139,34	2	97,99	0,128
585	CP012523	90538	90710	JUNC00000009	4	?	90538	90710	0,0,0	2	43,76	0,96
585	CP012523	90572	90870	JUNC00000010	230	?	90572	90870	192,96,154	2	98,99	0,199

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 number PRJNA274996.

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. Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila. PLoS Genet. 2015 Jun 26;11(6):e1005331.