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

Database: DperCAF1 Primary Table: regtools_junctions Row Count: 61,116 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	super_0	`varchar(255)`	values
`chromStart`	26831	`int(10) unsigned`	range
`chromEnd`	31042	`int(10) unsigned`	range
`name`	JUNC00000001	`varchar(255)`	values
`score`	6	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	26831	`int(10) unsigned`	range
`thickEnd`	31042	`int(10) unsigned`	range
`itemRgb`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	41,35	`longblob`
`chromStarts`	0,4176	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	super_0	26831	31042	JUNC00000001	6	-	26831	31042	0,0,0	2	41,35	0,4176
585	super_0	31933	32106	JUNC00000002	55	+	31933	32106	34,139,34	2	73,41	0,132
585	super_0	34721	34927	JUNC00000003	404	-	34721	34927	192,96,154	2	75,74	0,132
585	super_0	35003	35367	JUNC00000004	66	-	35003	35367	34,139,34	2	72,66	0,298
585	super_0	35130	35358	JUNC00000005	275	-	35130	35358	192,96,154	2	74,57	0,171
585	super_0	35146	35322	JUNC00000006	4	-	35146	35322	0,0,0	2	55,21	0,155
585	super_0	37728	38279	JUNC00000007	218	-	37728	38279	192,96,154	2	75,48	0,503
585	super_0	37765	38283	JUNC00000008	77	-	37765	38283	34,139,34	2	71,52	0,466
585	super_0	38353	38558	JUNC00000009	330	-	38353	38558	192,96,154	2	74,73	0,132
585	super_0	38981	39242	JUNC00000010	39	-	38981	39242	51,102,255	2	75,60	0,201

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 PRJNA388952.

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

The RNA-Seq data were produced by Dr. Brian Oliver's Developmental Genomics Lab at NIDDK, NIH.