Schema for FlyBase Exon Junctions - FlyBase RNA-Seq Exon Junctions

Database: dm6 Primary Table: fb_exon_junction Row Count: 71,183 Data last updated: 2022-10-21

field	example	SQL type	info
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	8041	`int(10) unsigned`	range
`chromEnd`	8239	`int(10) unsigned`	range
`name`	FBsf0000131040	`varchar(255)`	values
`score`	278	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	8041	`int(10) unsigned`	range
`thickEnd`	8239	`int(10) unsigned`	range
`itemRgb`	12607642	`int(10) unsigned`	range
`blockCount`	2	`int(11)`	range
`blockSizes`	75,47	`longblob`
`chromStarts`	0,151	`longblob`
`id`	FBsf0000131040	`varchar(255)`	values
`description`	BCM_1_RNAseq_junctions:2,mo...	`longblob`

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	id	description
chr2L	8041	8239	FBsf0000131040	278	+	8041	8239	192,96,154	2	75,47	0,151	FBsf0000131040	BCM_1_RNAseq_junctions:2,modENCODE_mRNA-Seq_U_junctions:276
chr2L	8106	8238	FBsf0000175585	23	+	8106	8238	51,102,255	2	10,10	0,122	FBsf0000175585	modENCODE_mRNA-Seq_U_junctions:23
chr2L	11264	11475	FBsf0000139959	2335	-	11264	11475	200,45,24	2	80,66	0,145	FBsf0000139959	BCM_1_RNAseq_junctions:30,modENCODE_mRNA-Seq_U_junctions:2305
chr2L	11334	11788	FBsf0000172621	53	-	11334	11788	34,139,34	2	10,10	0,444	FBsf0000172621	modENCODE_mRNA-Seq_U_junctions:53
chr2L	11452	11872	FBsf0000105354	6159	-	11452	11872	200,45,24	2	66,94	0,326	FBsf0000105354	BCM_1_RNAseq_junctions:133,modENCODE_mRNA-Seq_U_junctions:6026
chr2L	12151	12370	FBsf0000131992	12302	-	12151	12370	200,45,24	2	70,85	0,134	FBsf0000131992	BCM_1_RNAseq_junctions:86,modENCODE_mRNA-Seq_U_junctions:12216
chr2L	12330	12426	FBsf0000176045	11	-	12330	12426	51,102,255	2	10,10	0,86	FBsf0000176045	modENCODE_mRNA-Seq_U_junctions:11
chr2L	12875	13587	FBsf0000132883	21109	-	12875	13587	200,45,24	2	53,68	0,644	FBsf0000132883	BCM_1_RNAseq_junctions:146,modENCODE_mRNA-Seq_U_junctions:20963
chr2L	12908	19900	FBsf0000146990	1000	-	12908	19900	200,45,24	2	20,21	0,6971	FBsf0000146990	BCM_1_RNAseq_junctions:0
chr2L	12918	13692	FBsf0000183914	37	-	12918	13692	51,102,255	2	10,10	0,764	FBsf0000183914	modENCODE_mRNA-Seq_U_junctions:37

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

FlyBase Exon Junctions (fb_exon_junction) Track Description

Description

This track shows the exon junction predictions based on RNA-Seq data produced by the modENCODE project and the Baylor College of Medicine - Human Genome Sequencing Center. The exon junction predictions were obtained from the D. melanogaster release 6.13 produced by FlyBase.

The exon junctions are color-coded based on the number of reads supporting the junction:

Thanks to FlyBase for providing these annotations.

St Pierre SE, Ponting L, Stefancsik R, McQuilton P; FlyBase Consortium. FlyBase 102 — advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014 Jan;42(Database issue):D780-8