Schema for Geneid Genes (BUSCO) - Geneid Gene Predictions with CEGMA Training Set

Database: DmirGB2 Primary Table: geneidCEGMA Row Count: 14,848 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-CM001516_1	`varchar(255)`	values
`chrom`	CM001516	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	1943	`int(10) unsigned`	range
`txEnd`	2232	`int(10) unsigned`	range
`cdsStart`	1943	`int(10) unsigned`	range
`cdsEnd`	2232	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	1943,2181,	`longblob`
`exonEnds`	2138,2232,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-CM001516_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-CM001516_1	CM001516	-	1943	2232	1943	2232	2	1943,2181,	2138,2232,	geneid_cegma-CM001516_1	unk	unk	0,0,
585	mRNA_geneid_cegma-CM001516_2	CM001516	-	4412	14427	4412	14427	4	4412,6209,7078,14408,	4899,6276,7108,14427,	geneid_cegma-CM001516_2	unk	unk	2,1,1,0,
585	mRNA_geneid_cegma-CM001516_3	CM001516	+	15164	15968	15164	15968	3	15164,15381,15810,	15315,15759,15968,	geneid_cegma-CM001516_3	unk	unk	0,1,1,
585	mRNA_geneid_cegma-CM001516_4	CM001516	+	16490	18026	16490	18026	2	16490,16925,	16742,18026,	geneid_cegma-CM001516_4	unk	unk	0,0,
585	mRNA_geneid_cegma-CM001516_5	CM001516	+	18571	21013	18571	21013	5	18571,18878,19130,19783,20817,	18644,19050,19643,20737,21013,	geneid_cegma-CM001516_5	unk	unk	0,1,2,2,2,
585	mRNA_geneid_cegma-CM001516_6	CM001516	+	23489	29360	23489	29360	8	23489,24309,24698,25430,25969,26350,26512,29252,	24243,24596,25178,25922,26296,26439,28247,29360,	geneid_cegma-CM001516_6	unk	unk	0,1,0,0,0,0,2,0,
585	mRNA_geneid_cegma-CM001516_7	CM001516	-	30530	40570	30530	40570	4	30530,31094,31826,40462,	31017,31757,32299,40570,	geneid_cegma-CM001516_7	unk	unk	2,2,0,0,
585	mRNA_geneid_cegma-CM001516_8	CM001516	+	41785	44350	41785	44350	3	41785,42274,42504,	41886,42415,44350,	geneid_cegma-CM001516_8	unk	unk	0,2,2,
585	mRNA_geneid_cegma-CM001516_9	CM001516	+	46343	46843	46343	46843	2	46343,46539,	46465,46843,	geneid_cegma-CM001516_9	unk	unk	0,2,
585	mRNA_geneid_cegma-CM001516_10	CM001516	+	48663	50124	48663	50124	1	48663,	50124,	geneid_cegma-CM001516_10	unk	unk	0,

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

Geneid Genes (BUSCO) (geneidCEGMA) Track Description


	Description This track shows the gene predictions produced by geneid using species-specific parameters. Methods The species-specific geneid parameters were produced by CEGMA. References Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007 May 1;23(9):1061-7. Parra G, Blanco E, Guigó R. GeneID in Drosophila. Genome Res. 2000 Apr;10(4):511-5.

Description