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

Database: DobsGB1 Primary Table: geneidCEGMA Row Count: 18,552 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	mRNA_geneid_cegma-BDQP01000...	`varchar(255)`	values
`chrom`	BDQP01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	2090	`int(10) unsigned`	range
`txEnd`	2438	`int(10) unsigned`	range
`cdsStart`	2090	`int(10) unsigned`	range
`cdsEnd`	2438	`int(10) unsigned`	range
`exonCount`	1	`int(10) unsigned`	range
`exonStarts`	2090,	`longblob`
`exonEnds`	2438,	`longblob`
`score`	0	`int(11)`	range
`name2`	geneid_cegma-BDQP01000001_1	`varchar(255)`	values
`cdsStartStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`cdsEndStat`	unk	`enum('none', 'unk', 'incmpl', 'cmpl')`	values
`exonFrames`	0,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	mRNA_geneid_cegma-BDQP01000001_1	BDQP01000001	+	2090	2438	2090	2438	1	2090,	2438,	geneid_cegma-BDQP01000001_1	unk	unk	0,
585	mRNA_geneid_cegma-BDQP01000001_2	BDQP01000001	+	6016	32204	6016	32204	14	6016,18205,18970,20245,23291,23671,25913,26185,26487,27912,29149,30315,30773,31448,	6058,18323,19158,20281,23346,23987,26047,26361,26722,28683,29245,30687,31387,32204,	geneid_cegma-BDQP01000001_2	unk	unk	0,0,1,0,0,1,2,1,0,1,1,1,1,0,
585	mRNA_geneid_cegma-BDQP01000001_3	BDQP01000001	-	37921	41098	37921	41098	9	37921,38186,38378,38594,39369,39863,39984,40149,40864,	38092,38264,38536,38694,39408,39925,40091,40805,41098,	geneid_cegma-BDQP01000001_3	unk	unk	0,0,1,0,0,1,2,0,0,
585	mRNA_geneid_cegma-BDQP01000001_4	BDQP01000001	-	42804	44219	42804	44219	4	42804,43483,43884,44134,	43414,43812,44039,44219,	geneid_cegma-BDQP01000001_4	unk	unk	2,0,1,0,
585	mRNA_geneid_cegma-BDQP01000001_5	BDQP01000001	-	46003	54552	46003	54552	11	46003,46501,46772,46886,47177,49733,49970,50335,50566,51679,54535,	46428,46695,46821,47100,47350,49898,50265,50488,51616,51869,54552,	geneid_cegma-BDQP01000001_5	unk	unk	1,2,1,0,1,1,0,0,0,2,0,
585	mRNA_geneid_cegma-BDQP01000001_6	BDQP01000001	+	55919	73985	55919	73985	3	55919,73000,73214,	55967,73141,73985,	geneid_cegma-BDQP01000001_6	unk	unk	0,0,0,
585	mRNA_geneid_cegma-BDQP01000001_7	BDQP01000001	+	74955	76079	74955	76079	3	74955,75061,75725,	74987,75215,76079,	geneid_cegma-BDQP01000001_7	unk	unk	0,2,0,
585	mRNA_geneid_cegma-BDQP01000001_8	BDQP01000001	+	78088	80743	78088	80743	6	78088,78665,79350,79729,80424,80733,	78594,79283,79667,80364,80618,80743,	geneid_cegma-BDQP01000001_8	unk	unk	0,2,2,1,0,2,
585	mRNA_geneid_cegma-BDQP01000001_9	BDQP01000001	-	81261	85756	81261	85756	12	81261,81336,82353,82732,83244,83591,83870,84469,84855,85127,85499,85712,	81287,82302,82670,83181,83534,83811,83964,84795,85067,85437,85647,85756,	geneid_cegma-BDQP01000001_9	unk	unk	1,1,2,0,1,0,2,0,1,0,2,0,
585	mRNA_geneid_cegma-BDQP01000001_10	BDQP01000001	+	86299	87784	86299	87784	1	86299,	87784,	geneid_cegma-BDQP01000001_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

Methods

References