Schema for mgcGenes

Schema for mgcGenes

Database: bosTau4 Primary Table: mgcGenes Row Count: 9,701
Format description: A gene prediction with some additional info.

field	example	SQL type	info	description
`bin`	586	`smallint unsigned`	range	Indexing field to speed chromosome range queries.
`name`	BC105155	`varchar(255)`	values	Name of gene (usually transcript_id from GTF)
`chrom`	chrUn.004.137	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	198008	`int unsigned`	range	Transcription start position
`txEnd`	202339	`int unsigned`	range	Transcription end position
`cdsStart`	198071	`int unsigned`	range	Coding region start
`cdsEnd`	199927	`int unsigned`	range	Coding region end
`exonCount`	4	`int unsigned`	range	Number of exons
`exonStarts`	198008,199244,199575,199759,	`longblob`		Exon start positions
`exonEnds`	198090,199336,199632,202339,	`longblob`		Exon end positions
`score`	0	`int`	range
`name2`	BET1L	`varchar(255)`	values	Alternate name (e.g. gene_id from GTF)
`cdsStartStat`	cmpl	`enum('none','unk','incmpl','cmpl')`	values	enum('none','unk','incmpl','cmpl')
`cdsEndStat`	cmpl	`enum('none','unk','incmpl','cmpl')`	values	enum('none','unk','incmpl','cmpl')
`exonFrames`	0,1,0,0,	`longblob`		Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields


	bosTau4.all_mrna.qName (via mgcGenes.name) bosTau4.gbCdnaInfo.acc (via mgcGenes.name) bosTau4.gbSeq.acc (via mgcGenes.name) bosTau4.gbStatus.acc (via mgcGenes.name) bosTau4.imageClone.acc (via mgcGenes.name) bosTau4.mgcFullMrna.qName (via mgcGenes.name) bosTau4.mrnaOrientInfo.name (via mgcGenes.name)

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
586	BC105155	chrUn.004.137	+	198008	202339	198071	199927	4	198008,199244,199575,199759,	198090,199336,199632,202339,	BET1L	cmpl	cmpl	0,1,0,0,
858	BC149285	chr5	+	35815644	35815949	35815949	35815949	1	35815644,	35815949,	RPAP3	unk	unk	-1,
972	BC151396	chrX	-	50801010	50834218	50802428	50811814	13	50801010,50802693,50802970,50804178,50804684,50805070,50805675,50806323,50808355,50809277,50811757,50814971,50834046,	50802546,50802870,50803188,50804403,50804799,50805281,50805874,50806483,50808531,50810413,50811821,50815043,50834218,	STARD8	cmpl	cmpl	2,2,0,0,2,1,0,2,0,0,0,-1,-1,
16	BC140569	chrX	-	59768792	59769601	59768792	59769100	1	59768792,	59769601,	FGD1	incmpl	cmpl	0,
585	BC111156	chrUn.004.2096	+	1989	13589	2013	12063	6	1989,2786,4286,10836,11069,11929,	2032,2932,4949,10983,11199,13589,	SUV39H1	cmpl	cmpl	0,1,0,0,0,1,
1041	BC102363	chrX	+	59799917	59828224	59802355	59828097	16	59799917,59802306,59809460,59810416,59811663,59812511,59812757,59813807,59816480,59819043,59819627,59819883,59820669,59822937,59 ...	59800000,59802374,59809501,59810524,59811780,59812595,59812893,59813911,59816625,59819131,59819802,59820026,59820806,59823065,59 ...	GNL3L	cmpl	cmpl	-1,0,1,0,0,0,0,1,0,1,2,0,2,1,0,1,
1273	BC111208	chr5	-	90190360	90213646	90190695	90209993	5	90190360,90191431,90194188,90209890,90213563,	90190817,90191576,90195078,90210096,90213646,	RASSF8	cmpl	cmpl	1,0,1,0,-1,
1006	BC103120	chrX	-	55303281	55306344	55303670	55306241	5	55303281,55303891,55304719,55304920,55306145,	55303693,55303982,55304815,55305073,55306344,	PLP2	cmpl	cmpl	1,0,0,0,0,
660	BC114833	chr3	+	9900433	9939481	9900514	9938849	7	9900433,9909184,9911450,9924834,9929494,9937120,9938798,	9900590,9909523,9911735,9924933,9929568,9937213,9939481,	SLAMF1	cmpl	cmpl	0,1,1,1,1,0,0,
855	BC114912	chr10	-	35476928	35483432	35481330	35483307	4	35476928,35480149,35481330,35483135,	35477022,35480199,35481365,35483432,	GPR176	cmpl	cmpl	-1,-1,1,0,

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