Schema for Ensembl Genes - Ensembl Gene Predictions

Schema for Ensembl Genes - Ensembl Gene Predictions

Database: bosTau4 Primary Table: ensGene Row Count: 29,802
Format description: A gene prediction.

field	example	SQL type	info	description
`bin`	585	`smallint unsigned`	range	Indexing field to speed chromosome range queries.
`name`	ENSBTAT00000052762	`varchar(255)`	values	Name of gene
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	37235	`int unsigned`	range	Transcription start position
`txEnd`	38165	`int unsigned`	range	Transcription end position
`cdsStart`	38165	`int unsigned`	range	Coding region start
`cdsEnd`	38165	`int unsigned`	range	Coding region end
`exonCount`	3	`int unsigned`	range	Number of exons
`exonStarts`	37235,37500,37934,	`longblob`		Exon start positions
`exonEnds`	37499,37932,38165,	`longblob`		Exon end positions
`score`	0	`int`	range
`name2`	ENSBTAG00000039257	`varchar(255)`	values
`cdsStartStat`	none	`enum('none','unk','incmpl','cmpl')`	values
`cdsEndStat`	none	`enum('none','unk','incmpl','cmpl')`	values
`exonFrames`	-1,-1,-1,	`longblob`

Connected Tables and Joining Fields


	bosTau4.ensGtp.transcript (via ensGene.name) bosTau4.ensPep.name (via ensGene.name)

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
585	ENSBTAT00000052762	chr1	+	37235	38165	38165	38165	3	37235,37500,37934,	37499,37932,38165,	ENSBTAG00000039257	none	none	-1,-1,-1,
585	ENSBTAT00000057271	chr1	+	41242	42175	42175	42175	4	41242,41292,41519,41947,	41290,41517,41945,42175,	ENSBTAG00000038953	none	none	-1,-1,-1,-1,
585	ENSBTAT00000051913	chr1	+	52417	55107	52417	55107	3	52417,52800,55079,	52798,53333,55107,	ENSBTAG00000006858	cmpl	incmpl	0,0,2,
585	ENSBTAT00000009004	chr1	+	52417	54073	52417	54073	3	52417,52800,54057,	52798,53345,54073,	ENSBTAG00000006858	cmpl	incmpl	0,0,2,
585	ENSBTAT00000053790	chr1	+	52417	54057	52417	54057	3	52417,52806,54020,	52804,53318,54057,	ENSBTAG00000006858	cmpl	incmpl	0,0,2,
585	ENSBTAT00000057220	chr1	-	61174	62822	61174	62822	2	61174,61905,	61202,62822,	ENSBTAG00000035349	incmpl	cmpl	2,0,
585	ENSBTAT00000008992	chr1	-	61236	62825	61236	62825	3	61236,61494,61905,	61250,61511,62825,	ENSBTAG00000035349	incmpl	incmpl	1,2,0,
585	ENSBTAT00000056519	chr1	-	61648	62828	61648	62828	2	61648,61905,	61697,62828,	ENSBTAG00000035349	cmpl	incmpl	2,0,
73	ENSBTAT00000002299	chr1	-	103391	158259	103395	158259	6	103391,114362,115700,116377,117418,156978,	103557,114544,115807,116503,117528,158259,	ENSBTAG00000001753	cmpl	cmpl	0,1,2,2,0,0,
586	ENSBTAT00000052024	chr1	+	179265	181213	179265	181213	3	179265,179809,181111,	179321,179831,181213,	ENSBTAG00000038575	incmpl	incmpl	0,2,0,

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

Ensembl Genes (ensGene) Track Description

Description

These gene predictions were generated by Ensembl.

Methods

For a description of the methods used in Ensembl gene prediction, refer to Hubbard, T. et al. (2002) in the References section below.

Credits

Thanks to Ensembl for providing this annotation.

References

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41.