Schema for ensGene

Database: anoGam3 Primary Table: ensGene Row Count: 15,632 Data last updated: 2018-01-07
Format description: Ensembl gene predictions.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	586	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`name`	AGAP004677-RB	`varchar(255)`	values	Ensembl transcript ID
`chrom`	chr2L	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	-	`char(1)`	values	+ or - for strand
`txStart`	157347	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	186936	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	157495	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	159356	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	4	`int(10) unsigned`	range	Number of exons
`exonStarts`	157347,157678,159191,186859,	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	157623,158297,159366,186936,	`longblob`		Exon end positions (or start positions for minus strand item)
`score`	0	`int(11)`	range	always 0 for Ensembl genes
`name2`	AGAP004677	`varchar(255)`	values	Ensembl gene ID
`cdsStartStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values	Status of CDS start annotation (none, unknown, incomplete, or complete)
`cdsEndStat`	cmpl	`enum('none', 'unk', 'incmpl', 'cmpl')`	values	Status of CDS end annotation (none, unknown, incomplete, or complete)
`exonFrames`	1,0,0,-1,	`longblob`		Exon frame {0,1,2}, or -1 if no frame for exon

To download this table in different text formats or to intersect or correlate it with other tables, use the Table Browser.

Connected Tables and Joining Fields


	anoGam3.ensGtp.transcript (via ensGene.name) anoGam3.ensPep.name (via ensGene.name) anoGam3.ensemblSource.name (via ensGene.name) anoGam3.ensemblToGeneName.name (via ensGene.name) knownGeneV39.knownToEnsembl.value (via ensGene.name)

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds	name2	cdsStartStat	cdsEndStat	exonFrames
586	AGAP004677-RB	chr2L	-	157347	186936	157495	159356	4	157347,157678,159191,186859,	157623,158297,159366,186936,	AGAP004677	cmpl	cmpl	1,0,0,-1,
586	AGAP004677-RA	chr2L	-	157347	181305	157495	181213	4	157347,157678,159191,180908,	157623,158297,159366,181305,	AGAP004677	cmpl	cmpl	1,0,2,0,
586	AGAP004678-RA	chr2L	+	203778	205293	203865	204956	2	203778,203980,	203924,205293,	AGAP004678	cmpl	cmpl	0,2,
586	AGAP004679-RB	chr2L	+	207893	210460	208416	210276	6	207893,208392,208638,208896,209472,209876,	207953,208581,208824,209394,209816,210460,	AGAP004679	cmpl	cmpl	-1,0,0,0,0,2,
586	AGAP004679-RA	chr2L	+	208182	210460	208416	210276	5	208182,208638,208896,209472,209876,	208581,208824,209394,209816,210460,	AGAP004679	cmpl	cmpl	0,0,0,0,2,
587	AGAP004680-RA	chr2L	+	271284	271815	271284	271815	1	271284,	271815,	AGAP004680	cmpl	cmpl	0,
587	AGAP004681-RA	chr2L	-	358328	359280	358639	359145	2	358328,358976,	358881,359280,	AGAP004681	cmpl	cmpl	1,0,
588	AGAP004682-RA	chr2L	-	433502	461627	433502	461082	3	433502,460184,461513,	434254,461391,461627,	AGAP004682	cmpl	cmpl	1,0,-1,
588	AGAP028431-RA	chr2L	-	477920	484647	482630	483384	5	477920,482617,482788,483375,483974,	479912,482709,483015,483905,484647,	AGAP028431	cmpl	cmpl	-1,2,0,0,-1,
588	AGAP004683-RA	chr2L	-	485697	488369	485736	488369	2	485697,486670,	486245,488369,	AGAP004683	cmpl	cmpl	1,0,

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. For more information on the different gene tracks, see our Genes FAQ. Methods For a description of the methods used in Ensembl gene predictions, please refer to Hubbard et al. (2002), also listed in the References section below. Data access Ensembl Gene data can be explored interactively using the Table Browser or the Data Integrator. For local downloads, the genePred format files for hg19 are available in our downloads directory as ensGene.txt.gz or in our genes download directory in GTF format. For programmatic access, the data can be queried from the REST API or directly from our public MySQL servers. Instructions on this method are available on our MySQL help page and on our blog. Previous versions of this track can be found on our archive download server. Credits We would like to thank Ensembl for providing these gene annotations. For more information, please see Ensembl's genome annotation page. 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. PMID: 11752248; PMC: PMC99161

Description

Methods

Data access

Credits

References