Schema for Ensembl Genes - Ensembl Genes
  Database: xenTro9    Primary Table: ensGene    Row Count: 56,323   Data last updated: 2020-08-31
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
name ENSXETT00000061673.2varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 133269int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 152620int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 133269int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 152620int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 133269,140925,143199,146043...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 134186,141049,143427,146880...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ENSXETG00000030302.2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 1,0,0,0,2,0,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
586ENSXETT00000061673.2chr1-1332691526201332691526206133269,140925,143199,146043,151249,152381,134186,141049,143427,146880,151541,152620,0ENSXETG00000030302.2cmplcmpl1,0,0,0,2,0,
587ENSXETT00000095917.1chr1-3293053294703293053294701329305,329470,0ENSXETG00000037036.1cmplcmpl0,
589ENSXETT00000005165.4chr1+5872726129795872726129796587272,590379,592510,608841,610834,612068,587457,590671,593335,609069,610961,612979,0ENSXETG00000002418.4cmplcmpl0,2,0,0,0,1,
589ENSXETT00000076283.1chr1+6203656215736203656215733620365,621143,621222,620385,621174,621573,0ENSXETG00000039580.1cmplcmpl0,2,0,
73ENSXETT00000005128.3chr1-6540776557156540776557151654077,655715,0ENSXETG00000002403.4cmplincmpl0,
590ENSXETT00000085750.1chr1-7089947091617091617091611708994,709161,0ENSXETG00000040274.1nonenone-1,
601ENSXETT00000062078.2chr1+217983121952872179831219528782179831,2180696,2181041,2182684,2187941,2191157,2192293,2194382,2179928,2180862,2181060,2182963,2188754,2191385,2192417,2195287,0ENSXETG00000033450.2cmplcmpl0,1,2,0,0,0,0,1,
601ENSXETT00000079655.1chr1-218975721906612189757219066142189757,2189906,2190053,2190627,2189846,2189986,2190168,2190661,0ENSXETG00000037881.1cmplincmpl1,2,1,0,
76ENSXETT00000060370.2chr1+3201001410918432010074108941253201001,3258251,3280425,3294882,3296012,3308889,3599671,3797439,3841232,3970526,3970929,3975166,3976584,3976771,3976859,3977307, ...3201109,3258447,3280592,3295002,3296279,3309093,3599707,3797520,3841385,3970619,3971086,3975367,3976606,3976779,3976916,3977338, ...0ENSXETG00000040099.1cmplcmpl0,0,1,0,0,0,0,0,0,0,0,1,1,2,1,1,2,0,0,0,0,2,0,0,0,
610ENSXETT00000082420.1chr1-328454632879803284546328798033284546,3286000,3287863,3284570,3286963,3287980,0ENSXETG00000038255.1cmplincmpl0,0,0,

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 xenTro9 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.

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