Schema for Ensembl Genes - Ensembl Genes
  Database: proCap1    Primary Table: ensGene    Row Count: 37,004   Data last updated: 2019-01-11
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
name ENSPCAT00000002217.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_0varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 7247int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 282389int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 7247int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 282389int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 325int(10) unsigned range Number of exons
exonStarts 7247,7683,8529,8772,8969,10...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 7546,7995,8683,8967,9463,10...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ENSPCAG00000000833.1varchar(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 1,1,0,0,1,0,0,0,2,0,0,0,0,0...longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields
        proCap1.ensGtp.transcript (via ensGene.name)
      proCap1.ensPep.name (via ensGene.name)
      proCap1.ensemblSource.name (via ensGene.name)
      proCap1.ensemblToGeneName.name (via ensGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
73ENSPCAT00000002217.1scaffold_0-724728238972472823893257247,7683,8529,8772,8969,10332,10594,13966,15760,15762,15810,15821,15835,15840,15847,16564,17932,18463,19133,19549,19990,20670,2 ...7546,7995,8683,8967,9463,10489,13732,15757,15761,15806,15819,15833,15838,15843,16434,17158,18461,18507,19433,19855,20575,20973,2 ...0ENSPCAG00000000833.1cmplcmpl1,1,0,0,1,0,0,0,2,0,0,0,0,0,1,1,0,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,0,0,0,0,0,2,0,0,1,1,1,1,1,2, ...
587ENSPCAT00000002278.1scaffold_0-31169635914331169635914313311696,320572,320592,320615,324074,326804,329454,346337,348901,351075,352994,353309,358969,312572,320590,320614,320692,324187,326988,329649,346487,349084,351264,353120,353486,359143,0ENSPCAG00000002282.1cmplincmpl0,0,2,0,1,0,0,0,0,0,0,0,0,
585ENSPCAT00000006862.1scaffold_1+36652109561366521095613436652,73545,81362,84974,89396,89560,89801,90187,90390,91083,91124,91776,91992,97928,98080,98234,98409,99351,105946,106243,106442 ...36769,73605,81407,85116,89447,89660,89960,90295,90469,91117,91140,91848,92067,98003,98152,98306,98471,99428,106044,106334,106505 ...0ENSPCAG00000006738.1cmplcmpl0,0,0,0,2,2,0,0,0,1,2,0,0,0,0,0,0,2,2,1,2,2,1,1,0,0,0,0,0,2,1,2,1,0,
585ENSPCAT00000006666.1scaffold_1+1161341200431161341200436116134,116568,116591,116602,116646,119838,116566,116589,116600,116644,116981,120043,0ENSPCAG00000006711.1cmplcmpl0,0,0,0,0,2,
585ENSPCAT00000006632.1scaffold_1-1215051233381215051233383121505,122705,123211,122009,122743,123338,0ENSPCAG00000006688.1cmplcmpl0,1,0,
585ENSPCAT00000006617.1scaffold_1+12412712711812412712711811124127,124767,124945,125274,125749,125960,126167,126309,126489,126821,127050,124205,124859,125114,125383,125886,126058,126204,126403,126607,126964,127118,0ENSPCAG00000006617.1cmplcmpl0,0,2,0,1,0,2,0,1,2,1,
73ENSPCAT00000006540.1scaffold_1+12858313216112858313216114128583,128609,128673,128941,129811,130053,130228,130468,130646,131094,131425,131642,131878,132085,128607,128672,128675,129050,129928,130107,130366,130557,130747,131267,131551,131764,132004,132161,0ENSPCAG00000006538.1cmplcmpl0,0,0,2,0,0,0,0,2,1,0,0,2,2,
586ENSPCAT00000006479.1scaffold_1+13279414127213279414127210132794,133027,134890,139910,139927,139938,139943,140064,140394,141125,133025,133043,134997,139925,139936,139941,139962,140275,140510,141272,0ENSPCAG00000006499.1cmplcmpl0,0,1,0,0,0,0,0,1,0,
586ENSPCAT00000006433.1scaffold_1+1430611446471430611446473143061,144289,144581,143216,144410,144647,0ENSPCAG00000006487.1cmplcmpl0,2,0,
586ENSPCAT00000006415.1scaffold_1+1508491531821508491531823150849,152285,152768,151770,152375,153182,0ENSPCAG00000006458.1cmplcmpl0,0,0,

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 proCap1 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