Schema for Ensembl Genes - Ensembl Genes
  Database: calJac3    Primary Table: ensGene    Row Count: 55,116   Data last updated: 2016-10-18
Format description: Ensembl gene predictions.
fieldexampleSQL type info description
bin 587smallint(5) unsigned range Indexing field to speed chromosome range queries.
name ENSCJAT00000051294.1varchar(255) values Ensembl transcript ID
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 280482int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 280589int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 280589int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 280589int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 280482,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 280589,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range always 0 for Ensembl genes
name2 ENSCJAG00000030309.1varchar(255) values Ensembl gene ID
cdsStartStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields
        calJac3.ensGtp.transcript (via ensGene.name)
      calJac3.ensPep.name (via ensGene.name)
      calJac3.ensemblSource.name (via ensGene.name)
      calJac3.ensemblToGeneName.name (via ensGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
587ENSCJAT00000051294.1chr1-2804822805892805892805891280482,280589,0ENSCJAG00000030309.1nonenone-1,
588ENSCJAT00000048144.1chr1+3955723957133957133957131395572,395713,0ENSCJAG00000027159.1nonenone-1,
589ENSCJAT00000041746.2chr1+6088796098676098676098672608879,608940,608939,609867,0ENSCJAG00000021223.2nonenone-1,-1,
590ENSCJAT00000015848.2chr1+6966076975726966076975723696607,697224,697332,697219,697275,697572,0ENSCJAG00000031552.1cmplcmpl0,0,0,
590ENSCJAT00000057358.1chr1-7508957510017510017510011750895,751001,0ENSCJAG00000033063.1nonenone-1,
592ENSCJAT00000006122.2chr1-9756739832599768789796453975673,979589,982825,979351,979669,983259,0ENSCJAG00000003187.2cmplcmpl2,0,-1,
606ENSCJAT00000058771.1chr1+286153828685122864308286718262861538,2864300,2866638,2866678,2866698,2866705,2861750,2866636,2866677,2866696,2866704,2868512,0ENSCJAG00000003189.2cmplcmpl-1,0,0,0,0,0,
606ENSCJAT00000006138.1chr1+286214728672242862384286718262862147,2865126,2866638,2866678,2866698,2866705,2862479,2866636,2866677,2866696,2866704,2867224,0ENSCJAG00000003189.2cmplcmpl0,2,0,0,0,0,
606ENSCJAT00000006127.2chr1+286430828671822864308286718232864308,2866632,2866754,2866630,2866681,2867182,0ENSCJAG00000003189.2cmplcmpl0,0,1,
611ENSCJAT00000046399.1chr1+351974735198223519822351982213519747,3519822,0ENSCJAG00000025414.1nonenone-1,

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 calJac3 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