Schema for FlyBase Genes - FlyBase Protein-Coding Genes
  Database: dm3    Primary Table: flyBaseGene    Row Count: 21,243   Data last updated: 2008-10-21
Format description: A gene prediction.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name CG11023-RAvarchar(255) values Name of gene
chrom chr2Lvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 7528int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 9491int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 7679int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 9276int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 7528,8228,8667,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 8116,8589,9491,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        dm3.arbExpDistance.query (via flyBaseGene.name)
      dm3.arbExpDistance.target (via flyBaseGene.name)
      dm3.ceBlastTab.query (via flyBaseGene.name)
      dm3.drBlastTab.query (via flyBaseGene.name)
      dm3.flyBase2004Xref.name (via flyBaseGene.name)
      dm3.flyBaseBlastTab.query (via flyBaseGene.name)
      dm3.flyBaseBlastTab.target (via flyBaseGene.name)
      dm3.flyBaseCanonical.transcript (via flyBaseGene.name)
      dm3.flyBaseIsoforms.transcript (via flyBaseGene.name)
      dm3.flyBaseNoncoding.name (via flyBaseGene.name)
      dm3.flyBasePep.name (via flyBaseGene.name)
      dm3.flyBaseToCG.name (via flyBaseGene.name)
      dm3.flyBaseToDescription.name (via flyBaseGene.name)
      dm3.flyBaseToPfam.name (via flyBaseGene.name)
      dm3.flyBaseToRefSeq.name (via flyBaseGene.name)
      dm3.flyBaseToUniProt.name (via flyBaseGene.name)
      dm3.flyP2P.query (via flyBaseGene.name)
      dm3.flyP2P.target (via flyBaseGene.name)
      dm3.hgBlastTab.query (via flyBaseGene.name)
      dm3.mmBlastTab.query (via flyBaseGene.name)
      dm3.rnBlastTab.query (via flyBaseGene.name)
      dm3.scBlastTab.query (via flyBaseGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
585CG11023-RAchr2L+752894917679927637528,8228,8667,8116,8589,9491,
585CG2671-RCchr2L-983518583112141713699835,11409,11778,12285,13519,13682,14932,17052,18260,11344,11518,12221,12928,13625,14874,15711,17212,18583,
585CG2671-RBchr2L-983521372112141994499835,11409,11778,12285,13519,13682,14932,19884,21135,11344,11518,12221,12928,13625,14874,15711,20020,21372,
585CG2671-RFchr2L-9835213721121415648109835,11409,11778,12285,13519,13682,14932,19879,21065,21348,11344,11518,12221,12928,13625,14874,15711,20020,21200,21372,
585CG2671-REchr2L-983521372112141564899835,11409,11778,12285,13519,13682,14932,19879,21065,11344,11518,12221,12928,13625,14874,15711,20015,21372,
585CG2671-RAchr2L-9835185831121417136109835,11409,11778,12285,13519,13682,14932,17052,18025,18260,11344,11518,12221,12928,13625,14874,15711,17212,18168,18583,
585CG2671-RDchr2L-983521372112141564899835,11409,11778,12285,13519,13682,14932,19879,21065,11344,11518,12221,12928,13625,14874,15711,20020,21372,
585CG2657-RBchr2L-21918251512191825151521918,22742,22993,23928,24746,22687,22935,23873,24210,25151,
585CG31973-REchr2L-254015924226520581501325401,26765,27052,28410,28732,28981,33844,34557,34719,38534,39300,58080,59189,26688,26964,27490,28639,28926,29068,34288,34604,35212,38731,39857,58182,59242,
585CG31973-RBchr2L-254015924226520581501425401,26765,27052,28014,28732,28981,30393,33844,34557,34719,38534,39300,58080,59189,26688,26964,27490,28240,28926,29068,33270,34288,34604,35212,38731,39857,58182,59242,

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

FlyBase Genes (flyBaseGene) Track Description
 

Description

This track shows protein-coding genes annotated by FlyBase and the Drosophila Heterochromatin Genome Project (DHGP). Annotations on both heterochromatin and euchromatic sequences were downloaded from FlyBase D. melanogaster version 5.12.

Credits

Thanks to FlyBase and DHGP for providing these annotations.

References

Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM; FlyBase Consortium. FlyBase: genomes by the dozen. Nucleic Acids Res. 2007 Jan;35(Database issue):D486-91.

Smith CD, Shu S, Mungall CJ, Karpen GH. The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin. Science. 2007 Jun 15;316(5831):1586-91.