Schema for Genscan Genes - Genscan Gene Predictions
  Database: dm3gene    Primary Table: genscan    Row Count: 3
fieldexampleSQL type info
bin 585smallint(5) unsigned range
name contig1.1varchar(255) values
chrom contig1varchar(255) values
strand +char(1) values
txStart 9int(10) unsigned range
txEnd 360int(10) unsigned range
cdsStart 9int(10) unsigned range
cdsEnd 360int(10) unsigned range
exonCount 1int(10) unsigned range
exonStarts 9,longblob  
exonEnds 360,longblob  

Sample Rows

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

Genscan Genes (genscan) Track Description


This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks.

The track description page offers the following filter and configuration options:

  • Color track by codons: Select the genomic codons option to color and label each codon in a zoomed-in display to facilitate validation and comparison of gene predictions. Go to the Coloring Gene Predictions and Annotations by Codon page for more information about this feature.


For a description of the Genscan program and the model that underlies it, refer to Burge and Karlin (1997) in the References section below. The splice site models used are described in more detail in Burge (1998) below.


Thanks to Chris Burge for providing the Genscan program.


Burge C. Modeling Dependencies in Pre-mRNA Splicing Signals. In: Salzberg S, Searls D, Kasif S, editors. Computational Methods in Molecular Biology. Amsterdam: Elsevier Science; 1998. p. 127-163.

Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997 Apr 25;268(1):78-94.