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  Schema for Genscan Genes - Genscan Gene Predictions
  Database: bosTau4    Primary Table: genscan    Row Count: 49,598
Format description: A gene prediction.
fieldexampleSQL type info description
bin 585smallint unsigned range Indexing field to speed chromosome range queries.
name chr1.1varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 27289int unsigned range Transcription start position
txEnd 28224int unsigned range Transcription end position
cdsStart 27289int unsigned range Coding region start
cdsEnd 28224int unsigned range Coding region end
exonCount 2int unsigned range Number of exons
exonStarts 27289,28092,longblob   Exon start positions
exonEnds 27574,28224,longblob   Exon end positions

  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. Click here 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 these data.


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