Schema for Genscan Genes - Genscan Gene Predictions
  Database: mm9    Primary Table: genscan    Row Count: 45,189   Data last updated: 2007-08-10
Format description: A gene prediction.
fieldexampleSQL type info description
bin 608smallint(5) 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 3018706int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3044814int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3018706int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3044814int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 3018706,3044213,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3018786,3044814,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        mm9.genscanPep.name (via genscan.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
608chr1.1chr1+301870630448143018706304481423018706,3044213,3018786,3044814,
9chr1.2chr1-308524331892283085243318922843085243,3109302,3188693,3189178,3085390,3109416,3188784,3189228,
609chr1.3chr1+319714932011913197149320119123197149,3201057,3197174,3201191,
609chr1.4chr1-320610232142923206102321429223206102,3214258,3207049,3214292,
610chr1.5chr1-327996133609993279961336099933279961,3311577,3360948,3280112,3311738,3360999,
76chr1.6chr1-338705034217293387050342172953387050,3401224,3411782,3414294,3421571,3387254,3401313,3411982,3414414,3421729,
611chr1.7chr1-350705335225813507053352258143507053,3521730,3522035,3522444,3507097,3521979,3522286,3522581,
612chr1.8chr1+354447636251293544476362512943544476,3565147,3585405,3624871,3544570,3565258,3585557,3625129,
612chr1.18chr1-362759836614293627598366142933627598,3660632,3661307,3627845,3661130,3661429,
76chr1.19chr1+374431838242813744318382428123744318,3824093,3744361,3824281,

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

Genscan Genes (genscan) Track Description
 

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.

For more information on the different gene tracks, see our Genes FAQ.

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.

Methods

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.

Credits

Thanks to Chris Burge for providing the Genscan program.

References

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. PMID: 9149143