Schema for Genscan Genes - Genscan Gene Predictions

Database: DyakCAF1 Primary Table: genscan Row Count: 19,789 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	chr2L.1	`varchar(255)`	values
`chrom`	chr2L	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	9271	`int(10) unsigned`	range
`txEnd`	14684	`int(10) unsigned`	range
`cdsStart`	9271	`int(10) unsigned`	range
`cdsEnd`	14684	`int(10) unsigned`	range
`exonCount`	6	`int(10) unsigned`	range
`exonStarts`	9271,9784,10693,10856,12106...	`longblob`
`exonEnds`	9722,10349,10799,12048,1288...	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	chr2L.1	chr2L	-	9271	14684	9271	14684	6	9271,9784,10693,10856,12106,14600,	9722,10349,10799,12048,12885,14684,
585	chr2L.2	chr2L	-	16689	19686	16689	19686	3	16689,17769,19281,	17393,18649,19686,
585	chr2L.3	chr2L	-	20962	29753	20962	29753	12	20962,21194,21490,22503,22905,23238,24943,27371,27591,28097,28211,29220,	21130,21393,21928,22803,23134,23432,25710,27541,27815,28144,28554,29753,
585	chr2L.4	chr2L	-	29805	47705	29805	47705	4	29805,32040,32502,47635,	31957,32237,33059,47705,
585	chr2L.5	chr2L	+	55250	65401	55250	65401	9	55250,56099,56413,56602,59103,61859,62894,64196,64380,	55348,56277,56545,59046,59300,62173,63083,64312,65401,
585	chr2L.6	chr2L	+	65718	67377	65718	67377	2	65718,67150,	66871,67377,
585	chr2L.7	chr2L	-	72463	76384	72463	76384	3	72463,75690,76311,	73485,75882,76384,
585	chr2L.8	chr2L	+	84208	93127	84208	93127	13	84208,84337,84480,84698,87227,87873,89130,90107,90361,90594,91893,92369,92879,	84249,84419,84650,87178,87814,88833,89862,90288,90540,90965,92246,92798,93127,
585	chr2L.9	chr2L	-	93839	96016	93839	96016	3	93839,94881,95315,	94285,95285,96016,
585	chr2L.10	chr2L	+	98063	102729	98063	102729	6	98063,99782,99927,100177,101826,102620,	98187,99860,100050,100351,102556,102729,

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

Description