Schema for SGP Genes - SGP Gene Predictions Using Mouse/Human Homology
  Database: mm9    Primary Table: sgpGene    Row Count: 35,983   Data last updated: 2007-10-01
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 609smallint(5) unsigned range Indexing field to speed chromosome range queries.
name chr1_1.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 3206102int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3211122int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3206102int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3211122int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 3206102,3211094,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3207049,3211122,longblob   Exon end positions (or start positions for minus strand item)
id 20897int(10) unsigned range  
name2 chr1_1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 1,0,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsidname2cdsStartStatcdsEndStatexonFrames
609chr1_1.1chr1-320610232111223206102321112223206102,3211094,3207049,3211122,20897chr1_1cmplcmpl1,0,
609chr1_2.1chr1-323999732593253239997325932523239997,3259284,3240025,3259325,20896chr1_2cmplcmpl2,0,
76chr1_3.1chr1-335380434200293353804342002943353804,3391491,3411782,3420000,3353847,3391519,3411982,3420029,20895chr1_3cmplcmpl2,1,2,0,
611chr1_4.1chr1+352187535228013521875352280133521875,3522003,3522385,3521983,3522358,3522801,20894chr1_4cmplcmpl0,0,1,
76chr1_5.1chr1-365233437199603652334371996053652334,3660632,3664599,3696254,3719947,3652356,3661130,3664618,3696281,3719960,20893chr1_5cmplcmpl2,2,1,1,0,
9chr1_6.1chr1-3989637424945639896374249456233989637,3997736,4009150,4014816,4031968,4046242,4082697,4109748,4110095,4132692,4137892,4138734,4153935,4160285,4187614,4196740, ...3989698,3997818,4009229,4014971,4032188,4046359,4082861,4109793,4110154,4132847,4138044,4138825,4154022,4160485,4187722,4196918, ...20892chr1_6cmplcmpl2,1,0,1,0,0,1,1,2,0,1,0,0,1,1,0,0,0,1,2,1,0,0,
617chr1_7.1chr1-425006743227194250067432271974250067,4250380,4257549,4274846,4283006,4301350,4322712,4250179,4250592,4257701,4274979,4283093,4301514,4322719,20891chr1_7cmplcmpl2,0,1,0,0,1,0,
618chr1_8.1chr1-433468043429064334680434290634334680,4341990,4342282,4340094,4342162,4342906,20890chr1_8cmplcmpl1,0,0,
619chr1_9.1chr1-448179644834874481796448348724481796,4483180,4482749,4483487,20889chr1_9cmplcmpl1,0,
77chr1_10.1chr1+451324446014874513244460148774513244,4514758,4515864,4534101,4562453,4600691,4601403,4513436,4515451,4516105,4534283,4562493,4600972,4601487,20888chr1_10cmplcmpl0,0,0,1,0,1,0,

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

SGP Genes (sgpGene) Track Description
 

Description

This track shows gene predictions from the SGP2 homology-based gene prediction program developed by Roderic Guigó's "Computational Biology of RNA Processing" group, which is part of the Centre de Regulació Genòmica (CRG) in Barcelona, Catalunya, Spain. To predict genes in a genomic query, SGP2 combines geneid predictions with tblastx comparisons of the genome of the target species against genomic sequences of other species (reference genomes) deemed to be at an appropriate evolutionary distance from the target.

Credits

Thanks to the "Computational Biology of RNA Processing" group for providing these data.