Schema for SGP Genes - SGP Gene Predictions Using Rat/Human Homology
  Database: rn6    Primary Table: sgpGene    Row Count: 37,981   Data last updated: 2015-07-30
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 587smallint(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 328914int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 353008int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 328914int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 353008int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 328914,353004,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 329731,353008,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 chr1_1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('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 1,2,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
587chr1_1.1chr1+3289143530083289143530082328914,353004,329731,353008,0chr1_1incmplcmpl1,2,
588chr1_2.1chr1+4087944096764087944096761408794,409676,0chr1_2cmplcmpl0,
590chr1_3.1chr1+6740037080656740037080654674003,702859,704512,707158,674009,703663,704598,708065,0chr1_3cmplcmpl0,0,0,2,
590chr1_4.1chr1-7154187625967154187625964715418,744738,751870,762590,716252,745499,752195,762596,0chr1_4cmplcmpl0,1,0,0,
591chr1_5.1chr1-8048618105048048618105044804861,808330,809266,810450,805768,808416,810070,810504,0chr1_5cmplcmpl2,0,0,0,
73chr1_6.1chr1-8896199507258896199507256889619,892832,893164,894244,928661,950634,890311,892881,893218,894985,928681,950725,0chr1_6cmplcmpl1,0,0,0,1,0,
74chr1_7.1chr1+117053012078501170530120785041170530,1198755,1205870,1207807,1170621,1199004,1205904,1207850,0chr1_7cmplcmpl0,1,1,2,
74chr1_8.1chr1-126377713160281263777131602861263777,1265585,1289882,1292411,1306799,1316015,1263789,1265680,1289905,1292479,1306948,1316028,0chr1_8cmplcmpl0,1,2,0,1,0,
595chr1_9.1chr1-139083513949561390835139495621390835,1394865,1391110,1394956,0chr1_9cmplcmpl1,0,
74chr1_10.1chr1-141436814747681414368147476861414368,1440382,1456812,1472803,1473328,1474758,1414502,1440643,1457073,1473067,1473589,1474768,0chr1_10cmplcmpl1,1,1,1,1,0,

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 SGP program, developed at the Genome Bioinformatics Laboratory (GBL), which is part of the Grup de Recerca en Informàtica Biomèdica (GRIB) at Institut Municipal d'Investigació Mèdica (IMIM) / Centre de Regulació Genòmica (CRG) in Barcelona. To predict genes in a genomic query, SGP combines geneid predictions with tblastx comparisons of the genomic query against other genomic sequences.

Credits

Thanks to GRIB for providing these gene predictions.