Schema for SGP Genes - SGP Gene Predictions Using Rat/Human Homology
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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
field | example | SQL type | info | description |
bin | 587 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | chr1_1.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 328914 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 353008 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 328914 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 353008 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 2 | int(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 | 0 | int(11) | range | score |
name2 | chr1_1 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | cmpl | enum('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. |
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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587 | chr1_1.1 | chr1 | + | 328914 | 353008 | 328914 | 353008 | 2 | 328914,353004, | 329731,353008, | 0 | chr1_1 | incmpl | cmpl | 1,2, |
588 | chr1_2.1 | chr1 | + | 408794 | 409676 | 408794 | 409676 | 1 | 408794, | 409676, | 0 | chr1_2 | cmpl | cmpl | 0, |
590 | chr1_3.1 | chr1 | + | 674003 | 708065 | 674003 | 708065 | 4 | 674003,702859,704512,707158, | 674009,703663,704598,708065, | 0 | chr1_3 | cmpl | cmpl | 0,0,0,2, |
590 | chr1_4.1 | chr1 | - | 715418 | 762596 | 715418 | 762596 | 4 | 715418,744738,751870,762590, | 716252,745499,752195,762596, | 0 | chr1_4 | cmpl | cmpl | 0,1,0,0, |
591 | chr1_5.1 | chr1 | - | 804861 | 810504 | 804861 | 810504 | 4 | 804861,808330,809266,810450, | 805768,808416,810070,810504, | 0 | chr1_5 | cmpl | cmpl | 2,0,0,0, |
73 | chr1_6.1 | chr1 | - | 889619 | 950725 | 889619 | 950725 | 6 | 889619,892832,893164,894244,928661,950634, | 890311,892881,893218,894985,928681,950725, | 0 | chr1_6 | cmpl | cmpl | 1,0,0,0,1,0, |
74 | chr1_7.1 | chr1 | + | 1170530 | 1207850 | 1170530 | 1207850 | 4 | 1170530,1198755,1205870,1207807, | 1170621,1199004,1205904,1207850, | 0 | chr1_7 | cmpl | cmpl | 0,1,1,2, |
74 | chr1_8.1 | chr1 | - | 1263777 | 1316028 | 1263777 | 1316028 | 6 | 1263777,1265585,1289882,1292411,1306799,1316015, | 1263789,1265680,1289905,1292479,1306948,1316028, | 0 | chr1_8 | cmpl | cmpl | 0,1,2,0,1,0, |
595 | chr1_9.1 | chr1 | - | 1390835 | 1394956 | 1390835 | 1394956 | 2 | 1390835,1394865, | 1391110,1394956, | 0 | chr1_9 | cmpl | cmpl | 1,0, |
74 | chr1_10.1 | chr1 | - | 1414368 | 1474768 | 1414368 | 1474768 | 6 | 1414368,1440382,1456812,1472803,1473328,1474758, | 1414502,1440643,1457073,1473067,1473589,1474768, | 0 | chr1_10 | cmpl | cmpl | 1,1,1,1,1,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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SGP Genes (sgpGene) Track Description
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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.
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