Schema for ncbiRefSeqCurated
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Database: otoGar3 Primary Table: ncbiRefSeqCurated Row Count: 13   Data last updated: 2020-04-08
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 11 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | NM_001301729.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | GL873523 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 24087461 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 24125424 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 24109620 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 24123179 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 12 | int(10) unsigned | range | Number of exons |
exonStarts | 24087461,24092047,24109525,... | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 24087937,24092185,24109722,... | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | AZIN1 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | cmpl | 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,-1,0,0,0,2,2,0,0,1,0,2, | 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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Connected Tables and Joining Fields
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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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11 | NM_001301729.1 | GL873523 | + | 24087461 | 24125424 | 24109620 | 24123179 | 12 | 24087461,24092047,24109525,24113804,24114417,24116253,24117806,24118190,24119206,24121152,24121772,24123067, | 24087937,24092185,24109722,24113978,24114590,24116388,24117888,24118265,24119369,24121268,24121987,24125424, | 0 | AZIN1 | cmpl | cmpl | -1,-1,0,0,0,2,2,0,0,1,0,2, |
11 | NM_001291492.1 | GL873523 | + | 24087461 | 24125424 | 24109620 | 24123179 | 13 | 24087461,24092047,24100039,24109525,24113804,24114417,24116253,24117806,24118190,24119206,24121152,24121772,24123067, | 24087937,24092185,24100185,24109722,24113978,24114590,24116388,24117888,24118265,24119369,24121268,24121987,24125424, | 0 | AZIN1 | cmpl | cmpl | -1,-1,-1,0,0,0,2,2,0,0,1,0,2, |
754 | NM_001291038.1 | GL873524 | + | 22228474 | 22237246 | 22228751 | 22236176 | 2 | 22228474,22234966, | 22228756,22237246, | 0 | PEG10 | cmpl | cmpl | 0,2, |
715 | NM_001289994.1 | GL873530 | - | 17068227 | 17086447 | 17069330 | 17086217 | 6 | 17068227,17069701,17070871,17073137,17073219,17086197, | 17069461,17069787,17071047,17073218,17073295,17086447, | 0 | OAZ2 | cmpl | cmpl | 1,2,0,0,2,0, |
816 | NM_001308456.1 | GL873532 | - | 30309955 | 30384372 | 30309955 | 30384372 | 35 | 30309955,30321490,30324585,30324885,30327418,30330025,30330859,30332695,30334827,30338994,30341196,30341572,30344057,30345914,30 ... | 30310009,30321658,30324774,30324951,30327533,30330078,30330934,30332824,30334923,30339222,30341388,30341659,30344145,30346048,30 ... | 0 | AOX2 | cmpl | cmpl | 0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0, |
12 | NM_001308455.1 | GL873532 | - | 30396145 | 30467569 | 30396145 | 30467569 | 35 | 30396145,30396996,30398924,30401958,30402191,30402792,30403978,30409409,30412692,30416017,30417653,30418027,30418432,30419752,30 ... | 30396199,30397164,30399110,30402024,30402306,30402845,30404053,30409538,30412788,30416245,30417845,30418114,30418520,30419886,30 ... | 0 | AOX4 | cmpl | cmpl | 0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0, |
818 | NM_001308454.1 | GL873532 | - | 30568198 | 30637429 | 30568251 | 30637428 | 35 | 30568198,30569143,30569760,30571560,30572682,30573964,30575468,30576220,30579216,30582100,30584019,30585045,30588049,30589333,30 ... | 30568302,30569311,30569949,30571626,30572797,30574017,30575543,30576349,30579312,30582328,30584211,30585132,30588137,30589467,30 ... | 0 | AOX1 | cmpl | cmpl | 0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0, |
700 | NM_001289715.1 | GL873548 | + | 15127123 | 15130443 | 15127202 | 15130003 | 6 | 15127123,15128748,15128807,15129242,15129672,15129869, | 15127348,15128806,15128894,15129415,15129758,15130443, | 0 | OAZ1 | cmpl | cmpl | 0,2,0,0,2,1, |
612 | NM_001281858.1 | GL873565 | + | 3607596 | 3629076 | 3607609 | 3629002 | 7 | 3607596,3612465,3613687,3618527,3619782,3627219,3628975, | 3607621,3612548,3613832,3618617,3619914,3627348,3629076, | 0 | TVP23B | cmpl | cmpl | 0,0,2,0,0,0,0, |
75 | NM_001285809.1 | GL873658 | - | 2617985 | 2627955 | 2617985 | 2627915 | 8 | 2617985,2619136,2619831,2620404,2622698,2624391,2626150,2627787, | 2618072,2619261,2619916,2620459,2622798,2624559,2626266,2627955, | 0 | RNASEH1 | cmpl | cmpl | 0,1,0,2,1,1,2,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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