Schema for ncbiRefSeqCurated
  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
fieldexampleSQL type info description
bin 11smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001301729.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom GL873523varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 24087461int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 24125424int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 24109620int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 24123179int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(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 0int(11) range score
name2 AZIN1varchar(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,-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.

Connected Tables and Joining Fields
        otoGar3.ncbiRefSeq.name (via ncbiRefSeqCurated.name)
      otoGar3.ncbiRefSeqCds.id (via ncbiRefSeqCurated.name)
      otoGar3.ncbiRefSeqLink.id (via ncbiRefSeqCurated.name)
      otoGar3.ncbiRefSeqPredicted.name (via ncbiRefSeqCurated.name)
      otoGar3.ncbiRefSeqPsl.qName (via ncbiRefSeqCurated.name)
      otoGar3.seqNcbiRefSeq.acc (via ncbiRefSeqCurated.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
11NM_001301729.1GL873523+240874612412542424109620241231791224087461,24092047,24109525,24113804,24114417,24116253,24117806,24118190,24119206,24121152,24121772,24123067,24087937,24092185,24109722,24113978,24114590,24116388,24117888,24118265,24119369,24121268,24121987,24125424,0AZIN1cmplcmpl-1,-1,0,0,0,2,2,0,0,1,0,2,
11NM_001291492.1GL873523+240874612412542424109620241231791324087461,24092047,24100039,24109525,24113804,24114417,24116253,24117806,24118190,24119206,24121152,24121772,24123067,24087937,24092185,24100185,24109722,24113978,24114590,24116388,24117888,24118265,24119369,24121268,24121987,24125424,0AZIN1cmplcmpl-1,-1,-1,0,0,0,2,2,0,0,1,0,2,
754NM_001291038.1GL873524+22228474222372462222875122236176222228474,22234966,22228756,22237246,0PEG10cmplcmpl0,2,
715NM_001289994.1GL873530-17068227170864471706933017086217617068227,17069701,17070871,17073137,17073219,17086197,17069461,17069787,17071047,17073218,17073295,17086447,0OAZ2cmplcmpl1,2,0,0,2,0,
816NM_001308456.1GL873532-303099553038437230309955303843723530309955,30321490,30324585,30324885,30327418,30330025,30330859,30332695,30334827,30338994,30341196,30341572,30344057,30345914,30 ...30310009,30321658,30324774,30324951,30327533,30330078,30330934,30332824,30334923,30339222,30341388,30341659,30344145,30346048,30 ...0AOX2cmplcmpl0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0,
12NM_001308455.1GL873532-303961453046756930396145304675693530396145,30396996,30398924,30401958,30402191,30402792,30403978,30409409,30412692,30416017,30417653,30418027,30418432,30419752,30 ...30396199,30397164,30399110,30402024,30402306,30402845,30404053,30409538,30412788,30416245,30417845,30418114,30418520,30419886,30 ...0AOX4cmplcmpl0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0,
818NM_001308454.1GL873532-305681983063742930568251306374283530568198,30569143,30569760,30571560,30572682,30573964,30575468,30576220,30579216,30582100,30584019,30585045,30588049,30589333,30 ...30568302,30569311,30569949,30571626,30572797,30574017,30575543,30576349,30579312,30582328,30584211,30585132,30588137,30589467,30 ...0AOX1cmplcmpl0,0,0,0,2,0,0,0,0,0,0,0,2,0,1,0,0,2,0,0,2,0,1,0,1,1,0,0,0,1,0,2,1,0,0,
700NM_001289715.1GL873548+15127123151304431512720215130003615127123,15128748,15128807,15129242,15129672,15129869,15127348,15128806,15128894,15129415,15129758,15130443,0OAZ1cmplcmpl0,2,0,0,2,1,
612NM_001281858.1GL873565+360759636290763607609362900273607596,3612465,3613687,3618527,3619782,3627219,3628975,3607621,3612548,3613832,3618617,3619914,3627348,3629076,0TVP23Bcmplcmpl0,0,2,0,0,0,0,
75NM_001285809.1GL873658-261798526279552617985262791582617985,2619136,2619831,2620404,2622698,2624391,2626150,2627787,2618072,2619261,2619916,2620459,2622798,2624559,2626266,2627955,0RNASEH1cmplcmpl0,1,0,2,1,1,2,0,

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