Schema for ncbiRefSeq
  Database: xenTro9    Primary Table: ncbiRefSeq    Row Count: 43,724   Data last updated: 2021-02-11
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 586smallint(5) unsigned range Indexing field to speed chromosome range queries.
name XM_012956089.1varchar(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 133269int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 152620int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 133269int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 152620int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 133269,140925,143199,146034...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 134186,141049,143418,146880...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC100490505varchar(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 1,0,0,0,2,0,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
        xenTro9.ncbiRefSeqCds.id (via ncbiRefSeq.name)
      xenTro9.ncbiRefSeqCurated.name (via ncbiRefSeq.name)
      xenTro9.ncbiRefSeqLink.id (via ncbiRefSeq.name)
      xenTro9.ncbiRefSeqPredicted.name (via ncbiRefSeq.name)
      xenTro9.ncbiRefSeqPsl.qName (via ncbiRefSeq.name)
      xenTro9.seqNcbiRefSeq.acc (via ncbiRefSeq.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
586XM_012956089.1chr1-1332691526201332691526206133269,140925,143199,146034,151249,152381,134186,141049,143418,146880,151541,152620,0LOC100490505cmplcmpl1,0,0,0,2,0,
586XM_018090860.1chr1-1584691744331584691744335158469,160350,162164,170432,174037,159374,160474,162386,171221,174433,0LOC100490675cmplcmpl1,0,0,0,0,
586XM_012956191.2chr1-1923491951091925181950112192349,194935,193426,195109,0LOC100489075cmplcmpl1,0,
586XM_002941730.2chr1-2114822120222114822120221211482,212022,0LOC100488911cmplcmpl0,
586XM_012956192.2chr1+2182272436232182272436235218227,233350,235322,238854,242715,218478,233453,235619,238978,243623,0LOC100488739cmplcmpl0,2,0,0,1,
587XM_012956193.2chr1+2863133035092863133035094286313,289920,291982,303393,286394,290044,292879,303509,0LOC105946480cmplcmpl0,0,1,1,
588XM_012956142.2chr1+4352414611384352544611386435241,448180,453999,456506,459382,460233,435499,448472,454833,456725,459506,461138,0LOC100487968cmplcmpl0,2,0,0,0,1,
588XM_012956143.1chr1-5104295229605104295229606510429,512239,517796,518541,521348,522766,511337,512363,518024,519342,521640,522960,0LOC105946420cmplcmpl1,0,0,0,2,0,
589XM_018090861.1chr1+5639215794245639215794245563921,569617,571441,577976,578522,564046,569753,572263,578100,579424,0LOC108645644cmplcmpl0,2,0,0,1,
589XM_018090862.1chr1+5872216158575872216158577587221,590379,592510,608841,610756,612068,615393,587457,590671,593335,609069,610961,612974,615857,0LOC100498444cmplcmpl0,2,0,0,0,1,1,

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