Schema for ncbiRefSeq
  Database: calMil1    Primary Table: ncbiRefSeq    Row Count: 30,695   Data last updated: 2020-04-01
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name XR_489181.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom AAVX02039917varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 43042int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 47028int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 47028int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 47028int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 43042,46899,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 43198,47028,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC103190692varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,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
        calMil1.ncbiRefSeqCds.id (via ncbiRefSeq.name)
      calMil1.ncbiRefSeqCurated.name (via ncbiRefSeq.name)
      calMil1.ncbiRefSeqLink.id (via ncbiRefSeq.name)
      calMil1.ncbiRefSeqPredicted.name (via ncbiRefSeq.name)
      calMil1.ncbiRefSeqPsl.qName (via ncbiRefSeq.name)
      calMil1.seqNcbiRefSeq.acc (via ncbiRefSeq.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585XR_489181.1AAVX02039917-43042470284702847028243042,46899,43198,47028,0LOC103190692nonenone-1,-1,
585XM_007911773.1AAVX02040487+8731562952259954428238731,13871,22597,26713,27400,28962,29989,32508,33342,33634,34478,36022,38654,41182,43654,44675,45951,46994,47803,50386,51982,537 ...9328,14033,22693,26797,27573,29147,30092,32635,33452,33747,34597,36078,38861,41306,43813,44849,46062,47170,47941,50491,52075,538 ...0LOC103190869cmplcmpl-1,-1,0,1,1,0,2,0,1,0,2,1,0,0,1,1,1,1,0,0,0,0,2,
585XM_007911910.1AAVX02040794+244255346244254944162442,2874,13346,15182,24028,26746,27640,28722,29052,29213,30604,31847,33806,35432,36087,52986,2511,3103,13402,15308,24184,26841,27767,28969,29108,29296,30753,31986,34004,35669,36244,55346,0LOC103190984cmplcmpl1,1,2,1,1,1,0,1,2,1,0,2,0,0,0,1,
585XM_007912056.1AAVX02041197-40891328372291255464089,6742,9711,11261,12113,13266,4099,7475,9879,11789,12572,13283,0LOC103191103cmplcmpl-1,0,0,0,0,-1,
585XM_007912054.1AAVX02041197-40891642172291255464089,6742,9711,11261,12113,16261,4099,7475,9879,11789,12572,16421,0LOC103191103cmplcmpl-1,0,0,0,0,-1,
585XM_007912055.1AAVX02041197-59761642172291255455976,9711,11261,12113,16261,7475,9879,11789,12572,16421,0LOC103191103cmplcmpl0,0,0,0,-1,
585XM_007912057.1AAVX02041197-26026342732657631394526026,28805,29641,30953,34062,26846,28970,30169,31412,34273,0LOC103191104cmplcmpl0,0,0,0,-1,
585XM_007912103.1AAVX02041304-19320313952033430395419320,22982,30347,31225,21650,23148,30424,31395,0LOC103191140cmplcmpl1,0,0,-1,
585XM_007912102.1AAVX02041304-19320320602033430395419320,22982,30347,31988,21650,23148,30424,32060,0LOC103191140cmplcmpl1,0,0,-1,
585XM_007912101.1AAVX02041304+32193422894029441626332193,35817,40290,32254,35904,42289,0leng9cmplcmpl-1,-1,0,

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