Schema for ncbiRefSeqPredicted
  Database: ochPri3    Primary Table: ncbiRefSeqPredicted    Row Count: 26,227   Data last updated: 2020-03-20
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 XM_004599723.1varchar(255) values Name of gene (usually transcript_id from GTF)
chrom ALIT01119338varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 8906int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 14354int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 8906int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 14354int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 8906,14141,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 9092,14354,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC101532914varchar(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,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
        ochPri3.ncbiRefSeq.name (via ncbiRefSeqPredicted.name)
      ochPri3.ncbiRefSeqCds.id (via ncbiRefSeqPredicted.name)
      ochPri3.ncbiRefSeqCurated.name (via ncbiRefSeqPredicted.name)
      ochPri3.ncbiRefSeqLink.id (via ncbiRefSeqPredicted.name)
      ochPri3.ncbiRefSeqPsl.qName (via ncbiRefSeqPredicted.name)
      ochPri3.seqNcbiRefSeq.acc (via ncbiRefSeqPredicted.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585XM_004599723.1ALIT01119338-89061435489061435428906,14141,9092,14354,0LOC101532914cmplcmpl1,1,
585XM_004599725.1ALIT01119401-36802358536802354833680,10494,23404,3783,10607,23585,0LOC101533391cmplcmpl2,0,0,
585XM_004599726.1ALIT01119402-80052202480052202458005,8895,14072,19073,21935,8164,9111,14408,19329,22024,0LMCD1cmplcmpl0,0,0,2,0,
585XM_012931245.1ALIT01119634+10140208461014020846610140,11729,14283,17156,17936,20765,10231,11893,14389,17231,17974,20846,0LOC105942638cmplcmpl0,1,0,1,1,0,
585XM_004599732.2ALIT01119880+81032551281592551248103,20021,23488,25352,8225,20055,23653,25512,0LOC101536068cmplcmpl0,0,1,1,
585XM_004599741.1ALIT01120075-12231408012231408051223,5519,7750,10710,14017,1581,5624,7854,10791,14080,0LOC101518198cmplcmpl2,2,0,0,0,
585XM_012931252.1ALIT01120092-735988957359889517359,8895,0LOC101518444cmplcmpl0,
585XM_004599743.1ALIT01120252-467707246770724467,1100,5696,7014,722,1364,6047,7072,0LOC101519416cmplcmpl1,1,1,0,
585XM_012931254.1ALIT01120281-160618701606175611606,1870,0LOC105942642cmplcmpl0,
585XM_004599744.1ALIT01120286-758763375876335758,2906,3719,6947,7538,815,3029,3819,7316,7633,0LOC101520153cmplcmpl0,0,2,2,0,

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