Schema for xenoRefGene
  Database: panTro2    Primary Table: xenoRefGene    Row Count: 340,768   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1003smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001256409varchar(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 54890195int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 54913702int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 54896038int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 54913473int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 54890195,54891826,54896024,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 54890371,54891863,54896511,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LRRC42varchar(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,-1,0,2,2,1,0,0,1,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
        hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)
      panTro2.all_est.qName (via xenoRefGene.name)
      panTro2.all_mrna.qName (via xenoRefGene.name)
      panTro2.refGene.name (via xenoRefGene.name)
      panTro2.refSeqAli.qName (via xenoRefGene.name)
      panTro2.xenoMrna.qName (via xenoRefGene.name)
      panTro2.xenoRefFlat.name (via xenoRefGene.name)
      panTro2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1003NM_001256409chr1+54890195549137025489603854913473954890195,54891826,54896024,54902175,54905911,54907588,54907850,54911831,54913198,54890371,54891863,54896511,54902307,54906030,54907677,54907964,54911916,54913702,0LRRC42cmplcmpl-1,-1,0,2,2,1,0,0,1,
1932NR_027767chr3-1765736091766673681766673681766673682176573609,176666966,176573675,176667368,0TNIKunkunk-1,-1,
1932NM_001378456chr2b+17661809617667908517662049817667855517176618096,176620489,176623120,176638216,176643890,176646422,176656656,176656961,176657231,176657828,176658858,176659345,17665975 ...176618215,176620561,176623238,176638307,176643950,176646538,176656752,176657124,176657331,176657954,176659005,176659459,17665989 ...0DYNC1I2cmplcmpl-1,0,0,1,2,2,1,1,2,0,0,0,0,2,0,0,0,
648NR_110805chr17+830668583103338310333831033368306685,8307192,8307426,8307580,8309806,8310291,8307049,8307273,8307519,8307926,8309841,8310333,0LINC02075unkunk-1,-1,-1,-1,-1,-1,
969NR_024504chr11+50412662504259985042599850425998650412662,50413080,50421762,50424541,50425769,50425939,50412703,50413163,50421880,50424642,50425914,50425998,0LOC646813unkunk-1,-1,-1,-1,-1,-1,
1450NM_030069chr11+1134621501134854351134621501134854324113462150,113476690,113484308,113484896,113462249,113477323,113484510,113485435,0Nxpe2incmplcmpl1,0,0,1,
1628NM_200966chr3+1367210931367223991367210991367223963136721093,136721758,136721829,136721758,136721829,136722399,0psmc2cmplcmpl0,0,0,
1372NM_200966chr7+10323047310324455910323047310324455611103230473,103231413,103232241,103238444,103239174,103239841,103240639,103242575,103243916,103244214,103244396,103230508,103231497,103232343,103238577,103239249,103239934,103240804,103242665,103244117,103244309,103244559,0psmc2incmplcmpl0,2,2,2,0,0,0,0,0,0,2,
1037NR_030185chr19+59358947593590345935903459359034159358947,59359034,0MIR519Eunkunk-1,
756NR_023915chr15+22521005225269122252691222526912722521005,22522701,22523498,22524586,22525244,22525835,22526508,22521971,22522816,22524250,22525111,22525564,22526164,22526912,0IPWunkunk-1,-1,-1,-1,-1,-1,-1,

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