Schema for xenoRefFlat
  Database: dipOrd1    Primary Table: xenoRefFlat    Row Count: 666,567   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName DLGAP2varchar(255) Name of gene as it appears in genome browser.
name NM_001346810varchar(255) Name of gene
chrom scaffold_22357varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 283int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 1157int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 1157int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 1157int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned Number of exons
exonStarts 283,352,880,1041,longblob Exon start positions (or end positions for minus strand item)
exonEnds 331,380,928,1157,longblob Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        dipOrd1.xenoMrna.qName (via xenoRefFlat.name)
      dipOrd1.xenoRefGene.name (via xenoRefFlat.name)
      dipOrd1.xenoRefSeqAli.qName (via xenoRefFlat.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
DLGAP2NM_001346810scaffold_22357+2831157115711574283,352,880,1041,331,380,928,1157,
LOC108579106NM_001365301scaffold_15658+20236252312023625231620236,21018,21894,23259,24069,25135,20362,21156,21972,23313,24195,25231,
nkcc-1NM_001276883scaffold_95+18789779881878977988718789,23455,32465,34917,65667,65935,77856,18909,23563,32564,35016,65707,65955,77988,
POLR2MNM_015532scaffold_9461-4849681558516815144849,4935,5320,5550,5727,5756,5847,5940,5971,6038,6293,6386,6498,6765,4926,4990,5499,5691,5746,5814,5931,5970,6016,6104,6326,6493,6761,6815,
CTRB1NM_001105330scaffold_42461+595875425958753955958,6170,6546,6795,7377,6070,6242,6691,6909,7542,
TrhdeNM_001108991scaffold_16250+615164306151643016151,6430,
MffNM_001310697scaffold_367-1787291796871788561795109178729,178772,178872,179063,179361,179384,179427,179461,179630,178750,178872,179052,179359,179382,179426,179459,179598,179687,
Rgs3NM_001310706scaffold_2415+84708103104102161103104984708,102161,102313,102388,102436,102474,102608,102632,102781,84810,102283,102373,102413,102466,102493,102623,102719,103104,
lrp8NM_001256393scaffold_3319+519116354551911635451251911,53762,53924,54101,54275,54322,54725,54948,57427,58352,60916,63452,51968,53882,54008,54215,54280,54443,54837,55079,57545,58498,60958,63545,
casq2NM_001002682scaffold_15223-27781302662778130266327781,28779,30161,27886,28845,30266,

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