Schema for xenoRefGene
  Database: petMar3    Primary Table: xenoRefGene    Row Count: 200,903   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 623smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001320018varchar(255) values Name of gene (usually transcript_id from GTF)
chrom PIZI01000052v1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 4999186int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 5005088int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 4999186int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 5005088int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 4999186,4999621,4999677,500...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 4999303,4999624,4999770,500...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC106573729varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,0,0,0,0,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
        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)
      petMar3.all_est.qName (via xenoRefGene.name)
      petMar3.all_mrna.qName (via xenoRefGene.name)
      petMar3.xenoRefFlat.name (via xenoRefGene.name)
      petMar3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
623NM_001320018PIZI01000052v1+499918650050884999186500508894999186,4999621,4999677,5000137,5002508,5002589,5003774,5004230,5004968,4999303,4999624,4999770,5000203,5002583,5002706,5003924,5004380,5005088,0LOC106573729incmplincmpl0,0,0,0,0,0,0,0,0,
686NM_030795PIZI01000017v1+13317709133193861331770913319386613317709,13317805,13318060,13318511,13318834,13319341,13317781,13317880,13318063,13318700,13318837,13319386,0STMN4incmplincmpl0,0,0,0,0,0,
626NM_001330624PIZI01000061v1+5422054545796754220545457967225422054,5427279,5428068,5430966,5431799,5432276,5432707,5433881,5435494,5435896,5436259,5438361,5439453,5439669,5441459,5442350, ...5422090,5427390,5428158,5431032,5431874,5432433,5432799,5433964,5435564,5436013,5436262,5438549,5439562,5439777,5441543,5442458, ...0CUL4Bincmplcmpl0,0,0,0,0,0,1,0,2,0,0,0,2,0,0,0,0,0,0,2,0,0,
91NM_001110787PIZI01000005v1-196426901969154519642690196915452519642690,19643167,19644148,19645576,19645905,19646162,19646711,19648491,19650831,19650990,19651892,19654173,19654725,19657468,19 ...19643134,19643470,19644160,19645693,19645908,19646260,19646844,19648537,19650893,19651101,19651919,19654350,19654809,19657579,19 ...0SCN9Aincmplincmpl0,0,2,0,0,1,0,2,0,0,0,0,0,0,0,2,0,0,0,0,1,0,0,0,0,
685NM_001174838PIZI01000006v1+13200455132026711320045513202671513200455,13201154,13201515,13202201,13202578,13200554,13201265,13201644,13202267,13202671,0LOC100382075incmplincmpl0,0,0,0,0,
596NM_001369211PIZI01000063v1+149464715172431494647151724391494647,1494752,1495778,1496055,1496497,1496769,1497049,1510162,1517078,1494710,1494800,1495961,1496181,1496678,1496858,1497280,1510354,1517243,0Tncincmplincmpl0,0,0,0,0,1,0,0,0,
81NM_006946PIZI01000041v1-8649682877841386496828778413258649682,8649802,8655110,8657265,8660359,8662979,8663220,8667537,8671092,8673360,8676928,8677153,8677373,8677571,8680164,8685258, ...8649784,8649868,8655152,8657331,8660545,8663084,8663259,8667763,8671170,8673477,8677090,8677341,8677535,8677667,8680348,8685372, ...0SPTBN2incmplincmpl0,0,0,0,0,2,0,0,0,0,0,1,0,0,2,0,0,1,0,0,1,0,0,1,0,
640NM_153313PIZI01000046v1-728605973170077286059731700727286059,7316797,7286293,7317007,0Cyp2d1incmplincmpl0,0,
623NM_173971PIZI01000009v1+498765649912554987656499125544987656,4989783,4989855,4990751,4987803,4989798,4989866,4991255,0VITincmplincmpl0,0,0,0,
601NM_176244PIZI01000038v1+2167333218261621673332182616172167333,2168641,2169535,2171565,2171749,2172168,2172455,2172497,2172874,2173518,2173773,2173828,2174417,2181676,2181884,2182152, ...2167441,2168746,2169565,2171592,2171920,2172303,2172458,2172662,2173063,2173650,2173775,2174009,2174465,2181749,2182060,2182340, ...0domincmplincmpl0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,2,

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