Schema for xenoRefGene
  Database: myoLuc2    Primary Table: xenoRefGene    Row Count: 437,480   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 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001082139varchar(255) values Name of gene (usually transcript_id from GTF)
chrom AAPE02055386varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 8354int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 11424int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 11369int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 11422int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 8354,11369,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 8402,11424,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 LOC100008880varchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,0,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)
      myoLuc2.all_mrna.qName (via xenoRefGene.name)
      myoLuc2.xenoMrna.qName (via xenoRefGene.name)
      myoLuc2.xenoRefFlat.name (via xenoRefGene.name)
      myoLuc2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NM_001082139AAPE02055386-835411424113691142228354,11369,8402,11424,0LOC100008880cmplincmpl-1,0,
585NM_001082139AAPE02055386-39700775447748977542239700,77489,39748,77544,0LOC100008880cmplincmpl-1,0,
648NM_001138170GL429777+828768682904048287686829040458287686,8289195,8289780,8290102,8290321,8287731,8289264,8289843,8290190,8290404,0LOC100193000incmplincmpl0,0,0,0,1,
585NM_001082092AAPE02055386-3972210964375786109643339722,75786,109595,39750,75843,109643,0LOC100008792incmplincmpl-1,2,1,
585NM_001082723AAPE02055386-95837964809583796480295837,96423,95876,96480,0LOC100009480cmplincmpl2,0,
675NM_001105193GL429786-11840411118489581184135511843085811840411,11841355,11841412,11841516,11841540,11842122,11842900,11848877,11840490,11841391,11841451,11841534,11842107,11842884,11843095,11848958,0AMER3cmplincmpl-1,0,2,0,1,0,0,-1,
589NM_001122829GL430078+55257659305855257659186225552576,567909,569761,571971,572502,576935,577710,577969,578575,578781,579044,580206,580460,581305,581867,586690,587172,587930,58 ...552742,568046,569851,572139,572683,577097,577828,578067,578684,578941,579163,580368,580578,581449,582081,586808,587329,588073,58 ...0Upf1incmplcmpl2,0,2,2,2,0,0,1,1,2,0,2,2,0,0,1,2,0,2,2,1,0,0,-1,-1,
608NR_031844GL429826-301809030181743018174301817413018090,3018174,0Mir30c2unkunk-1,
73NM_001087449GL430107+8557819244068557819244063855781,895400,924290,855890,895589,924406,0lin28a.Sincmplincmpl0,1,1,
594NM_001102641GL430096-126849412702921268494127029231268494,1269677,1270223,1268572,1269833,1270292,0krt98incmplincmpl0,0,0,

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