Schema for xenoRefGene
  Database: danRer6    Primary Table: xenoRefGene    Row Count: 319,946   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1051smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001113697varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr6varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 61095279int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 61104236int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 61095285int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 61104236int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 61095279,61095323,61098399,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 61095315,61095326,61098567,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 PRELID3Bvarchar(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 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
        danRer6.all_est.qName (via xenoRefGene.name)
      danRer6.all_mrna.qName (via xenoRefGene.name)
      danRer6.refGene.name (via xenoRefGene.name)
      danRer6.refSeqAli.qName (via xenoRefGene.name)
      danRer6.xenoMrna.qName (via xenoRefGene.name)
      danRer6.xenoRefFlat.name (via xenoRefGene.name)
      danRer6.xenoRefSeqAli.qName (via xenoRefGene.name)
      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)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1051NM_001113697chr6+61095279611042366109528561104236661095279,61095323,61098399,61103595,61103756,61104134,61095315,61095326,61098567,61103667,61103858,61104236,0PRELID3Bcmplincmpl0,0,0,0,0,0,
937NM_001253045chr12+46228657462299804622865746229980446228657,46228741,46229534,46229800,46228711,46228762,46229687,46229980,0LOC100820541incmplincmpl0,0,0,0,
728NM_001094407chr8-187554141876585718755414187658571118755414,18757257,18757389,18758891,18759517,18759801,18762453,18762722,18763626,18764418,18765806,18755474,18757320,18757546,18758963,18759588,18759987,18762621,18762876,18763821,18764510,18765857,0dmap1.Lcmplcmpl0,0,2,2,0,0,0,2,2,0,0,
984NM_001109892chr8-523723975241979452372397524197941752372397,52374326,52374335,52374990,52375213,52376941,52377144,52378995,52379338,52379424,52381290,52383584,52392276,52399990,52 ...52372463,52374330,52374437,52375128,52375284,52377064,52377335,52379104,52379341,52379545,52381357,52383666,52392411,52399993,52 ...0Fgfr2incmplincmpl0,2,2,2,0,0,1,0,0,2,0,2,0,0,1,0,0,
653NM_001109902chr5+9010051903500290100519035002109010051,9010315,9010469,9015010,9015296,9019359,9019518,9030909,9033292,9034867,9010098,9010382,9010490,9015119,9015370,9019513,9019519,9031060,9033397,9035002,0Rnft2incmplcmpl0,2,0,0,1,0,1,2,0,0,
764NM_001252900chr3-23506460235117522350646023511752723506460,23506505,23507395,23509321,23509325,23509655,23511704,23506496,23506643,23507517,23509322,23509515,23509741,23511752,0LOC100820006incmplincmpl0,0,1,0,2,0,0,
657NM_001164593chr23-947314495586479473144955864789473144,9473363,9473624,9474131,9474506,9476175,9477059,9558494,9473309,9473591,9473756,9474209,9474620,9476235,9477152,9558647,0Pdzrn4incmplcmpl0,0,0,0,0,0,0,0,
653NM_001244666chr14+8938131894890889381318948767108938131,8939843,8940023,8942524,8942782,8943089,8945491,8946960,8947139,8948739,8938197,8939896,8940079,8942595,8942899,8943146,8945557,8947016,8947263,8948908,0STX5incmplcmpl0,0,2,1,0,0,0,0,2,2,
696NM_208073chr3+14621852146251901462185214625190514621852,14622841,14622991,14624893,14625127,14621942,14622907,14623156,14625034,14625190,0AGOS_AAR177Wincmplincmpl0,0,0,0,0,
878NM_208077chr20+38404699384105783840469938410578438404699,38406057,38410371,38410437,38404732,38406087,38410422,38410578,0AGOS_AAR181Wincmplincmpl1,0,0,0,

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