Schema for xenoRefGene
  Database: oviAri3    Primary Table: xenoRefGene    Row Count: 226,920   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 956smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001018012varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr19varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 48656107int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 48668837int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 48656107int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 48668837int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 48656107,48657416,48658271,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 48656263,48657575,48658544,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ALAS1varchar(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 0,0,0,0,0,0,0,0,1,0,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)
      oviAri3.all_est.qName (via xenoRefGene.name)
      oviAri3.all_mrna.qName (via xenoRefGene.name)
      oviAri3.refGene.name (via xenoRefGene.name)
      oviAri3.refSeqAli.qName (via xenoRefGene.name)
      oviAri3.xenoMrna.qName (via xenoRefGene.name)
      oviAri3.xenoRefFlat.name (via xenoRefGene.name)
      oviAri3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
956NM_001018012chr19-486561074866883748656107486688371048656107,48657416,48658271,48660482,48660966,48661676,48662707,48663732,48664652,48668723,48656263,48657575,48658544,48660641,48661146,48661862,48662929,48663843,48664780,48668837,0ALAS1cmplcmpl0,0,0,0,0,0,0,0,1,0,
11NM_001018011chr15+240587862426166724061826242559343724058786,24061730,24062847,24155439,24190987,24247684,24253261,24255706,24256300,24256547,24256731,24256931,24257205,24257261,24 ...24058844,24062847,24063074,24155532,24191079,24247780,24253435,24255935,24256402,24256614,24256758,24257020,24257235,24257284,24 ...0ZBTB16cmplcmpl-1,0,0,2,2,1,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NM_001171292chr8+396466008439646600841239646,42189,42487,47198,49384,49591,50021,50807,51095,55391,58244,59983,39851,42389,42605,47488,49493,49786,50150,51014,51262,55509,58405,60084,0MTO1incmplincmpl0,1,0,1,0,1,1,1,1,0,1,0,
663NM_001261155chr14-102514241029609110252476102960721110251424,10251528,10251646,10251673,10251802,10252053,10252154,10252343,10270472,10295644,10295995,10251490,10251546,10251664,10251736,10251879,10252074,10252228,10252594,10270623,10295727,10296091,0COTL1cmplcmpl-1,-1,-1,-1,-1,-1,-1,2,1,2,0,
1819NM_001261154chr3-16178012316179256516178186016179249020161780123,161780171,161780389,161780637,161780928,161781144,161781185,161781248,161781662,161781847,161782128,161782402,16178259 ...161780158,161780363,161780485,161780787,161781104,161781157,161781230,161781583,161781827,161781941,161782234,161782546,16178266 ...0PIP4K2Ccmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,0,2,2,0,0,0,0,0,2,0,0,
641NM_001360530chr20-736779473700407367794737004047367794,7368082,7369773,7369833,7367871,7368346,7369809,7370040,0H2-DMaincmplincmpl1,1,0,0,
2096NM_001194237chr1-1981422681981451581981422681981451582198142268,198145024,198142677,198145158,0RTP4incmplincmpl2,0,
1387NM_001204113chr3+1052080611052317661052080761052084623105208061,105208368,105231700,105208200,105208462,105231766,0BCL2L11cmplincmpl0,1,-1,
114NM_001376504chr15+433001484342177943361553434210222443300148,43300253,43361528,43387374,43399089,43401615,43402354,43403388,43403489,43404778,43405078,43407789,43408384,43412018,43 ...43300238,43300287,43361633,43387511,43399236,43401717,43402399,43403450,43403573,43404888,43405148,43407867,43408525,43412167,43 ...0DENND2Bcmplcmpl-1,-1,0,2,1,1,1,1,0,0,2,0,0,0,2,0,0,1,1,1,-1,-1,-1,-1,
1004NM_001179481chr14+54974243549746285497424354974628254974243,54974541,54974327,54974628,0RPL16Aincmplincmpl0,0,

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