Schema for xenoRefGene
  Database: oryCun2    Primary Table: xenoRefGene    Row Count: 345,704   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 800smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001383085varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr12varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 28303764int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 28303977int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 28303764int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 28303977int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 28303764,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 28303977,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 cyc-2.1varchar(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,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)
      oryCun2.all_est.qName (via xenoRefGene.name)
      oryCun2.all_mrna.qName (via xenoRefGene.name)
      oryCun2.refGene.name (via xenoRefGene.name)
      oryCun2.refSeqAli.qName (via xenoRefGene.name)
      oryCun2.xenoMrna.qName (via xenoRefGene.name)
      oryCun2.xenoRefFlat.name (via xenoRefGene.name)
      oryCun2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
800NM_001383085chr12-28303764283039772830376428303977128303764,28303977,0cyc-2.1incmplincmpl0,
100NM_001369chr12+285490402885966828549040288596685728549040,28563883,28567676,28581277,28589540,28645115,28648701,28649903,28652001,28653859,28655780,28659808,28663770,28665917,28 ...28549217,28563992,28567714,28581346,28589636,28645358,28648807,28650061,28652165,28653962,28655942,28660033,28663934,28666099,28 ...0DNAH5incmplcmpl0,0,1,0,0,0,0,1,0,2,0,0,0,2,1,0,2,0,1,0,1,0,1,0,2,0,0,0,0,0,2,0,2,0,0,0,1,0,0,0,0,0,1,0,0,0,2,0,0,0,2,1,2,0,0,1,0,
1327NM_001170797chr3-97344799973606379734479997360617797344799,97353814,97355353,97355529,97356231,97357169,97360562,97344973,97353939,97355442,97355657,97356271,97357212,97360637,0ZFAND1cmplincmpl0,1,2,0,2,1,0,
871NM_001204292chr13+37503603375079143750365537507911837503603,37503679,37506038,37506363,37506611,37506657,37506820,37507839,37503669,37503706,37506071,37506417,37506626,37506738,37506973,37507914,0MUC1cmplcmpl0,0,2,2,0,0,0,0,
788NM_001088259chrX+26696188266995382669618826699538626696188,26696639,26697125,26698290,26699124,26699520,26696260,26696678,26697275,26698350,26699247,26699538,0ddx4.Lincmplincmpl0,0,0,0,0,0,
585NM_001088257chrUn0329-67299102391672991023911667299,71943,81182,81324,88833,89873,91574,91899,92220,94072,95032,98260,100462,101288,101300,102311,67395,71997,81290,81345,88941,89989,91899,92022,92256,94225,95122,98415,100586,101291,101394,102391,0ctdp1.Lincmplincmpl0,0,0,2,0,1,0,0,0,0,0,1,0,0,2,0,
589NM_001243259chrUn0125+59027560320959634560237913590275,596339,596489,599922,600414,600702,601346,601511,601713,601938,602300,602513,603173,590332,596489,596517,600154,600522,600855,601424,601632,601848,602068,602504,602744,603209,0HINFPcmplcmpl-1,0,0,0,1,1,1,1,2,2,2,-1,-1,
10NM_001012805chr19+146644001469377514664403146934181714664400,14664508,14666699,14668797,14676195,14679106,14679469,14680167,14685825,14686437,14688505,14688571,14691781,14691850,14 ...14664454,14664586,14666765,14668903,14676325,14679179,14679529,14680276,14685925,14686519,14688538,14688802,14691823,14691944,14 ...0NCBP3cmplcmpl0,0,0,0,1,2,0,0,1,2,0,0,0,0,1,0,-1,
1333NM_024911chr13+980506909816783298050965981670341898050690,98050912,98096941,98129164,98135230,98136479,98140592,98142255,98142668,98145784,98147082,98155314,98166924,98167146,98 ...98050833,98051071,98097215,98129287,98135392,98136617,98140760,98142353,98142732,98145928,98147166,98155468,98167034,98167364,98 ...0WLScmplcmpl-1,0,1,0,0,0,0,0,2,0,0,0,1,-1,-1,-1,-1,-1,
820NM_001133603chr20-308157503093178230816830309317791030815750,30816073,30816280,30816672,30816779,30915573,30917519,30920751,30921993,30931748,30815813,30816106,30816653,30816711,30816886,30915655,30917586,30920789,30922062,30931782,0LIN52cmplcmpl-1,-1,-1,-1,1,1,0,1,1,0,

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