Schema for xenoRefGene
  Database: ci2    Primary Table: xenoRefGene    Row Count: 164,807   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 597smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001035658varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr04qvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1653846int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1654119int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1653996int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1654119int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 1653846,1653996,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1653990,1654119,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 NFU4varchar(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 -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
        ci2.all_est.qName (via xenoRefGene.name)
      ci2.all_mrna.qName (via xenoRefGene.name)
      ci2.refGene.name (via xenoRefGene.name)
      ci2.refSeqAli.qName (via xenoRefGene.name)
      ci2.xenoMrna.qName (via xenoRefGene.name)
      ci2.xenoRefFlat.name (via xenoRefGene.name)
      ci2.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
597NM_001035658chr04q-165384616541191653996165411921653846,1653996,1653990,1654119,0NFU4incmplincmpl-1,0,
613NM_001035317chr05q+3790073379984037900733799840133790073,3790520,3791121,3792176,3792692,3793795,3794581,3796963,3797726,3798608,3798861,3799109,3799744,3790196,3790601,3791152,3792313,3792703,3793806,3794707,3797164,3797843,3798758,3798864,3799349,3799840,0MVPincmplincmpl0,0,0,1,0,0,0,0,0,0,0,0,0,
598NM_001276316chr01q+1738271175032117382711750321181738271,1741263,1741784,1742397,1743825,1744213,1744363,1744378,1744554,1744682,1745119,1746259,1746761,1748605,1749224,1749699, ...1738454,1741334,1741920,1742505,1743894,1744346,1744368,1744464,1744558,1744838,1745311,1746337,1746875,1748788,1749317,1749711, ...0Uba1incmplincmpl0,0,2,0,0,0,1,0,2,0,0,0,0,0,0,0,0,0,
585NM_001276303scaffold_3690-320548803205488033205,3723,4778,3328,3774,4880,0NACAincmplincmpl0,0,0,
590NM_202864scaffold_55-7332307340917332307340912733230,733998,733926,734091,0T12H17.110; T12H17_110incmplincmpl0,0,
627NM_202863chr04q+555418655544565554186555445625554186,5554363,5554327,5554456,0ORP2Aincmplincmpl0,0,
610NM_080463chr05q+340342134038173403421340381723403421,3403616,3403538,3403817,0Pofut1incmplincmpl0,0,
607NM_079460chr14q+296063529646192960635296461962960635,2960755,2961359,2962320,2963436,2964450,2960731,2960776,2961540,2962541,2963471,2964619,0Psnincmplincmpl0,0,0,1,0,2,
585NM_079459chr09p-837895068378950668378,8560,8886,9015,9121,9329,8504,8632,8985,9059,9278,9506,0Lasincmplincmpl0,0,0,1,0,0,
586NM_079455chr12p+2522022563202522022563205252202,253069,253993,255948,256258,252343,253195,254182,256027,256320,0poloincmplincmpl0,0,0,0,1,

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