Schema for xenoRefGene
  Database: galGal3    Primary Table: xenoRefGene    Row Count: 262,009   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 171smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001384692varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr2varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 103132984int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 103220794int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 103133014int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 103218481int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 29int(10) unsigned range Number of exons
exonStarts 103132984,103133143,1031411...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 103133050,103133212,1031413...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 EPB41L3varchar(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 0,0,2,0,0,1,2,2,0,0,2,2,0,0...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
        galGal3.all_est.qName (via xenoRefGene.name)
      galGal3.all_mrna.qName (via xenoRefGene.name)
      galGal3.refGene.name (via xenoRefGene.name)
      galGal3.refSeqAli.qName (via xenoRefGene.name)
      galGal3.xenoMrna.qName (via xenoRefGene.name)
      galGal3.xenoRefFlat.name (via xenoRefGene.name)
      galGal3.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
171NM_001384692chr2+10313298410322079410313301410321848129103132984,103133143,103141119,103164995,103173305,103176628,103177928,103178229,103181844,103184014,103185061,103187850,10320501 ...103133050,103133212,103141315,103165100,103173348,103176704,103178147,103178317,103181997,103184112,103185235,103187922,10320507 ...0EPB41L3cmplcmpl0,0,2,0,0,1,2,2,0,0,2,2,0,0,0,0,0,0,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1,
1091NM_001280602chr3-66426861664356136642686166435613966426861,66428332,66430213,66431402,66432492,66434101,66434114,66435403,66435545,66426974,66428402,66430333,66431480,66432534,66434103,66434181,66435407,66435613,0rwdd1.Scmplcmpl1,0,0,0,0,1,0,2,0,
9NM_020505chr8-9924151114278994073111427826992415,993878,994073,995726,1006090,1008726,1010394,1014932,1020628,1050074,1052730,1068572,1069009,1069510,1070581,1072825,1074 ...992448,993956,994115,995882,1006219,1008841,1010427,1015002,1020766,1050171,1052831,1068683,1069144,1069558,1070668,1072894,1074 ...0Vav3incmplcmpl-1,-1,0,0,0,2,1,0,0,2,0,0,0,0,0,0,0,2,0,2,0,0,2,2,0,0,
73NM_001090079chr15+52066653793252066653133112520666,522444,525550,527494,527973,529914,531223,533559,534758,534885,534974,537890,520850,522632,525667,527609,528105,530024,531331,533663,534852,534955,535010,537932,0mapk1.Sincmplincmpl0,1,0,0,1,1,0,-1,-1,-1,-1,-1,
595NM_001045221chr27+1395011142491713950111424917141395011,1395873,1396658,1399114,1399580,1399813,1400183,1403197,1404152,1405096,1410122,1415429,1415537,1424770,1395217,1395972,1396823,1399172,1399728,1399928,1400354,1403270,1404225,1405229,1410290,1415507,1415558,1424917,0myo1gincmplincmpl0,2,0,0,1,2,0,0,1,2,0,0,0,0,
76NM_001080115chr6+338507234548933385072345489073385072,3414801,3434880,3435093,3449963,3451085,3454793,3385164,3414955,3434994,3435095,3450130,3451122,3454893,0LDB3cmplcmpl0,2,0,0,2,1,2,
861NM_146262chrUn_random-36283365362969513628336536296951236283365,36296804,36283449,36296951,0Olfr1290incmplincmpl0,0,
73NM_008902chrE22C19W28_E50C23+4650765957694650764665287465076,465327,465679,466075,466420,466935,595736,465157,465468,465778,466213,466528,466951,595769,0Endouincmplincmpl0,0,0,0,0,-1,-1,
188NM_008892chr1-12129687912148636912129687912148636937121296879,121338130,121356733,121398938,121406789,121410404,121411126,121412392,121412555,121413250,121414937,121451286,12145164 ...121296957,121338201,121356850,121399082,121406966,121410536,121411255,121412396,121412757,121413347,121414951,121451414,12145178 ...0Pola1incmplincmpl0,0,0,0,0,0,0,2,1,0,0,1,0,1,0,0,2,0,0,0,0,0,1,0,0,2,2,0,0,1,0,1,0,0,1,0,0,
672NM_008095chr15+114398621149356011439862114418151011439862,11440088,11440392,11440629,11440783,11441151,11441386,11441593,11441747,11493529,11439971,11440126,11440483,11440697,11440924,11441186,11441481,11441674,11441815,11493560,0Nipsnap2incmplcmpl0,1,0,1,0,0,2,1,1,-1,

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