Schema for xenoRefGene
  Database: bosTau8    Primary Table: xenoRefGene    Row Count: 332,093   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 13smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_019438varchar(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 38766002int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 38811946int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 38766013int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 38811941int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 22int(10) unsigned range Number of exons
exonStarts 38766002,38767250,38767869,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 38766124,38767445,38768110,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Ncapgvarchar(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 0,0,0,1,0,1,2,2,2,0,0,0,0,0...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
        bosTau8.all_est.qName (via xenoRefGene.name)
      bosTau8.all_mrna.qName (via xenoRefGene.name)
      bosTau8.refGene.name (via xenoRefGene.name)
      bosTau8.refSeqAli.qName (via xenoRefGene.name)
      bosTau8.xenoRefFlat.name (via xenoRefGene.name)
      bosTau8.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
13NM_019438chr6+387660023881194638766013388119412238766002,38767250,38767869,38770057,38770486,38771547,38772218,38776543,38777247,38779246,38779651,38784701,38787020,38793473,38 ...38766124,38767445,38768110,38770203,38770571,38771740,38772368,38776684,38777371,38779336,38779831,38784812,38787140,38793608,38 ...0Ncapgcmplcmpl0,0,0,1,0,1,2,2,2,0,0,0,0,0,2,0,1,0,0,0,0,2,
126NM_001282749chr8+558365945599380055837628559921022855836594,55837015,55837252,55838506,55839687,55840961,55876273,55918932,55920379,55973005,55974095,55974642,55976230,55976734,55 ...55836970,55837222,55837673,55838604,55839751,55841006,55876336,55919134,55920396,55973125,55974149,55974795,55976363,55976877,55 ...0TLE4cmplcmpl-1,-1,0,0,2,0,0,0,1,0,0,0,0,1,0,0,0,0,2,0,1,0,-1,-1,-1,-1,-1,-1,
1249NM_001142503chrX-870495998713193587050779871317752487049599,87049840,87049940,87050005,87050116,87050706,87051044,87051321,87052529,87053035,87053421,87054026,87054678,87056700,87 ...87049638,87049904,87049984,87050070,87050477,87050897,87051221,87051539,87052754,87053150,87053632,87054229,87054834,87056876,87 ...0STARD8cmplcmpl-1,-1,-1,-1,-1,2,2,0,0,2,1,2,2,0,0,2,1,0,1,1,0,0,0,-1,
140NM_001164736chr7-70600793707253537060080770725353470600793,70693468,70694423,70725010,70600880,70693504,70694498,70725353,0HAVCR1incmplcmpl2,0,0,0,
821NM_001251887chr3+310123703101352831012370310130781031012370,31012506,31012850,31012939,31012991,31013149,31013305,31013376,31013412,31013504,31012502,31012834,31012938,31012981,31013111,31013296,31013353,31013386,31013423,31013528,0KNSTRNincmplcmpl1,2,1,2,0,-1,-1,-1,-1,-1,
800NM_001293292chr25+28271655282942492827165528294249528271655,28275533,28276933,28288506,28294159,28271691,28275630,28277031,28288563,28294249,0CRCPincmplincmpl0,0,1,0,0,
143NM_001293301chr2-734882337376255173491070737234874973488233,73488416,73488875,73488946,73489284,73490738,73490869,73491016,73491070,73501779,73503172,73512507,73514490,73516732,73 ...73488384,73488433,73488911,73488962,73489304,73490752,73490993,73491035,73491157,73501896,73503379,73512636,73514681,73516916,73 ...0Clasp1cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,0,0,0,0,1,0,0,2,0,0,0,2,0,2,0,1,1,1,1,0,0,2,0,0,0,2,0,0,1,0,2,0,2,0,1,0,0,-1,-1,-1,-1,
1017NM_001283270chr18-56703946567259105670394956705512656703946,56704714,56705011,56705054,56705215,56725745,56704654,56705002,56705048,56705127,56705548,56725910,0NUP62cmplcmpl0,0,2,1,0,-1,
104NM_001283267chr20+33030319332302033303053933229553833030319,33157649,33229399,33229617,33229871,33229897,33230050,33230140,33030636,33158364,33229560,33229849,33229882,33230030,33230131,33230203,0PLCXD3cmplcmpl0,1,2,-1,-1,-1,-1,-1,
788NM_001283266chr5-267027062672339726703579267214901626702706,26703574,26708767,26709653,26711178,26712472,26715515,26716623,26718033,26720127,26720775,26720897,26721478,26721560,26 ...26702918,26703620,26708937,26709706,26711251,26712514,26715602,26716752,26718165,26720244,26720808,26720921,26721531,26721621,26 ...0PCBP2cmplcmpl-1,1,0,1,0,0,0,0,0,0,0,0,0,-1,-1,-1,

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