Schema for xenoRefGene
  Database: danRer4    Primary Table: xenoRefGene    Row Count: 290,059   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 1255smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001184699varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr14varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 87918000int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 87942885int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 87918000int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 87942885int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 87918000,87920868,87921594,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 87918240,87921011,87921670,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 CPXM1varchar(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 0,1,0,0,1,0,1,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
        danRer4.all_est.qName (via xenoRefGene.name)
      danRer4.all_mrna.qName (via xenoRefGene.name)
      danRer4.refGene.name (via xenoRefGene.name)
      danRer4.refSeqAli.qName (via xenoRefGene.name)
      danRer4.xenoMrna.qName (via xenoRefGene.name)
      danRer4.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1255NM_001184699chr14-87918000879428858791800087942885787918000,87920868,87921594,87923832,87924207,87929547,87942772,87918240,87921011,87921670,87923931,87924398,87929671,87942885,0CPXM1incmplincmpl0,1,0,0,1,0,1,
845NM_001163984chr24+34092285341011733409228534101173434092285,34100927,34101038,34101122,34092332,34101032,34101119,34101173,0PRKAG2incmplincmpl1,0,0,0,
937NM_001145832chr18-461890954619852246189095461985221146189095,46189411,46190461,46191734,46193136,46193344,46193467,46194486,46194716,46194896,46198348,46189328,46189541,46190588,46191862,46193241,46193434,46193502,46194598,46194808,46195044,46198522,0Kifc3incmplincmpl1,0,2,0,0,0,1,0,1,0,0,
937NM_001145831chr18-461890954619852246189095461985221146189095,46189411,46190461,46191734,46193136,46193352,46193467,46194486,46194716,46194896,46198348,46189328,46189541,46190588,46191862,46193243,46193434,46193502,46194598,46194808,46195044,46198522,0Kifc3incmplincmpl1,0,2,0,1,0,1,0,1,0,0,
103NM_001192840chr19+32069556321453013206955632145301732069556,32106357,32111753,32116608,32125682,32134144,32145223,32069658,32106498,32111840,32116704,32125751,32134219,32145301,0TRIT1incmplincmpl0,0,0,0,0,0,0,
839NM_001191549chr2+333913463341415533391346334141552133391346,33391594,33394655,33398672,33398862,33399116,33399346,33400370,33401365,33401523,33402761,33402818,33403115,33403199,33 ...33391467,33391722,33394832,33398744,33399013,33399249,33399508,33400454,33401413,33401646,33402788,33402884,33403184,33403257,33 ...0Smg7incmplcmpl1,2,1,1,1,2,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,
680NM_001102703chr13+125604161256843312560416125684331512560416,12564801,12564998,12565282,12565566,12566032,12566273,12567037,12567246,12567379,12567814,12567974,12568094,12568310,12 ...12560524,12564894,12565117,12565460,12565906,12566136,12566387,12567184,12567249,12567538,12567844,12567986,12568307,12568355,12 ...0eif3aincmplincmpl0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,
711NM_001256554chr22-16548473165498801654847316549880716548473,16548661,16548709,16548834,16549061,16549573,16549793,16548641,16548691,16548719,16548972,16549130,16549720,16549880,0SAFB2incmplincmpl0,1,0,0,0,0,0,
794NM_001256552chr25+27518375275210312751837527521031627518375,27518690,27519912,27520368,27520837,27520998,27518564,27518704,27520038,27520416,27520909,27521031,0NEIL1incmplincmpl0,0,0,0,0,0,
911NM_001256551chr1-427802094283948442780209428394841542780209,42780471,42780732,42780980,42781853,42782015,42783655,42783897,42802725,42818545,42818919,42818936,42837252,42839211,42 ...42780338,42780597,42780817,42781081,42781935,42782053,42783727,42783933,42802783,42818655,42818922,42819077,42837315,42839285,42 ...0GK2incmplincmpl0,0,2,0,2,0,0,0,2,0,0,0,0,1,0,

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