Schema for xenoRefGene
  Database: caeJap1    Primary Table: xenoRefGene    Row Count: 203,513   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1306smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001108242varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrUnvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 94533223int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 94536251int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 94533223int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 94533841int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 94533223,94533727,94534220,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 94533370,94533841,94534283,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Slc9a7varchar(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 0,0,-1,-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
        caeJap1.all_est.qName (via xenoRefGene.name)
      caeJap1.all_mrna.qName (via xenoRefGene.name)
      caeJap1.xenoMrna.qName (via xenoRefGene.name)
      caeJap1.xenoRefFlat.name (via xenoRefGene.name)
      caeJap1.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
1306NM_001108242chrUn-94533223945362519453322394533841494533223,94533727,94534220,94536110,94533370,94533841,94534283,94536251,0Slc9a7incmplincmpl0,0,-1,-1,
894NM_074930chrUn+40592905405932984059290540593295240592905,40593184,40593124,40593298,0ZK218.3incmplcmpl0,0,
894NM_074754chrUn-40594979405953844059498540595384240594979,40595162,40595120,40595384,0F26D2.13incmplcmpl0,0,
1369NM_001267007chrUn+1028711011028751071028711011028751077102871101,102872336,102872533,102872742,102873039,102873111,102875050,102871146,102872459,102872605,102873018,102873081,102873246,102875107,0AP1G2incmplincmpl0,0,0,0,0,0,0,
1048NM_001348480chrUn+60789243607893336078924360789333160789243,60789333,0tsc22d3incmplincmpl0,
1161NM_001265869chrUn-75523037755236307552303775523630275523037,75523564,75523148,75523630,0CNOT2incmplincmpl0,0,
844NM_001265831chrUn-33980550339817783398055033981778533980550,33980794,33981308,33981433,33981619,33980748,33980938,33981362,33981469,33981778,0SLC1A1incmplincmpl0,0,0,0,0,
685NM_077948chrUn+132062351321329813206235132132981413206235,13207732,13207909,13208113,13208529,13208873,13210160,13210412,13210617,13210698,13211281,13212355,13212946,13213130,13206349,13207867,13208047,13208239,13208664,13208927,13210346,13210544,13210653,13210875,13211386,13212604,13212973,13213298,0F16B12.6incmplincmpl0,0,0,0,0,0,0,0,0,0,0,0,0,0,
685NM_001306239chrUn+132062381321254113206238132125411213206238,13207729,13207909,13208113,13208526,13210157,13210403,13210609,13210695,13211242,13212355,13212466,13206354,13207876,13208047,13208239,13208664,13210343,13210548,13210653,13210872,13211413,13212430,13212541,0Y48G1C.8incmplincmpl0,0,0,0,0,0,0,1,0,0,0,0,
1485NM_001083166chrUn-11806991811808084611807073511808083619118069918,118069981,118070010,118070077,118070126,118070230,118070401,118070735,118070892,118071490,118071687,118072008,11807922 ...118069937,118069999,118070037,118070095,118070137,118070297,118070423,118070831,118070999,118071638,118071795,118072542,11807944 ...0max-2cmplcmpl-1,-1,-1,-1,-1,-1,-1,0,1,0,0,0,0,2,1,0,0,1,0,

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