Schema for xenoRefGene
  Database: panTro4    Primary Table: xenoRefGene    Row Count: 343,020   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1591smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_177591varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 131903202int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 131916276int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 131903485int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 131916276int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 20int(10) unsigned range Number of exons
exonStarts 131903202,131903311,1319033...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 131903294,131903319,1319033...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Igsf1varchar(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 cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,2,1,1,0,1,1,1,1,1,...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
        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)
      panTro4.all_est.qName (via xenoRefGene.name)
      panTro4.all_mrna.qName (via xenoRefGene.name)
      panTro4.refGene.name (via xenoRefGene.name)
      panTro4.refSeqAli.qName (via xenoRefGene.name)
      panTro4.xenoMrna.qName (via xenoRefGene.name)
      panTro4.xenoRefFlat.name (via xenoRefGene.name)
      panTro4.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1591NM_177591chrX-13190320213191627613190348513191627620131903202,131903311,131903344,131903419,131903775,131904288,131904688,131905165,131905650,131906628,131907545,131908794,13190892 ...131903294,131903319,131903354,131903624,131903896,131904567,131904974,131905455,131905938,131906916,131907827,131908825,13190899 ...0Igsf1incmplcmpl-1,-1,-1,2,1,1,0,1,1,1,1,1,2,1,1,1,0,1,1,1,
585NR_130699chr1_GL389193_random+252829212921292112528,2921,0LINC01881unkunk-1,
585NR_130699chr1_GL389209_random-12410128041280412804112410,12804,0LINC01881unkunk-1,
585NR_130699chr1_GL389158_random-27385282842828428284227385,28268,27779,28284,0LINC01881unkunk-1,-1,
585NR_130699chr1_GL388976_random-222725692569256912227,2569,0LINC01881unkunk-1,
1205NM_001288799chr17-81296335812985288129722181298478381296335,81298258,81298470,81297286,81298377,81298528,0MCRIP1cmplcmpl1,2,0,
140NR_110827chr17+70894620709156637091566370915663670894620,70899499,70904279,70906106,70911269,70915112,70894995,70899604,70904372,70906243,70911858,70915663,0LINC02097unkunk-1,-1,-1,-1,-1,-1,
1662NR_045688chr5+1412899571412915281412915281412915283141289957,141290820,141291351,141290152,141291024,141291528,0slc35a4unkunk-1,-1,-1,
827NM_198959chr1+317395903174805831739629317474271231739590,31739968,31741279,31741914,31743956,31745437,31747236,31747317,31747775,31747866,31747987,31748010,31739828,31740147,31741523,31742030,31744183,31745559,31747290,31747468,31747817,31747902,31748001,31748058,0Hcrtr1cmplcmpl0,1,0,1,0,2,1,1,-1,-1,-1,-1,
1465NM_200614chrX-1153567701153590261153567701153590264115356770,115356827,115357263,115357793,115356809,115356956,115357728,115359026,0hsc70cmplcmpl0,0,0,0,

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