Schema for xenoRefGene
  Database: droPer1    Primary Table: xenoRefGene    Row Count: 259,434   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 593smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_061567varchar(255) values Name of gene (usually transcript_id from GTF)
chrom super_7varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1109823int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1110000int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1109823int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1110000int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1109823,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1110000,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Y51H7C.9varchar(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,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
        droPer1.xenoMrna.qName (via xenoRefGene.name)
      droPer1.xenoRefFlat.name (via xenoRefGene.name)
      droPer1.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
593NM_061567super_7+110982311100001109823111000011109823,1110000,0Y51H7C.9incmplincmpl0,
656NM_001030096super_1+934258793435389342587934353899342587,9342761,9342775,9342974,9343125,9343140,9343226,9343337,9343442,9342662,9342766,9342791,9343103,9343135,9343205,9343313,9343388,9343538,0tgm1l4incmplincmpl0,0,2,0,1,1,0,0,0,
586NM_001094470super_30-2453242457762453242457762245324,245644,245393,245776,0rhou.Lincmplincmpl0,0,
600NM_001145796super_3-209376120946132093761209461322093761,2094559,2093980,2094613,0SH2B1incmplincmpl0,0,
585NM_001162053super_40-37241379763724137976237241,37709,37670,37976,0LOC100162219incmplincmpl0,0,
588NM_177124super_42+4591534598254591534598252459153,459810,459350,459825,0Tnrc6bincmplincmpl0,2,
586NM_177611super_7+1768601772441768601772441176860,177244,0Psd4incmplincmpl0,
601NM_177606super_11+218230821892812182308218928162182308,2185097,2186065,2188085,2188456,2189212,2182428,2185110,2186167,2188310,2188630,2189281,0Plekhh2incmplincmpl0,0,0,0,0,0,
74NM_177595super_9-119879915921271592127159212741198799,1199930,1199990,1592081,1198819,1199935,1200017,1592127,0Mkxunkunk-1,-1,-1,-1,
597NM_177595super_9+166905616691911669056166919111669056,1669191,0Mkxincmplincmpl0,

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