Schema for xenoRefGene
  Database: monDom4    Primary Table: xenoRefGene    Row Count: 323,356   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 1429smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001042785varchar(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 110723731int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 110728644int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 110723731int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 110728644int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 110723731,110725299,1107275...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 110723944,110725455,1107276...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Ekarvarchar(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 0,0,0,0,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
        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)
      monDom4.all_est.qName (via xenoRefGene.name)
      monDom4.all_mrna.qName (via xenoRefGene.name)
      monDom4.refGene.name (via xenoRefGene.name)
      monDom4.refSeqAli.qName (via xenoRefGene.name)
      monDom4.xenoMrna.qName (via xenoRefGene.name)
      monDom4.xenoRefFlat.name (via xenoRefGene.name)
      monDom4.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1429NM_001042785chrUn-1107237311107286441107237311107286444110723731,110725299,110727556,110728605,110723944,110725455,110727655,110728644,0Ekarincmplincmpl0,0,0,0,
4088NM_001080655chr3-4592519864592532664592519864592532665459251986,459252197,459252445,459252672,459253200,459252103,459252278,459252596,459252812,459253266,0pnpla7aincmplincmpl0,0,2,0,0,
4039NM_001035422chr1+4527776154527781614527776154527781611452777615,452778161,0RNF183incmplcmpl0,
2723NM_001035421chr2+2803518672803527102803520082803527102280351867,280352563,280352548,280352710,0KCTD11cmplcmpl0,0,
2299NM_001035421chr7+2246987712246996142246989122246996142224698771,224699467,224699452,224699614,0KCTD11cmplcmpl0,0,
4054NM_001035420chr3-4547451194547650804547451194547650807454745119,454747467,454748808,454750712,454751078,454751764,454765017,454745315,454747610,454748930,454750845,454751144,454751887,454765080,0CNN2cmplincmpl2,0,1,0,0,0,0,
2830NR_129499chr8+2942725782942726382942726382942726381294272578,294272638,0MIR148Aunkunk-1,
2042NM_001163489chr2+19100846719103958319103076319103862613191008467,191030763,191031244,191033022,191033362,191033619,191034446,191035335,191036566,191036853,191038129,191038467,19103955 ...191008495,191030862,191031348,191033139,191033488,191033792,191034597,191035517,191036684,191036988,191038262,191038626,19103958 ...0Sema4aincmplincmpl-1,0,0,2,0,0,2,0,2,0,1,0,-1,
4443NM_001193351chr2-5057186925057188095057186925057188091505718692,505718809,0LYRM9cmplincmpl0,
622NM_194298chr1+485543348805154855452487864384855433,4863035,4867906,4874582,4874774,4874927,4878541,4880476,4855648,4863171,4868012,4874747,4874788,4875398,4878643,4880515,0SLC16A9cmplincmpl0,1,2,0,0,0,0,-1,

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