Schema for xenoRefFlat
  Database: otoGar3    Primary Table: xenoRefFlat    Row Count: 530,019   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName MIR9-1varchar(255) Name of gene as it appears in genome browser.
name NR_030833varchar(255) Name of gene
chrom GL873548varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 12716790int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 12716880int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 12716880int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 12716880int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned Number of exons
exonStarts 12716790,longblob Exon start positions (or end positions for minus strand item)
exonEnds 12716880,longblob Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)
      otoGar3.xenoMrna.qName (via xenoRefFlat.name)
      otoGar3.xenoRefGene.name (via xenoRefFlat.name)
      otoGar3.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MIR9-1NR_030833GL873548+12716790127168801271688012716880112716790,12716880,
LOC101927284NR_110754GL873739+134776713478481347848134784811347767,1347848,
Zfp944NM_001355280GL873542+853171485318308531714853183028531714,8531794,8531765,8531830,
RpL7NM_001043670GL873631-1323521332231323521332233132352,132494,133178,132421,132800,133223,
Vmn1r5NM_134174GL873823+5226335233175226335233173522633,523016,523194,522894,523044,523317,
Nxph1NM_012994GL873524+26289158265977052629036526596533826289158,26290255,26595771,26596550,26596663,26596798,26597193,26597282,26289435,26290419,26596540,26596654,26596771,26597160,26597259,26597705,
NAV1NM_020443GL873585+841999786892458689245868924528419997,8689173,8420027,8689245,
NAV1NM_020443GL873744+166654516667791666779166677921666545,1666689,1666614,1666779,
Stk19NM_019442GL873550+288398828900692883988288970872883988,2887527,2887917,2889098,2889307,2889669,2890033,2884123,2887622,2888058,2889196,2889453,2889711,2890069,
VARS2NM_020442GL873550+1076512108724510765301087219301076512,1076834,1077030,1077419,1077930,1078088,1078813,1079063,1079644,1080416,1080967,1081256,1081475,1081817,1082192,1082355, ...1076731,1076916,1077131,1077541,1077997,1078186,1078895,1079183,1079756,1080505,1081058,1081378,1081585,1081899,1082269,1082432, ...

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