Schema for xenoRefFlat
  Database: ci2    Primary Table: xenoRefFlat    Row Count: 164,807   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName 5SrRNA:CR33359varchar(255) values Name of gene as it appears in genome browser.
name NR_001886varchar(255) values Name of gene
chrom scaffold_3603varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 3103int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3222int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3222int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3222int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 3103,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3222,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        ci2.xenoMrna.qName (via xenoRefFlat.name)
      ci2.xenoRefGene.name (via xenoRefFlat.name)
      ci2.xenoRefSeqAli.qName (via xenoRefFlat.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
5SrRNA:CR33359NR_001886scaffold_3603-310332223222322213103,3222,
5SrRNA:CR33359NR_001886scaffold_36-5959855961035961035961031595985,596103,
5SrRNA:CR33359NR_001886scaffold_36+7947827948967948967948961794782,794896,
5SrRNA:CR33359NR_001886scaffold_3603-3134324324321313,432,
5SrRNA:CR33359NR_001886scaffold_3603-222523392339233912225,2339,
EPHB4NM_004444chr01p+167200316754811672003167548141672003,1673554,1674805,1675295,1672255,1673728,1674952,1675481,
EPHB4NM_004444chr01p-254850425516392548504255163952548504,2549066,2550378,2550600,2551522,2548657,2549249,2550582,2550627,2551639,
TYRP1NM_001042560chr08q+4443024458944443024458944444302,444404,445080,445759,444389,444533,445239,445894,
EIF4G2NM_001042559chr04q+434135343489584341353434895874341353,4341836,4342186,4342285,4342548,4342891,4348877,4341443,4341917,4342243,4342343,4342721,4342918,4348958,
Map2k7NM_001042557chr09p+379269537941143792695379411433792695,3793464,3793955,3792812,3793641,3794114,

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