Schema for refFlat
  Database: ornAna1    Primary Table: refFlat    Row Count: 690   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ORNANAV1R3279varchar(255) values Name of gene as it appears in genome browser.
name NM_001253671varchar(255) values Name of gene
chrom Ultra406varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 26601int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 27537int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 26601int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 27537int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 26601,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 27537,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      hgFixed.gbCdnaInfo.acc (via refFlat.name)
      hgFixed.gbSeq.acc (via refFlat.name)
      hgFixed.imageClone.acc (via refFlat.name)
      hgFixed.refLink.mrnaAcc (via refFlat.name)
      hgFixed.refSeqStatus.mrnaAcc (via refFlat.name)
      hgFixed.refSeqSummary.mrnaAcc (via refFlat.name)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)
      ornAna1.mrnaOrientInfo.name (via refFlat.name)
      ornAna1.refGene.name (via refFlat.name)
      ornAna1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
ORNANAV1R3279NM_001253671Ultra406+26601275372660127537126601,27537,
TVP23BNM_001281861Ultra151-147401414825661475110148256661474014,1476837,1478144,1479370,1482070,1482483,1475140,1476966,1478276,1479460,1482215,1482566,
MIR223NR_034755Contig3675+607261966196619616072,6196,
PALM2AKAP2NM_001370841Ultra84-115830015142561158300151425691158300,1170646,1186317,1361925,1373052,1373863,1436561,1449371,1514211,1158393,1170825,1188733,1362027,1373074,1373978,1436692,1449452,1514256,
MIR1329NR_034622chr1-28887188288873142888731428887314128887188,28887314,
MIR1328NR_034621chr1+21080347210804922108049221080492121080347,21080492,
MIR96NR_034625chr10-456876245688714568871456887114568762,4568871,
MIR1373NR_034778Contig59-211499621150712115071211507112114996,2115071,
MIR16BNR_034777Contig5755+797980808080808017979,8080,
MIR15BNR_034776Contig5755+781479447944794417814,7944,

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