Schema for refFlat
  Database: papHam1    Primary Table: refFlat    Row Count: 822   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName COX8Avarchar(255) values Name of gene as it appears in genome browser.
name NM_001112641varchar(255) values Name of gene
chrom scaffold15333varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 46436int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 46592int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 46477int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 46592int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 46436,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 46592,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)
      papHam1.mrnaOrientInfo.name (via refFlat.name)
      papHam1.refGene.name (via refFlat.name)
      papHam1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
COX8ANM_001112641scaffold15333+46436465924647746592146436,46592,
ESR1NM_001164587scaffold13339-18135184731813518473118135,18473,
SLC22A4NM_001168755scaffold4827+9727912653297279126532497279,115893,117344,126358,97672,115997,117499,126532,
GM-CSFNM_001168754scaffold11071+34849368603484936860434849,35110,35817,36752,35008,35152,35943,36860,
CCND3NM_001168753scaffold2941-1506381563311506381563315150638,151255,151932,155048,156133,150806,151392,152092,155264,156331,
BYSLNM_001168752scaffold2941+1369421477551369421477557136942,142431,145152,145654,146434,146766,147409,137210,142594,145291,145788,146595,146869,147755,
IL13NM_001168759scaffold2935+1334461355031334461355034133446,134642,134944,135395,133578,134696,135049,135503,
IL5NM_001168758scaffold2935-15581172051558117205415581,15785,16868,17109,15680,15914,16901,17205,
UGT2B45NM_001172144Contig147557+0287028720,166,163,287,
PGRNM_001164590scaffold10235-54357775705435777570554357,57251,64909,66480,77262,54450,57409,65040,66625,77570,

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