Schema for xenoRefFlat
  Database: dp3    Primary Table: xenoRefFlat    Row Count: 122,793   Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ZKSCAN1varchar(255) values Name of gene as it appears in genome browser.
name NM_001205510varchar(255) values Name of gene
chrom chrXR_group6varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 147914int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 148316int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 147914int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 148316int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 147914,148256,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 148157,148316,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        dp3.xenoMrna.qName (via xenoRefFlat.name)
      dp3.xenoRefGene.name (via xenoRefFlat.name)
      dp3.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
ZKSCAN1NM_001205510chrXR_group6-1479141483161479141483162147914,148256,148157,148316,
ZKSCAN1NM_001205510chr4_group3-865963686600208659636866002028659636,8659837,8659801,8660020,
SMAD9NM_001195510chr4_group4+146229914647491462299146474941462299,1462568,1463060,1464342,1462506,1462805,1463265,1464749,
RHOQNM_001205498chr2+377888537792563778885377925623778885,3779106,3778981,3779256,
RHOQNM_001205498chrXL_group1e+9416779422919416779422912941677,942078,941950,942291,
PAD1NM_001278992chrXL_group1e-10335992103367521033599210336752410335992,10336100,10336362,10336659,10336064,10336208,10336596,10336752,
PORNM_001129959chr4_group5-196708219705511967082197055191967082,1967169,1967397,1967643,1968214,1968337,1969819,1969972,1970537,1967137,1967379,1967613,1968126,1968234,1968457,1969945,1970144,1970551,
RXRGNM_001257610chrXL_group1a-254190125430592541901254305932541901,2542375,2542789,2542003,2542489,2543059,
KARS1NM_001257593chrXL_group3a+4532154550054532154550058453215,453365,453422,453518,453665,453964,454486,454972,453263,453373,453488,453617,453890,454411,454903,455005,
MAGOHNM_001257602chr3+17591236175917321759123617591732217591236,17591549,17591485,17591732,

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