Schema for xenoRefFlat
  Database: rn5    Primary Table: xenoRefFlat    Row Count: 219,545   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName rabgap1l.Svarchar(255) values Name of gene as it appears in genome browser.
name NM_001096453varchar(255) values Name of gene
chrom chr13varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 82887611int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 83416716int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 82887611int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 83416716int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 24int(10) unsigned range Number of exons
exonStarts 82887611,82890508,82895117,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 82887719,82890610,82895180,...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)
      rn5.xenoMrna.qName (via xenoRefFlat.name)
      rn5.xenoRefGene.name (via xenoRefFlat.name)
      rn5.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
rabgap1l.SNM_001096453chr13-828876118341671682887611834167162482887611,82890508,82895117,82898975,82900879,82909369,82918681,82996844,83051115,83099478,83101080,83109818,83130442,83281196,83 ...82887719,82890610,82895180,82899059,82900984,82909480,82918776,82996971,83051157,83099622,83101206,83109890,83130559,83281346,83 ...
GK2NM_001256933chrX-544311475448337754431147544833771954431147,54435034,54437416,54437669,54438371,54439458,54440740,54451502,54452157,54458430,54458898,54461859,54462086,54462801,54 ...54431236,54435118,54437556,54437790,54438452,54439540,54440819,54451583,54452200,54458498,54458934,54461924,54462090,54462913,54 ...
GzmmNM_008504chr7-13062467130682961306256713068001613062467,13063131,13063493,13064467,13067946,13068259,13062741,13063398,13063632,13064627,13068178,13068296,
Smkr-psNR_040264chr4+57035065570421965704219657042196357035065,57041762,57042156,57035178,57042145,57042196,
USP45NM_001346023chr5+405764324063938040576441406361443640576432,40579245,40580672,40582459,40595195,40595279,40596895,40603930,40616097,40619144,40620703,40621211,40626751,40626797,40 ...40576541,40579415,40580776,40582562,40595264,40595336,40597023,40604018,40616179,40619236,40620760,40621356,40626781,40626884,40 ...
PCM1NM_001352649chr16-537527445385121653754756538331865053752744,53753014,53753343,53753865,53753933,53753949,53754019,53754251,53754294,53754375,53754533,53754728,53755826,53756022,53 ...53752818,53753059,53753406,53753901,53753940,53753964,53754064,53754281,53754304,53754475,53754659,53754782,53755941,53756115,53 ...
SIRPANM_080792chr3-12786412912790165712786623712790163613127864129,127864861,127865344,127865542,127866162,127866305,127868450,127877750,127879830,127880497,127885380,127901566,12790159 ...127864236,127864929,127865415,127865635,127866303,127866480,127868492,127877843,127880096,127880639,127885506,127901590,12790165 ...
COL13A1NM_080801chr20-332551103339506333255419333945734333255110,33255210,33255337,33256781,33260155,33264874,33265820,33266822,33268990,33271831,33273081,33275820,33278093,33278498,33 ...33255182,33255300,33255422,33256820,33260242,33264910,33265874,33266876,33269026,33271912,33273125,33275865,33278237,33278545,33 ...
ATP6V0A1NM_001378534chr10+887128608876622288712866887649082588712860,88718223,88720363,88721146,88729316,88730141,88732160,88733306,88736660,88739659,88741392,88741896,88742916,88745359,88 ...88712983,88718304,88720459,88721275,88729420,88730268,88732243,88733400,88736873,88739810,88741532,88742040,88743006,88745476,88 ...
PTPN7NM_001040576chr13+57011944570212915701197157021291957011944,57012360,57012494,57013802,57015070,57015508,57017342,57019996,57021210,57012133,57012444,57012497,57013877,57015208,57015615,57017501,57020111,57021291,

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