Schema for xenoRefFlat
  Database: canFam1    Primary Table: xenoRefFlat    Row Count: 450,935   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 lzts2avarchar(255) values Name of gene as it appears in genome browser.
name NM_001145606varchar(255) values Name of gene
chrom chr24varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 21135750int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 21137508int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 21135750int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 21137508int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 21135750,21135927,21136329,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 21135819,21135975,21136494,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        canFam1.xenoMrna.qName (via xenoRefFlat.name)
      canFam1.xenoRefGene.name (via xenoRefFlat.name)
      canFam1.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
lzts2aNM_001145606chr24+21135750211375082113575021137508621135750,21135927,21136329,21136557,21136948,21137436,21135819,21135975,21136494,21136602,21137068,21137508,
LOC100786504NM_001255243chr6+19648748196510191964874819651019419648748,19649901,19650410,19650953,19648820,19649976,19650497,19651019,
Kng1NM_001102411chr34+223680342239570022368046223957001122368034,22376890,22392634,22394956,22395061,22395136,22395258,22395269,22395331,22395509,22395565,22368241,22377034,22392733,22395044,22395133,22395249,22395268,22395306,22395342,22395545,22395700,
chmp4c.LNM_001092411chr24+25922579259742412592257925974241325922579,25970732,25974196,25922713,25970913,25974241,
etf1.SNM_001090894chrUn-56192856561940715619285656194053156192856,56194071,
Vipas39NM_001101004chr8-531508595317124153150899531712331853150859,53151641,53152159,53152831,53154199,53154808,53155886,53156461,53158655,53161461,53162970,53163576,53166077,53166844,53 ...53150920,53151746,53152249,53152918,53154289,53154856,53156015,53156537,53158729,53161489,53163073,53163610,53166134,53166909,53 ...
znf143.SNM_001090904chr21+350205513507930435020551350793041535020551,35021495,35038114,35038451,35039354,35039964,35041320,35052421,35053275,35054078,35058308,35062705,35067271,35078181,35 ...35020614,35021502,35038216,35038524,35039433,35040047,35041520,35052505,35053351,35054204,35058488,35062932,35067322,35078264,35 ...
RPS6KA5NM_001322237chr24-19772886198003021980030219800302319772886,19791329,19800273,19772915,19791351,19800302,
RPS6KA5NM_001322237chr12+38258097387945793879457938794579438258097,38551712,38552625,38794561,38258139,38551727,38552641,38794579,
CDANM_001193110chr2-78983856790057237898424479005709678983856,78984237,78984287,78987552,78993444,79005563,78983973,78984273,78984361,78987610,78993564,79005723,

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