Schema for xenoRefFlat
  Database: panTro5    Primary Table: xenoRefFlat    Row Count: 251,874   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 LOC101929172varchar(255) values Name of gene as it appears in genome browser.
name NR_104677varchar(255) values Name of gene
chrom chr8varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 20591372int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 20592561int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 20592561int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 20592561int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 20591372,20591821,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 20591637,20592561,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)
      panTro5.xenoMrna.qName (via xenoRefFlat.name)
      panTro5.xenoRefGene.name (via xenoRefFlat.name)
      panTro5.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
LOC101929172NR_104677chr8+20591372205925612059256120592561220591372,20591821,20591637,20592561,
abcg2aNM_001042775chr4-904728419051084790472841905108471290472841,90477819,90479725,90485678,90491788,90493468,90496293,90499816,90509280,90510018,90510758,90510789,90472949,90477946,90479812,90485744,90491884,90493561,90496422,90499972,90509434,90510128,90510763,90510847,
INTS10NM_001353519chr8+190761711911110419082923191108261819076171,19076493,19077214,19078595,19081460,19082323,19082900,19083836,19085464,19089441,19091069,19092208,19096090,19101873,19 ...19076461,19076683,19077363,19078699,19081542,19082464,19083072,19084006,19085598,19089595,19091152,19092361,19096199,19101953,19 ...
ZNF532NM_001353525chr2B-805753838058149780577372805812303680575383,80575670,80576188,80576570,80576667,80576724,80578564,80578658,80578687,80578789,80578834,80578908,80578955,80578998,80 ...80575449,80576107,80576526,80576650,80576713,80578563,80578658,80578687,80578779,80578833,80578908,80578955,80578996,80579025,80 ...
ZNF532NM_001353525chr18+562764525640173756333808563997285756276452,56276666,56276803,56278591,56333791,56334005,56334071,56334102,56334161,56334219,56334253,56334295,56334347,56334411,56 ...56276517,56276738,56276878,56278701,56334005,56334030,56334101,56334159,56334218,56334253,56334293,56334347,56334411,56334463,56 ...
LOC103447859NM_001293878chr20-65656507656668026565650765666796765656507,65657123,65658684,65662157,65663830,65664881,65666652,65656614,65657358,65658939,65662250,65664127,65665061,65666802,
Emc4NM_026519chr15+14491567144965811449158514496230714491567,14492007,14494140,14494876,14496194,14496407,14496539,14491671,14492122,14494294,14495037,14496243,14496482,14496581,
Fam122aNM_026520chr9+45944322459456544594443945945303445944322,45944532,45945333,45945359,45944484,45945318,45945341,45945654,
Rnf146NM_026518chr6+13109766413112117513111749413111857211131097664,131111051,131117494,131118494,131118872,131119011,131119113,131119175,131120009,131120134,131120751,131097774,131111178,131118458,131118850,131118990,131119052,131119137,131119250,131120026,131120155,131121175,
Rpl22l1NM_026517chr3-1745890821745910701745890821745910703174589082,174590691,174590976,174589227,174590813,174591070,

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