Schema for xenoRefFlat
  Database: panTro2    Primary Table: xenoRefFlat    Row Count: 340,768   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 GlySvarchar(255) values Name of gene as it appears in genome browser.
name NM_169610varchar(255) values Name of gene
chrom chr12varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 67451901int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 67489936int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 67451901int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 67489936int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 67451901,67455000,67461393,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 67452090,67455153,67461528,...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)
      panTro2.xenoMrna.qName (via xenoRefFlat.name)
      panTro2.xenoRefGene.name (via xenoRefFlat.name)
      panTro2.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
GlySNM_169610chr12+674519016748993667451901674899361167451901,67455000,67461393,67467057,67467358,67469900,67472068,67483908,67487778,67489775,67489864,67452090,67455153,67461528,67467168,67467466,67469999,67472185,67484026,67487874,67489798,67489936,
GlySNM_169610chr19-546816375470530454681637547053041054681637,54682014,54685616,54693907,54694358,54696958,54697349,54697457,54703662,54705258,54681709,54682112,54685737,54694015,54694481,54697099,54697427,54697496,54703703,54705304,
abcc1NM_001127001chr10+10015330010018967310015330010018967311100153300,100153453,100157369,100162337,100166925,100168397,100180840,100182685,100184502,100185842,100189483,100153390,100153558,100157525,100162415,100167090,100168571,100180972,100182757,100184658,100186006,100189673,
PRKXP1NR_073405chr15-985883229859171298591712985917121198588322,98588799,98588979,98589360,98589427,98590041,98590764,98590880,98591159,98591552,98591701,98588762,98588950,98589158,98589392,98589969,98590604,98590799,98591088,98591507,98591629,98591712,
Zcchc12NM_028325chrX+1183122621183146321183129121183140645118312262,118312905,118313896,118314334,118314572,118312289,118313849,118314064,118314350,118314632,
LOC102723517NR_110877chr17-71463679714872957148729571487295271463679,71487017,71463912,71487295,
SRRM1NM_001366570chr1+248736482490376924879225249027862224873648,24876325,24877018,24877430,24880344,24881949,24882957,24883436,24885382,24891246,24891835,24893186,24893709,24897321,24 ...24873694,24876415,24877141,24879381,24880460,24882153,24883152,24883556,24885651,24891327,24891919,24893331,24893751,24897432,24 ...
TMED10P1NR_002807chr8+1450189751450230191450230191450230195145018975,145020023,145021262,145022072,145022382,145020014,145020273,145022048,145022085,145023019,
PRKYNR_028062chrX-3554632364946736494673649467193554632,3555313,3555909,3556336,3556538,3556914,3557325,3557660,3558105,3558520,3558896,3558980,3562242,3566142,3576775,3595423, ...3555277,3555883,3556297,3556445,3556610,3557233,3557551,3557974,3558173,3558859,3558964,3559218,3562391,3566220,3576872,3595689, ...
ift122NM_212890chr3+13389766613397140713389766613397140731133897666,133906734,133907179,133909257,133909477,133910336,133914715,133921689,133921852,133921869,133922039,133923389,13392516 ...133897759,133906805,133907183,133909322,133909481,133910480,133914787,133921735,133921859,133921882,133922176,133923592,13392530 ...

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