Schema for xenoRefFlat
  Database: calJac1    Primary Table: xenoRefFlat    Row Count: 519,237   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName lbhvarchar(255) Name of gene as it appears in genome browser.
name NM_001011389varchar(255) Name of gene
chrom Contig247varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 296285int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 319154int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 296285int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 319154int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned Number of exons
exonStarts 296285,296969,318974,longblob Exon start positions (or end positions for minus strand item)
exonEnds 296369,296975,319154,longblob Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        calJac1.xenoMrna.qName (via xenoRefFlat.name)
      calJac1.xenoRefGene.name (via xenoRefFlat.name)
      calJac1.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
lbhNM_001011389Contig247+2962853191542962853191543296285,296969,318974,296369,296975,319154,
LOC410337NM_001126243Contig696-81421825988142182598381421,82486,82549,81469,82488,82598,
LoxNM_001286181Contig6415-655858008171083793421965585,65720,66054,66193,66284,66446,66825,66898,67103,67183,71083,71542,75072,76771,78250,78711,79120,79282,80013,65663,65786,66147,66256,66314,66464,66860,66960,67173,67236,71202,71638,75229,76909,78359,78973,79255,79342,80081,
ZFYVE9NM_007324Contig475+80670216164906042157121780670,90568,96574,126075,130375,136461,140865,143680,155423,158235,168185,197299,200649,204376,207148,213768,215550,80782,90674,98682,126175,130545,136580,140990,143836,155648,158318,168290,197450,200730,204539,207254,213945,216164,
RANBP3NM_007322Contig16416+5142877851977185115142,5274,5576,5958,6016,6369,7597,7745,7902,8048,8413,5274,5398,5643,6014,6364,7557,7732,7893,8037,8260,8778,
RANBP3NM_007322Contig17161+230255902341412192302,2418,2611,2860,2949,3302,4681,4838,4984,2418,2540,2649,2947,3302,4669,4829,4973,5590,
RANBP3NM_007322Contig12620+344790983483761193447,3560,6209,6353,6442,6795,8184,8342,8492,3560,3682,6247,6440,6795,8173,8333,8481,9098,
wnt4bNM_131500Contig1779+2543892636022543892636024254389,262222,262448,263245,254479,262357,262589,263602,
stat3NM_131479Contig3318-7582215323775822153237775822,79301,80558,83743,147139,150133,153183,75960,79436,80648,83833,147198,150230,153237,
Dctn6NM_001106085Contig7662+2174100702174977892174,2299,3874,3979,5698,7085,9679,10011,10049,2282,2302,3957,3981,5746,7228,9781,10038,10070,

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