Schema for refFlat
  Database: equCab2    Primary Table: refFlat    Row Count: 2,015   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName MYH2varchar(255) values Name of gene as it appears in genome browser.
name NM_001081760varchar(255) values Name of gene
chrom chr11varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 53001788int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 53027479int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 53001918int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 53025982int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 39int(10) unsigned range Number of exons
exonStarts 53001788,53003760,53003976,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 53002071,53003856,53004081,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      equCab2.mrnaOrientInfo.name (via refFlat.name)
      equCab2.refGene.name (via refFlat.name)
      equCab2.refSeqAli.qName (via refFlat.name)
      hgFixed.gbCdnaInfo.acc (via refFlat.name)
      hgFixed.gbSeq.acc (via refFlat.name)
      hgFixed.imageClone.acc (via refFlat.name)
      hgFixed.refLink.mrnaAcc (via refFlat.name)
      hgFixed.refSeqStatus.mrnaAcc (via refFlat.name)
      hgFixed.refSeqSummary.mrnaAcc (via refFlat.name)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MYH2NM_001081760chr11-530017885302747953001918530259823953001788,53003760,53003976,53004164,53004425,53005075,53005366,53005903,53006127,53006370,53007252,53007590,53008403,53009417,53 ...53002071,53003856,53004081,53004335,53004551,53005279,53005633,53006029,53006293,53006554,53007449,53007709,53008530,53009807,53 ...
GRIA2NM_001185087chr2-768694157701291976872391770124651676869415,76872388,76873781,76875281,76893265,76898087,76898937,76900639,76901421,76901788,76913950,76918542,76923019,76931769,77 ...76872001,76872637,76873896,76875529,76893464,76898458,76899144,76900750,76901526,76901956,76914112,76918596,76923216,76932009,77 ...
IFND2NM_001143796chr23+40338184403388284033831540338828140338184,40338828,
IFND1NM_001143795chr23+40302972403037204030318840303692140302972,40303720,
PKMNM_001143794chr1+12108952612111634512110000412111572311121089526,121099976,121100752,121105210,121105822,121106585,121108168,121108582,121112725,121114719,121115616,121089656,121100158,121100844,121105342,121106009,121106856,121108319,121108735,121112892,121114901,121116345,
MIP-2BETANM_001143793chr3-61699670617017526170032861701673461699670,61701134,61701336,61701555,61700344,61701218,61701460,61701752,
IL17ANM_001143792chr20+49863356498661974986335649866197349863356,49864510,49865959,49863383,49864707,49866197,
IL13NM_001143791chr14-429204904292253842920490429225381042920490,42920507,42920521,42920544,42920561,42920590,42920599,42920959,42921329,42922409,42920507,42920521,42920544,42920561,42920589,42920598,42920601,42921064,42921383,42922538,
EIF2AK2NM_001143800chr15+605377366056282060537752605622741460537736,60538229,60540663,60543486,60543735,60545423,60546874,60548439,60551352,60553177,60556831,60560284,60562001,60562133,60537871,60538347,60540811,60543567,60543832,60545446,60546937,60548562,60551472,60553358,60556960,60560386,60562055,60562820,
DRBNM_001142816chr20+33357075333757063335707533375706633357075,33364792,33367289,33368305,33368892,33375557,33357175,33365062,33367571,33368416,33368916,33375706,

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