Schema for refFlat
  Database: papAnu4    Primary Table: refFlat    Row Count: 509   Data last updated: 2019-05-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName AZIN2varchar(255) values Name of gene as it appears in genome browser.
name NM_001293719varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 31384217int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 31425790int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 31385344int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 31425443int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 31384217,31384492,31384724,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 31384399,31384613,31384937,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      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)
      papAnu4.mrnaOrientInfo.name (via refFlat.name)
      papAnu4.refGene.name (via refFlat.name)
      papAnu4.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
AZIN2NM_001293719chr1+313842173142579031385344314254431231384217,31384492,31384724,31385272,31387056,31395155,31396449,31397706,31400298,31401652,31423156,31425304,31384399,31384613,31384937,31385449,31387230,31395328,31396584,31397872,31400461,31401765,31423371,31425790,
SLC2A1NM_001173980chr1-41211164412432484121116441243248941211164,41211739,41213072,41213350,41213735,41214015,41214776,41215196,41243230,41211365,41211943,41213174,41213455,41213923,41214178,41215017,41215357,41243248,
UGT1A1NM_001112621chr12+1197384531197510281197384771197510065119738453,119745479,119746279,119746650,119750708,119739341,119745611,119746367,119746870,119751028,
UGT1A4NM_001112619chr12+1196926251197510281196926471197510065119692625,119745479,119746279,119746650,119750708,119693514,119745611,119746367,119746870,119751028,
SEMA6CNM_001168943chr1-12144339612145359512144339612145359518121443396,121444875,121445301,121445520,121445695,121446058,121446488,121446906,121447346,121447759,121448611,121448874,12144920 ...121444430,121444971,121445346,121445576,121445773,121446205,121446662,121447059,121447478,121447977,121448700,121448994,12144929 ...
LYSMD1NM_001168945chr1-1214722851214769821214722851214769823121472285,121473112,121476802,121472424,121473477,121476982,
SCNM1NM_001168946chr1+1214778761214816631214778761214816637121477876,121478201,121478628,121478812,121479017,121480135,121481563,121477927,121478272,121478717,121478910,121479106,121480330,121481663,
TMOD4NM_001168947chr1-1214826651214866371214826651214866379121482665,121483103,121483503,121484015,121484215,121484805,121485712,121486152,121486514,121482688,121483248,121483647,121484123,121484346,121484895,121485829,121486309,121486637,
VPS72NM_001168948chr1-1214884301215062691214884301215062696121488430,121489618,121496594,121498738,121499030,121506152,121488818,121489763,121496771,121498853,121499183,121506269,
PIP5K1ANM_001168949chr1+12151504612156327112151504612156327117121515046,121538937,121541605,121545395,121545974,121546277,121546349,121546359,121546384,121548493,121550949,121552620,12155387 ...121515131,121538969,121541686,121545526,121546092,121546348,121546359,121546384,121546421,121548795,121551155,121552704,12155392 ...

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