Schema for xenoRefFlat
  Database: ponAbe2    Primary Table: xenoRefFlat    Row Count: 353,597   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 LRRC2varchar(255) values Name of gene as it appears in genome browser.
name NM_001080311varchar(255) values Name of gene
chrom chr2bvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 64391345int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 64393073int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 64391412int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 64393049int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 64391345,64391796,64392091,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 64391494,64391810,64392333,...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)
      ponAbe2.xenoMrna.qName (via xenoRefFlat.name)
      ponAbe2.xenoRefGene.name (via xenoRefFlat.name)
      ponAbe2.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
LRRC2NM_001080311chr2b-64391345643930736439141264393049664391345,64391796,64392091,64392333,64392861,64392974,64391494,64391810,64392333,64392830,64392972,64393073,
LRRC2NM_001080311chr3+1000541351000890621000541551000887619100054135,100060987,100067012,100073179,100076501,100078994,100085075,100088711,100088827,100054280,100061192,100067171,100073316,100076647,100079150,100085212,100088766,100089062,
Vwa5b1NM_029401chr1_random+25009094250223022500909425022302725009094,25009775,25011629,25015306,25016506,25021340,25021984,25009289,25009900,25011815,25015351,25016702,25021484,25022302,
Rab4bNM_029391chr1-20377606203937432037760620393743620377606,20381464,20382906,20384643,20391337,20393661,20377722,20381560,20383061,20384708,20391450,20393743,
Rab4bNM_029391chr19+419296684194783141929801419380191041929668,41931448,41931813,41935179,41935326,41937719,41937905,41947459,41947549,41947816,41929817,41931529,41931928,41935242,41935360,41937818,41938034,41947490,41947798,41947831,
Shld2NM_029389chr10_random+328911923293358132891199329335591532891192,32891868,32892084,32892213,32892270,32892447,32897599,32913176,32913518,32913778,32918615,32922801,32929928,32933318,32 ...32891352,32892027,32892202,32892258,32892281,32892724,32897703,32913351,32913653,32913782,32918818,32923030,32930044,32933476,32 ...
anapc10NM_001267697chr1-1774977681774983261774977681774983261177497768,177498326,
Zfp709NM_145624chr19+120431841238088312043184123808831612043184,12044562,12045698,12090959,12124446,12161203,12161537,12248207,12248657,12289297,12291580,12306749,12307568,12308361,12 ...12043310,12044592,12045790,12091008,12124519,12161351,12161561,12248324,12248883,12289412,12291641,12306898,12307628,12308455,12 ...
anapc10NM_001267696chr4-1505087281506137911505087281506137913150508728,150594817,150613698,150508959,150594937,150613791,
anapc10NM_001267696chr1-1774977681774983261774977681774983261177497768,177498326,

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