Schema for xenoRefGene
  Database: rheMac2    Primary Table: xenoRefGene    Row Count: 350,277   Data last updated: 2016-02-16
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 115smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001105908varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr3varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 44148594int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 44183151int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 44148594int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 44167998int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 44148594,44152684,44153321,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 44148738,44152855,44153325,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Pms2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,2,0,0,0,-1,-1,-1,-1,-1,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)
      rheMac2.all_est.qName (via xenoRefGene.name)
      rheMac2.all_mrna.qName (via xenoRefGene.name)
      rheMac2.refGene.name (via xenoRefGene.name)
      rheMac2.refSeqAli.qName (via xenoRefGene.name)
      rheMac2.xenoMrna.qName (via xenoRefGene.name)
      rheMac2.xenoRefFlat.name (via xenoRefGene.name)
      rheMac2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
115NM_001105908chr3-441485944418315144148594441679981144148594,44152684,44153321,44153663,44157755,44167944,44176046,44179594,44180875,44181171,44183047,44148738,44152855,44153325,44153758,44157821,44168028,44176218,44179774,44180980,44181240,44183151,0Pms2cmplcmpl0,0,2,0,0,0,-1,-1,-1,-1,-1,
14NM_152814chr19-43749700440989114400743444098911543749700,44007434,44007809,44026417,44098789,43749730,44007725,44008041,44026551,44098911,0Zfp566incmplincmpl-1,0,2,0,0,
737NM_153106chr1+200167562003893120016756200389281420016756,20018027,20019260,20025577,20025899,20029631,20031567,20031728,20031890,20032536,20033112,20036176,20038116,20038694,20016825,20018102,20019380,20025661,20025996,20029747,20031675,20031730,20032043,20032681,20033235,20036335,20038119,20038931,0Padi6incmplcmpl0,0,1,0,0,1,0,0,2,2,0,0,0,0,
933NM_153105chr1-45629409456345664563030145634423945629409,45629515,45630107,45630220,45630300,45632592,45632782,45634200,45634548,45629464,45629603,45630131,45630233,45630464,45632675,45632949,45634495,45634566,0Cldn19cmplcmpl-1,-1,-1,-1,2,0,1,0,-1,
879NM_001033201chr15-385540933859076538554213385903022638554093,38554199,38555715,38556440,38558477,38560957,38562422,38563323,38564426,38566701,38569336,38569657,38570476,38571518,38 ...38554190,38554327,38555835,38556563,38558590,38561063,38562516,38563426,38564549,38566804,38569411,38569720,38570542,38571628,38 ...0Ncbp1cmplcmpl-1,0,0,0,1,0,2,1,1,2,2,2,2,0,0,0,0,2,0,0,2,0,1,0,-1,-1,
14NM_013141chr11+49184951494973354918495149185983549184951,49185918,49193941,49497271,49497318,49185026,49185983,49193977,49497285,49497335,0Ppardincmplincmpl0,0,-1,-1,-1,
1098NM_001005175chr14-67324834673257306732483467325730367324834,67324953,67325538,67324876,67325505,67325730,0OR52N4incmplincmpl0,0,0,
1547NM_001286737chr1+1261261621261310241261261621261310244126126162,126126291,126130883,126130958,126126252,126126513,126130949,126131024,0GNRHRincmplincmpl0,0,0,0,
1318NM_001286734chr5-961014209618918996101837961890994796101420,96104381,96106398,96109529,96110961,96114824,96117549,96127573,96128570,96131019,96133215,96135133,96135711,96136647,96 ...96101932,96104668,96106584,96109625,96111074,96115010,96117768,96127777,96128768,96131238,96133317,96135292,96136002,96136806,96 ...0CENPEcmplcmpl1,2,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,1,0,0,0,2,1,0,0,1,0,0,1,1,2,0,
1325NM_032327chr9+970364939704826397042313970477841197036493,97042308,97042727,97043050,97043522,97044155,97044426,97045330,97046239,97046551,97047669,97036716,97042556,97042922,97043139,97043551,97044289,97044474,97045416,97046363,97046622,97048263,0ZDHHC16cmplcmpl-1,0,0,0,2,1,0,0,2,0,2,

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