Schema for xenoRefGene
  Database: panTro3    Primary Table: xenoRefGene    Row Count: 343,294   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1590smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_073488varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 131817868int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 131823995int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 131823995int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 131823995int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 131817868,131819245,1318210...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 131818198,131819309,1318211...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 HINT1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -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)
      panTro3.all_est.qName (via xenoRefGene.name)
      panTro3.all_mrna.qName (via xenoRefGene.name)
      panTro3.refGene.name (via xenoRefGene.name)
      panTro3.refSeqAli.qName (via xenoRefGene.name)
      panTro3.xenoMrna.qName (via xenoRefGene.name)
      panTro3.xenoRefFlat.name (via xenoRefGene.name)
      panTro3.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1590NR_073488chr5-1318178681318239951318239951318239955131817868,131819245,131821066,131821201,131823718,131818198,131819309,131821106,131821318,131823995,0HINT1unkunk-1,-1,-1,-1,-1,
117NR_130778chr5+46210143462709994627099946270999746210143,46268656,46268933,46269226,46269548,46270856,46270972,46210283,46268802,46268983,46269430,46269623,46270883,46270999,0LINC02198unkunk-1,-1,-1,-1,-1,-1,-1,
89NM_001378415chr7+171661671751567617166167175156761917166167,17171159,17172335,17174735,17210123,17215430,17225496,17229254,17229322,17229395,17328598,17341722,17372928,17409217,17 ...17166365,17171312,17172389,17174844,17210257,17215469,17225550,17229269,17229380,17229455,17328730,17341839,17373036,17409273,17 ...0HDAC4incmplincmpl0,0,0,0,1,0,0,2,2,0,0,0,0,0,2,0,2,0,0,
630NR_110777chr18-591154359165075916507591650755911543,5913709,5914008,5914865,5916259,5913555,5913994,5914617,5915119,5916507,0LOC101927410unkunk-1,-1,-1,-1,-1,
145NM_198429chr18+75745722758027927574572275802792975745722,75745836,75746715,75768199,75784005,75784531,75786822,75787544,75802660,75745833,75746703,75746822,75768359,75784205,75784534,75786995,75787684,75802792,0Nfatc1incmplincmpl0,0,0,2,0,2,2,1,0,
14NM_198089chr19+49164075493206354916416349320635549164075,49212341,49212715,49294251,49320495,49164178,49212468,49212806,49295474,49320635,0ZNF155cmplincmpl0,0,1,2,1,
997NR_024231chr19+54013340540133855401338554013385154013340,54013385,0SNAR-B1unkunk-1,
2072NR_024242chr3-1949683841949685031949685031949685031194968384,194968503,0SNAR-A14unkunk-1,
2072NR_024242chr3-1949699381949700571949700571949700571194969938,194970057,0SNAR-A14unkunk-1,
1407NR_033557chr6-1077602691078308451078308451078308454107760269,107761030,107777050,107830559,107760891,107761064,107777091,107830845,0LINC02532unkunk-1,-1,-1,-1,

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