Schema for xenoRefGene
  Database: aptMan1    Primary Table: xenoRefGene    Row Count: 445,279   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 661smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001081281varchar(255) values Name of gene (usually transcript_id from GTF)
chrom NW_013991102v1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 9965409int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 9993850int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 9965409int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 9993850int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 9965409,9970817,9971853,997...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 9965532,9970847,9972000,997...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Trim55varchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,0,0,0,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
        aptMan1.all_mrna.qName (via xenoRefGene.name)
      aptMan1.refGene.name (via xenoRefGene.name)
      aptMan1.refSeqAli.qName (via xenoRefGene.name)
      aptMan1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
661NM_001081281NW_013991102v1-996540999938509965409999385089965409,9970817,9971853,9976522,9978594,9992736,9992823,9993682,9965532,9970847,9972000,9976609,9978756,9992739,9992997,9993850,0Trim55cmplincmpl0,0,0,0,0,0,0,0,
1027NM_137339NW_013995860v1-58053767580572645805376758057264258053767,58057123,58053821,58057264,0CG9646incmplincmpl0,0,
661NR_037718NW_013997969v1+10034010100773841007738410077384310034010,10034242,10077291,10034054,10034329,10077384,0EFEMP2unkunk-1,-1,-1,
679NM_001321878NW_013990105v1+123392981244258712339342124393042412339298,12395430,12396642,12396714,12396865,12399179,12401337,12402412,12418721,12422097,12428147,12430600,12431193,12438986,12 ...12339364,12395672,12396678,12396783,12396866,12399307,12401446,12402417,12418856,12422190,12428257,12430774,12431409,12439121,12 ...0HDAC9cmplcmpl0,1,0,0,0,1,0,1,0,0,1,0,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NM_001281621NW_013993267v1-32940364113294036411532940,33526,33913,35431,36255,33026,33685,34119,35574,36411,0Raraincmplincmpl1,1,2,0,0,
587NM_001281619NW_013992704v1-2971882976552971882976553297188,297359,297550,297347,297470,297655,0Rassf1incmplincmpl0,0,0,
585NM_200353NW_013996691v1-68648701456864870145668648,69386,69535,69703,69780,69968,68774,69451,69607,69766,69783,70145,0ucp3incmplincmpl0,0,0,0,0,0,
597NM_001135281NW_014002486v1-1598871161091115994311610911131598871,1599267,1599348,1599784,1599827,1600605,1600666,1604263,1605866,1608584,1609052,1609122,1610810,1599245,1599308,1599592,1599824,1599947,1600608,1600888,1604416,1605937,1608656,1609055,1609160,1610911,0ZNF207incmplcmpl-1,-1,1,0,0,0,0,0,2,0,0,1,2,
692NM_001315776NW_013992144v1-14074758141310681407475814131068614074758,14096066,14107130,14119034,14122231,14130933,14074932,14096192,14107214,14119088,14122291,14131068,0RBKSincmplcmpl0,0,0,0,0,0,
585NM_001017461NW_013999854v1-155275323815527532382115527,15808,17467,21369,21427,25779,26273,26551,26946,27467,27862,29316,29870,30908,32187,33109,34135,35965,44370,53049,53154,15683,15972,17537,21372,21545,25851,26452,26679,27097,27596,27965,29469,30053,31091,32278,33256,34290,36081,44473,53136,53238,0Ogdhincmplincmpl0,1,0,0,2,0,1,2,1,1,0,0,0,0,2,2,0,1,0,0,0,

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