Schema for xenoRefGene
  Database: gorGor5    Primary Table: xenoRefGene    Row Count: 338,535   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 74smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001287295varchar(255) values Name of gene (usually transcript_id from GTF)
chrom CYUI01000058v1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1546468int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1577592int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1546468int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1577592int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 18int(10) unsigned range Number of exons
exonStarts 1546468,1549465,1555811,155...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1546543,1549602,1555887,155...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 TRAP1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('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 0,0,2,0,1,0,0,2,0,0,0,2,0,0...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
        gorGor5.all_mrna.qName (via xenoRefGene.name)
      gorGor5.refGene.name (via xenoRefGene.name)
      gorGor5.refSeqAli.qName (via xenoRefGene.name)
      gorGor5.xenoRefFlat.name (via xenoRefGene.name)
      gorGor5.xenoRefSeqAli.qName (via xenoRefGene.name)
      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)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
74NM_001287295CYUI01000058v1+1546468157759215464681577592181546468,1549465,1555811,1557944,1559464,1560209,1561110,1562154,1562803,1563828,1563860,1569471,1571128,1572025,1572615,1573473, ...1546543,1549602,1555887,1558107,1559577,1560281,1561259,1562161,1562917,1563860,1563904,1569619,1571317,1572151,1572702,1573614, ...0TRAP1incmplcmpl0,0,2,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,
605NR_135323CYUI01015388v1-2702524273436327343632734363122702524,2702668,2705030,2707271,2708246,2709384,2710549,2713035,2717989,2724699,2733533,2734277,2702596,2702992,2705104,2707404,2708313,2709449,2710596,2713169,2718097,2724821,2733695,2734363,0PHF11unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
590NM_004749CYUI01015540v1+67162668318467406968295911671626,674019,677525,678580,679035,679845,680793,681214,681670,681912,682857,671681,674480,677849,678752,679193,679956,680938,681460,681782,682027,683184,0TBRG4cmplcmpl-1,0,0,0,1,0,0,1,1,2,0,
647NM_004748CYUI01015082v1-8185271823649781895518217587118185271,8187463,8188420,8188737,8195235,8201803,8206966,8208321,8213386,8217527,8235984,8187157,8187498,8188597,8190997,8195357,8202055,8207168,8208398,8213501,8217596,8236497,0CCPG1cmplcmpl-1,-1,-1,0,1,1,0,1,0,0,-1,
78NM_004747CYUI01015089v1+5906036604153559062916039883415906036,5906148,5906286,5906380,5963078,5975429,5977949,5978782,5988582,5990094,5996392,5998272,6001442,6001971,6002785,6003329, ...5906136,5906208,5906380,5906593,5963147,5975592,5978093,5978966,5988842,5990407,5996577,5998398,6001575,6002099,6002961,6003433, ...0DLG5cmplcmpl-1,-1,0,1,1,1,2,2,0,2,0,2,2,0,2,1,0,1,1,2,1,1,0,0,2,1,1,1,2,0,2,2,0,2,2,1,1,0,2,1,-1,
9NM_030595CYUI01015047v1+5577782630001755782846298278725577782,5578215,5578407,5677594,5681608,5681967,5685257,5686974,5692678,5695376,5695426,5706906,5707716,5733961,5744654,5746321, ...5577834,5578299,5578578,5677826,5681709,5682063,5685379,5687101,5692798,5695426,5695522,5707104,5707848,5734063,5744810,5746491, ...0Nbeacmplcmpl-1,0,0,0,1,0,0,2,0,0,0,0,0,0,0,0,2,0,0,0,1,2,0,1,2,0,0,0,2,1,1,2,0,1,2,2,1,2,1,0,1,0,2,1,1,0,1,2,0,0,0,0,0,0,0,1,1,1,1,1,0,2,-1, ...
695NM_001276711CYUI01014933v1-14513940145178601451394014517860914513940,14514230,14514618,14515500,14516029,14516245,14517307,14517486,14517821,14514060,14514251,14514729,14515596,14516065,14516344,14517337,14517585,14517860,0Nfkb1incmplincmpl0,0,0,0,0,0,0,0,0,
76NM_001300977CYUI01015087v1+405200640728324052964407097894052006,4056799,4064368,4064421,4068606,4069613,4070967,4071197,4072711,4053022,4056963,4064421,4064475,4068726,4069749,4071052,4071838,4072832,0ANKRD42cmplcmpl0,1,0,0,0,0,1,-1,-1,
599NM_031522CYUI01015528v1-189762419005961897627190059661897624,1897950,1898347,1899097,1899910,1900563,1897854,1898173,1898530,1899358,1900106,1900596,0Neu1incmplcmpl1,0,0,0,2,0,
76NM_001300972CYUI01015087v1+4052006411628340529644116081134052006,4056799,4064368,4064421,4068606,4069613,4083007,4085866,4094539,4098894,4103662,4108134,4116039,4053022,4056963,4064421,4064475,4068726,4069749,4083208,4085992,4094645,4099070,4103789,4108279,4116283,0ANKRD42cmplcmpl0,1,0,0,0,0,1,1,1,2,1,2,0,

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