Schema for xenoRefGene
  Database: nomLeu1    Primary Table: xenoRefGene    Row Count: 350,149   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 685smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_028054varchar(255) values Name of gene (usually transcript_id from GTF)
chrom GL397291varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 13229227int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 13230811int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 13230811int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 13230811int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 13229227,13229584,13230137,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 13229257,13229623,13230435,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 NGRNvarchar(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,-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)
      nomLeu1.all_mrna.qName (via xenoRefGene.name)
      nomLeu1.xenoMrna.qName (via xenoRefGene.name)
      nomLeu1.xenoRefFlat.name (via xenoRefGene.name)
      nomLeu1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
685NR_028054GL397291-13229227132308111323081113230811613229227,13229584,13230137,13230581,13230628,13230708,13229257,13229623,13230435,13230592,13230643,13230811,0NGRNunkunk-1,-1,-1,-1,-1,-1,
615NM_001252089GL397342+402669740281804026729402790154026697,4027065,4027597,4028027,4028103,4027056,4027597,4028010,4028069,4028180,0Rbmxl1cmplcmpl0,0,2,-1,-1,
621NM_001252089GL397347-4766002477165247662824771625124766002,4766099,4767228,4767398,4767402,4767616,4768578,4768622,4770116,4770176,4771215,4771516,4766086,4766593,4767310,4767401,4767529,4767726,4768582,4768690,4770167,4770287,4771322,4771652,0Rbmxl1cmplcmpl-1,1,0,0,2,0,2,0,0,0,1,0,
745NM_001252100GL397296-209811492103691920985926210365884020981149,20984659,20985926,20986541,20987325,20988598,20989033,20991359,20992778,20994860,20996667,20998793,20998945,21000251,21 ...20984557,20985862,20986026,20986741,20987496,20988716,20989198,20991540,20992915,20994899,20996781,20998868,20999151,21000312,21 ...0KIF21Bcmplcmpl-1,-1,2,0,0,2,2,1,2,2,2,2,0,2,1,0,0,0,2,0,0,0,1,1,1,1,2,1,1,1,0,2,2,0,0,0,2,0,-1,-1,
95NM_052985GL397298-231453002323259623145539232324893223145300,23146073,23146618,23148199,23150198,23151048,23153190,23157857,23159069,23161199,23162746,23165561,23170023,23173521,23 ...23145629,23146238,23146698,23148323,23150219,23151216,23153291,23157952,23159210,23161302,23162918,23165728,23170185,23173575,23 ...0IFT122cmplcmpl0,0,1,1,1,2,0,1,1,0,2,0,0,0,2,0,1,0,1,0,0,2,2,2,1,2,2,1,1,0,2,0,
733NM_001047010GL397291-19434439194355461943443919435546319434439,19434895,19435180,19434811,19435156,19435546,0LOC733015incmplcmpl0,0,0,
633NM_001102121GL397358+6409688642085464099816419438116409688,6409967,6409994,6410814,6411183,6415485,6417173,6419357,6420206,6420296,6420767,6409718,6409982,6410036,6411034,6411453,6415824,6417476,6419438,6420227,6420344,6420854,0TAPBPLcmplincmpl-1,0,0,0,1,1,1,1,-1,-1,-1,
596NM_210465GL397449-154031815457911540318154579161540318,1541923,1542303,1544197,1544457,1545653,1540402,1542061,1542378,1544347,1544598,1545791,0AGOS_AER254Wincmplincmpl0,0,0,0,0,0,
653NM_001097491GL397275-893798989401378937989894013748937989,8938443,8938924,8939871,8938082,8938721,8939203,8940137,0PCD1Bincmplincmpl0,1,1,0,
605NM_001280251GL397431-2644639273794726448012737850192644639,2645653,2646209,2646461,2647052,2648099,2648243,2648568,2648788,2656327,2662923,2664675,2666809,2667027,2676338,2678321, ...2644938,2645752,2646376,2646622,2647119,2648163,2648378,2648696,2648874,2656447,2663031,2664928,2666846,2667055,2676551,2678351, ...0MED15cmplcmpl1,1,2,0,2,1,1,2,0,0,2,2,0,1,1,1,0,2,0,

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