Schema for xenoRefGene
  Database: rheMac8    Primary Table: xenoRefGene    Row Count: 241,830   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 110smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_027466varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr14varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 38890307int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 39127492int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 39127492int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 39127492int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 38890307,38890336,39126525,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 38890322,38891939,39127492,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 CTAGE11Pvarchar(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,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)
      rheMac8.all_est.qName (via xenoRefGene.name)
      rheMac8.all_mrna.qName (via xenoRefGene.name)
      rheMac8.refGene.name (via xenoRefGene.name)
      rheMac8.refSeqAli.qName (via xenoRefGene.name)
      rheMac8.xenoRefFlat.name (via xenoRefGene.name)
      rheMac8.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
110NR_027466chr14+38890307391274923912749239127492338890307,38890336,39126525,38890322,38891939,39127492,0CTAGE11Punkunk-1,-1,-1,
79NR_125386chr8-6782170687513968751396875139126782170,6782595,6782788,6783942,6784164,6784514,6784991,6785567,6786731,6788047,6793595,6875094,6782538,6782643,6783452,6784130,6784218,6784968,6785145,6785636,6786823,6788247,6793757,6875139,0MCPH1-AS1unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
1236NM_001243078chr12+85399346854320388539956885428438585399346,85422805,85428311,85429567,85430383,85399620,85422932,85429262,85430161,85432038,0CD28cmplcmpl0,1,2,-1,-1,
1200NM_001076595chr10-80673413806880278067341380688027480673413,80674445,80674806,80687908,80673513,80674640,80674935,80688027,0josd1incmplcmpl2,2,2,0,
1665NM_001080273chr4-14159609914165753114159610414165751913141596099,141616309,141624985,141625235,141626648,141629577,141638488,141639411,141639778,141639959,141642234,141644431,14165744 ...141596236,141616429,141625118,141625308,141626813,141629658,141638645,141639546,141639871,141640041,141642308,141644497,14165753 ...0TRMT11cmplcmpl0,0,2,1,1,1,0,0,0,2,0,0,0,
138NM_001088639chr8-688014696883284568801469688328251168801469,68809512,68809918,68811067,68811175,68811279,68818714,68822145,68822366,68824570,68832708,68801544,68809603,68810052,68811172,68811176,68811352,68818796,68822244,68822465,68824633,68832845,0tram1.Scmplcmpl0,2,0,0,2,1,0,0,0,0,0,
1633NM_001102229chr5-13741643213742921113741776513742884111137416432,137416658,137416848,137417029,137417180,137417314,137417389,137417719,137425232,137425487,137426354,137416643,137416796,137416989,137417094,137417222,137417371,137417690,137418433,137425396,137425573,137429211,0PCDH18cmplcmpl-1,-1,-1,-1,-1,-1,-1,1,2,0,0,
601NR_003344chr7+215121621512982151298215129812151216,2151298,0SNORD115-29unkunk-1,
601NR_003344chr7+215631321563952156395215639512156313,2156395,0SNORD115-29unkunk-1,
585NR_003344chrUn_NW_014960451v1+050505010,50,0SNORD115-29unkunk-1,

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