Schema for xenoRefFlat
  Database: ornAna1    Primary Table: xenoRefFlat    Row Count: 585,080   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName UBQ13varchar(255) Name of gene as it appears in genome browser.
name NM_105209varchar(255) Name of gene
chrom Contig25783varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 1742int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 2198int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 1742int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 2198int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned Number of exons
exonStarts 1742,longblob Exon start positions (or end positions for minus strand item)
exonEnds 2198,longblob Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)
      ornAna1.xenoMrna.qName (via xenoRefFlat.name)
      ornAna1.xenoRefGene.name (via xenoRefFlat.name)
      ornAna1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
UBQ13NM_105209Contig25783-174221981742219811742,2198,
LRP8NM_001018054Contig120319+321376321376432,253,452,1337,122,328,488,1376,
zgc:173486NM_001115071Ultra301+7591511126775915111267575915,76671,110817,110884,111111,75975,76712,110863,110998,111267,
Zfp408NM_001033451Contig1021-35624357563562435756135624,35756,
Zfp408NM_001033451Contig1021-35813359933581335993135813,35993,
Zscan25NM_001384205Contig1411+1743471796771791461796774174347,179146,179421,179599,174540,179253,179437,179677,
nAChRa3NM_001109917Contig55346-311237303112373033112,3548,3607,3502,3559,3730,
PAK4NM_001014835Contig247251+13192192192213,93,82,192,
nAChRa3NM_001109917Contig19398-452649614526496124526,4850,4826,4961,
smim12NM_001013528Ultra467-126742512677191267425126770411267425,1267719,

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