Schema for xenoRefFlat
  Database: choHof1    Primary Table: xenoRefFlat    Row Count: 889,220   Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName CHD2varchar(255) Name of gene as it appears in genome browser.
name NM_001278454varchar(255) Name of gene
chrom scaffold_38719varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 6485int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 7455int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 6485int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 6546int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned Number of exons
exonStarts 6485,6586,6981,7164,longblob Exon start positions (or end positions for minus strand item)
exonEnds 6567,6620,7017,7455,longblob Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        choHof1.xenoMrna.qName (via xenoRefFlat.name)
      choHof1.xenoRefGene.name (via xenoRefFlat.name)
      choHof1.xenoRefSeqAli.qName (via xenoRefFlat.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
CHD2NM_001278454scaffold_38719-648574556485654646485,6586,6981,7164,6567,6620,7017,7455,
CCDC191NM_001353766scaffold_107754+1407461114073594131407,1970,2500,2805,2969,3162,3748,3852,4155,4278,4419,4506,4572,1508,2200,2800,2968,3161,3594,3815,3897,4237,4376,4496,4554,4611,
ARHGAP11ANM_001286480scaffold_107738-377738673867386713777,3867,
unc-31NM_001268737scaffold_30+65559152655591527655,17939,32320,33983,34457,58056,59047,796,18128,32419,34049,34580,58203,59152,
Agxt2NM_001031851scaffold_7044+192271281922710413192,1647,2910,3116,3647,9329,10454,13991,15195,16913,17153,22910,26996,315,1742,3001,3119,3765,9446,10547,14124,15285,17065,17156,23006,27128,
Vmn2r100NM_001104562scaffold_149455+281435532814355332814,3307,3412,2937,3367,3553,
Vmn2r101NM_001104563scaffold_54133-846698648466986438466,8563,9804,8529,8584,9864,
Galnt16NM_001081421scaffold_36868+712772597127725917127,7259,
hmgn6NM_001161336scaffold_52216-108912091089120921089,1194,1158,1209,
hmgn6NM_001161336scaffold_8133+16218166061621816326216218,16573,16326,16606,

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