Schema for xenoRefFlat
  Database: neoSch1    Primary Table: xenoRefFlat    Row Count: 446,526   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ehd4varchar(255) values Name of gene as it appears in genome browser.
name NM_001102972varchar(255) values Name of gene
chrom NW_018734356v1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 22790553int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 22866674int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 22790553int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 22866674int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 22790553,22798091,22806823,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 22791069,22798256,22807236,...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)
      neoSch1.xenoRefGene.name (via xenoRefFlat.name)
      neoSch1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
ehd4NM_001102972NW_018734356v1-22790553228666742279055322866674722790553,22798091,22806823,22836883,22846795,22866436,22866659,22791069,22798256,22807236,22836984,22846967,22866611,22866674,
ddx31.LNM_001094907NW_018734337v1+1926124197329519287331973295131926124,1926268,1928733,1934916,1937352,1938977,1939206,1940333,1941300,1941429,1954173,1967846,1973164,1926160,1926355,1928808,1934961,1937424,1939097,1939305,1940363,1941342,1941462,1954224,1967958,1973295,
PLCD3NM_001193028NW_018734318v1+21269659212806682126965921280668221269659,21280632,21269719,21280668,
Mxd4NM_001108364NW_018726556v1+8873101308873895828873,9968,8990,10130,
CNGA3NM_001079878NW_018734385v1+162620271629174116262051162900321816262027,16269900,16272223,16272453,16283248,16285539,16288622,16290089,16290293,16290376,16290461,16290616,16290783,16290837,16 ...16262084,16269975,16272416,16272456,16283349,16285648,16290035,16290102,16290304,16290407,16290596,16290742,16290792,16290858,16 ...
PBXIP1NM_001075265NW_018734287v1+4647430465435246474424653588124647430,4649078,4649603,4650994,4651352,4651846,4652435,4652641,4652803,4653064,4654147,4654301,4647493,4649204,4649734,4651230,4651370,4651939,4652636,4652795,4652886,4653588,4654160,4654352,
IDH3ANM_174644NW_018734280v1+285691812858344528569193285829831528569181,28572918,28575167,28576640,28577952,28578467,28579299,28579491,28580993,28581493,28582899,28583075,28583306,28583345,28 ...28569220,28572981,28575251,28576755,28578140,28578601,28579402,28579556,28581078,28581646,28583019,28583210,28583335,28583367,28 ...
Zfp788NM_023363NW_018734403v1+3161838383067331619343830673133161838,3167206,3167362,3317507,3317984,3318128,3318391,3483746,3755513,3755942,3756111,3830019,3830367,3161958,3167326,3167405,3317732,3318044,3318223,3318520,3483904,3755690,3756066,3756168,3830190,3830673,
cskNM_001077599NW_018734350v1-2638167264208126381672642081112638167,2638599,2638810,2639094,2639619,2639805,2639989,2640239,2641166,2641730,2641967,2638341,2638686,2639005,2639166,2639709,2639906,2640053,2640335,2641384,2641845,2642081,
RPL21NM_001191412NW_018734396v1+59448103594486005944811659448599159448103,59448600,

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