Schema for xenoRefFlat
  Database: gorGor3    Primary Table: xenoRefFlat    Row Count: 554,749   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName SPATA33varchar(255) Name of gene as it appears in genome browser.
name NM_001271910varchar(255) Name of gene
chrom chr16varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 80395519int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 80395976int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 80395976int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 80395976int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned Number of exons
exonStarts 80395519,80395546,longblob Exon start positions (or end positions for minus strand item)
exonEnds 80395537,80395976,longblob Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        gorGor3.xenoMrna.qName (via xenoRefFlat.name)
      gorGor3.xenoRefGene.name (via xenoRefFlat.name)
      gorGor3.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
SPATA33NM_001271910chr16+80395519803959768039597680395976280395519,80395546,80395537,80395976,
SPATA33NM_001271910chr16+80383540803961198038364880395199380383540,80383989,80395189,80383685,80384130,80396119,
HNRNPDLNM_001207000chr4-91231471912391549123495691238619791231471,91234934,91236074,91236322,91236907,91237167,91238176,91233780,91235027,91236189,91236454,91237069,91237336,91239154,
2010315B03RikNM_001243117chr19-125717701282574212699912128257421412571770,12699494,12699635,12699912,12700269,12700616,12764378,12764698,12764766,12764934,12765102,12825038,12825106,12825691,12571836,12699551,12699675,12700101,12700280,12700700,12764446,12764730,12764826,12764994,12765202,12825078,12825250,12825742,
tgfbiNM_001140391chr5+11950269411953449611950269411953449617119502694,119507297,119517589,119519852,119519941,119520094,119520376,119520799,119522985,119523402,119526449,119527487,11952829 ...119502754,119507396,119517645,119519916,119520018,119520097,119520541,119520898,119523120,119523404,119526664,119527624,11952840 ...
MAP2K1NM_001143716chr15+456997804581592445699877458150151345699780,45754708,45756431,45763005,45806159,45809391,45811637,45813611,45814112,45814901,45815211,45815349,45815828,45699957,45754919,45756578,45763086,45806286,45809595,45811699,45813673,45814158,45815156,45815322,45815797,45815924,
TNNT3NM_001169067chr11+1878947189131718789471891317121878947,1879177,1881672,1882361,1884972,1886552,1886762,1887163,1887377,1887660,1889789,1891262,1878963,1879192,1881696,1882380,1885018,1886669,1886840,1887277,1887487,1887751,1889828,1891317,
DCAF6NM_001349775chr1+14711848714726396614717836214726355818147118487,147142659,147155085,147163326,147178359,147183333,147191240,147191376,147210862,147226819,147231489,147233049,14723336 ...147118621,147142721,147155178,147163512,147178473,147183471,147191376,147191701,147210922,147226937,147231605,147233136,14723369 ...
RPL15NM_001244065chr3+24667939246707032466865024670297724667939,24668640,24669228,24669991,24670366,24670498,24670566,24667964,24668822,24669365,24670342,24670482,24670522,24670703,
RPL15NM_001244065chr4+48151289481529034815132448151938748151289,48151769,48152009,48152065,48152250,48152461,48152882,48151769,48151999,48152028,48152125,48152318,48152507,48152903,

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