Schema for xenoRefFlat
  Database: manPen1    Primary Table: xenoRefFlat    Row Count: 548,155   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type description
geneName Olfr1053varchar(255) Name of gene as it appears in genome browser.
name NM_001177857varchar(255) Name of gene
chrom JPTV01189992varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 0int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 537int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 0int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 537int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned Number of exons
exonStarts 0,362,longblob Exon start positions (or end positions for minus strand item)
exonEnds 289,537,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)
      manPen1.xenoRefGene.name (via xenoRefFlat.name)
      manPen1.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Olfr1053NM_001177857JPTV01189992-0537053720,362,289,537,
MCM3NM_001006421KN006122+540047261754004726161754004,55114,55655,56304,58387,59109,59912,60412,61138,63285,63800,64714,67056,68118,68813,72415,72563,54064,55228,55865,56433,58626,59218,60066,60546,61341,63464,63924,64868,67200,68160,68858,72532,72617,
il6st.SNM_001130940KN021677-754898227548982227548,9720,7620,9822,
LOC541695NM_001348558KN017283-43851446254385144625243851,44449,43921,44625,
IRAG2NM_001348560KN011379+46244499304624449930246244,49888,46289,49930,
SLC9A3R1NM_001143724KN005962+1893621895271893621895271189362,189527,
SLC9A3R1NM_001143724KN006165+1959422171301959482165299195942,211317,212602,214900,216006,216337,216630,217052,217105,196173,211478,212756,214941,216096,216536,216690,217070,217130,
CTNNA3NM_001199536KN012591-16819332521681933252216819,33180,16996,33252,
CTNNA3NM_001199536KN013074-39273394353927339435139273,39435,
CTNNA3NM_001199536KN015445-22675228672267522867122675,22867,

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