Schema for xenoRefFlat
  Database: rheMac3    Primary Table: xenoRefFlat    Row Count: 338,858   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName mcm-5varchar(255) values Name of gene as it appears in genome browser.
name NM_065457varchar(255) values Name of gene
chrom chr10varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 80211751int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 80224233int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 80211751int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 80224233int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 80211751,80213754,80213865,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 80211874,80213823,80213925,...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)
      rheMac3.xenoMrna.qName (via xenoRefFlat.name)
      rheMac3.xenoRefGene.name (via xenoRefFlat.name)
      rheMac3.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
mcm-5NM_065457chr10+80211751802242338021175180224233980211751,80213754,80213865,80215569,80216764,80218697,80219204,80219484,80224086,80211874,80213823,80213925,80215666,80216879,80218838,80219270,80219643,80224233,
CASP14NM_001093773chr19+15002847150054301500284715005430515002847,15003095,15004499,15004767,15005325,15002958,15003320,15004522,15004872,15005430,
ZNF519NM_145287chr19-21153331218822542127820621882254921153331,21153896,21154013,21278106,21515383,21696660,21863283,21863905,21882132,21153466,21153962,21154070,21278487,21515723,21696821,21863343,21863971,21882254,
cpne1NM_199699chr8+914231479145440291423147914544021191423147,91423911,91426115,91432595,91441877,91443569,91446418,91446557,91450837,91452168,91454336,91423246,91424088,91426193,91432682,91441961,91443701,91446475,91446611,91450951,91452405,91454402,
Col5a3NM_001317388chr19-995657710002063995658310002063719956577,9956685,9956822,9958682,9960499,9960715,9960892,9961523,9962455,9962577,9962936,9963197,9964013,9964309,9965052,9965064, ...9956682,9956729,9957063,9958752,9960606,9960862,9960931,9961577,9962491,9962631,9963044,9963251,9964114,9964354,9965055,9965124, ...
Tmem63cNM_001361704chr7+14075218414082950814079135314082677928140752184,140752287,140752345,140785894,140791353,140792013,140792527,140798038,140801021,140802860,140805820,140807774,14080805 ...140752217,140752336,140752453,140785966,140791458,140792080,140792607,140798074,140801166,140802909,140805914,140807845,14080805 ...
TMED7NM_001204309chr6-1129205001129320881129235971129314667112920500,112920918,112922558,112923094,112927436,112931312,112931904,112920890,112922514,112923028,112923834,112927682,112931466,112932088,
Nudt2NM_025539chr9-17684651176851331768466517685109117684651,17685133,
LOC101264240NM_001330775chr19+18627909186297701862790918629770418627909,18628274,18629491,18629676,18628010,18628363,18629594,18629770,
mspn-1NM_069460chr9-84882009849093548488200984909354484882009,84896664,84902118,84909152,84882090,84896736,84902201,84909354,

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