Schema for ORFeome Clones - ORFeome Collaboration Gene Clones
  Database: mm10    Primary Table: orfeomeMrna    Row Count: 2,273   Data last updated: 2018-10-16
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 619smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1259int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 1int(10) unsigned range Number of inserts in target
tBaseInsert 431int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName BC148437varchar(255) values Query sequence name
qSize 1321int(10) unsigned range Query sequence size
qStart 32int(10) unsigned range Alignment start position in query
qEnd 1292int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 195471971int(10) unsigned range Target sequence size
tStart 4491717int(10) unsigned range Alignment start position in target
tEnd 4493408int(10) unsigned range Alignment end position in target
blockCount 2int(10) unsigned range Number of blocks in alignment
blockSizes 951,309,longblob   Size of each block
qStarts 29,980,longblob   Start of each block in query.
tStarts 4491717,4493099,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via orfeomeMrna.qName)
      hgFixed.gbSeq.acc (via orfeomeMrna.qName)
      hgFixed.imageClone.acc (via orfeomeMrna.qName)
      mm10.all_mrna.qName (via orfeomeMrna.qName)
      mm10.mrnaOrientInfo.name (via orfeomeMrna.qName)
      mm10.orfeomeGenes.name (via orfeomeMrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
6191259100001431-BC1484371321321292chr1195471971449171744934082951,309,29,980,4491717,4493099,
6191259100001431-BC1530211321321292chr1195471971449171744934082951,309,29,980,4491717,4493099,
115530000016438915-BC1602861615331586chr11954719718363476880394417157,111,93,153,72,117,39,130,131,83,103,42,44,58,57,135,28,29,186,297,390,543,615,732,771,901,1032,1115,1218,1260,1304,1362,1419,1554,8363476,8414202,8445026,8447979,8463393,8465436,8554724,8583204,8595411,8607069,8624778,8677806,8677936,8679072,8681972,8782762, ...
8235530390002887466+BC1563493655343626chr119547197110045085101361432999,103,104,81,99,395,87,71,94,58,206,134,79,130,148,153,113,150,147,105,67,118,140,141,47,64,110,139,210,34,133,236,340,421,520,915,1002,1073,1167,1225,1431,1565,1644,1774,1922,2075,2188,2338,2485,2590,2657,2775,2915,3056,3103,3167,3 ...10045085,10047423,10058719,10064332,10065322,10066425,10074859,10077171,10082252,10083500,10085746,10088050,10088881,10090187,10 ...
72375300000620669-BC14878781434787chr119547197118115628181370507128,89,98,149,91,135,63,27,155,244,342,491,582,717,18115628,18122737,18124231,18128641,18130158,18134038,18136987,
72375100000620669-BC14150881434785chr119547197118115630181370507126,89,98,149,91,135,63,29,155,244,342,491,582,717,18115630,18122737,18124231,18128641,18130158,18134038,18136987,
724258000001713-BC14878231934292chr119547197118236472182374432188,70,27,215,18236472,18237373,
724256000001713-BC14150231934290chr119547197118236474182374432186,70,29,215,18236474,18237373,
72419000000113692-BC14032925031221chr119547197118251201182650832132,58,29,161,18251201,18265025,
7242000000014359-BC15675925931231chr119547197118260524182650832142,58,28,170,18260524,18265025,

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

ORFeome Clones (orfeomeMrna) Track Description
 

Description

This track shows alignments of mouse clones from the ORFeome Collaboration. The goal of the project is to be an "unrestricted source of fully sequence-validated full-ORF human cDNA clones in a format allowing easy transfer of the ORF sequences into virtually any type of expression vector. A major goal is to provide at least one fully-sequenced full-ORF clone for each human gene." This track is updated automatically as new clones become available.

Display Conventions and Configuration

The track follows the display conventions for gene prediction tracks.

Methods

ORFeome mouse clones were obtained from GenBank and aligned against the genome using the blat program. When a single clone aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits and References

Visit the ORFeome Collaboration members page for a list of credits and references.