Schema for Other mRNAs - Non-C. elegans mRNAs from GenBank
  Database: ce6    Primary Table: xenoMrna    Row Count: 1,045,030   Data last updated: 2020-02-05
Format description: Summary info about a patSpace alignment
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
matches 490int(10) unsigned Number of bases that match that aren't repeats
misMatches 146int(10) unsigned Number of bases that don't match
repMatches 0int(10) unsigned Number of bases that match but are part of repeats
nCount 0int(10) unsigned Number of 'N' bases
qNumInsert 0int(10) unsigned Number of inserts in query
qBaseInsert 0int(10) unsigned Number of bases inserted in query
tNumInsert 6int(10) unsigned Number of inserts in target
tBaseInsert 5223int(10) unsigned Number of bases inserted in target
strand +-char(2) + or - for strand. First character query, second target (optional)
qName EU726784varchar(255) Query sequence name
qSize 710int(10) unsigned Query sequence size
qStart 73int(10) unsigned Alignment start position in query
qEnd 709int(10) unsigned Alignment end position in query
tName chrIvarchar(255) Target sequence name
tSize 15072421int(10) unsigned Target sequence size
tStart 4274int(10) unsigned Alignment start position in target
tEnd 10133int(10) unsigned Alignment end position in target
blockCount 7int(10) unsigned Number of blocks in alignment
blockSizes 39,117,3,288,3,102,84,longblob Size of each block
qStarts 73,112,229,232,520,523,625,longblob Start of each block in query.
tStarts 15062288,15062575,15062699,...longblob Start of each block in target.

Connected Tables and Joining Fields
        ce6.all_est.qName (via xenoMrna.qName)
      ce6.all_mrna.qName (via xenoMrna.qName)
      ce6.refGene.name (via xenoMrna.qName)
      ce6.refSeqAli.qName (via xenoMrna.qName)
      ce6.xenoRefFlat.name (via xenoMrna.qName)
      ce6.xenoRefGene.name (via xenoMrna.qName)
      ce6.xenoRefSeqAli.qName (via xenoMrna.qName)
      hgFixed.gbCdnaInfo.acc (via xenoMrna.qName)
      hgFixed.gbMiscDiff.acc (via xenoMrna.qName)
      hgFixed.gbSeq.acc (via xenoMrna.qName)
      hgFixed.gbWarn.acc (via xenoMrna.qName)
      hgFixed.imageClone.acc (via xenoMrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585490146000065223+-EU72678471073709chrI15072421427410133739,117,3,288,3,102,84,73,112,229,232,520,523,625,15062288,15062575,15062699,15066094,15067029,15067125,15068063,
5851308600151148+-CR7143528259276chrI1507242160396303284,132,9,144,15066118,15066250,
5852851530021832375++JP545034911185806chrX1771885459886606993126,216,96,185,458,710,59886,60299,60603,
7358800002256500+-AK192597263103169chrI1507242142119298685333,9,24,103,136,145,14773736,14801404,15030278,
5858142000000++EZ91813822869192chrI1507242152288524111123,69,52288,
58527315600446242748++AB45128813532791170chrI1507242174622777995114,54,135,42,84,279,795,888,1035,1086,74622,76020,76949,77105,77715,
58527315600446242748++AB45142013502791170chrI1507242174622777995114,54,135,42,84,279,795,888,1035,1086,74622,76020,76949,77105,77715,
58527315600446242748++AB52757213672881179chrI1507242174622777995114,54,135,42,84,288,804,897,1044,1095,74622,76020,76949,77105,77715,
58527315600446242748++AK29769414432551146chrI1507242174622777995114,54,135,42,84,255,771,864,1011,1062,74622,76020,76949,77105,77715,
58527315600446242748++AK31266915584841375chrI1507242174622777995114,54,135,42,84,484,1000,1093,1240,1291,74622,76020,76949,77105,77715,

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

Other mRNAs (xenoMrna) Track Description
 

Description

This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than C. elegans.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The strand information (+/-) for this track is in two parts. The first + indicates the orientation of the query sequence whose translated protein produced the match (here always 5' to 3', hence +). The second + or - indicates the orientation of the matching translated genomic sequence. Because the two orientations of a DNA sequence give different predicted protein sequences, there are four combinations. ++ is not the same as --, nor is +- the same as -+.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page.

Methods

The mRNAs were aligned against the C. elegans genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518