Schema for Rhesus mRNAs - Rhesus mRNAs from GenBank
  Database: rheMac3    Primary Table: all_mrna    Row Count: 388,811   Data last updated: 2020-08-22
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 359int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(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 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName JU339375varchar(255) values Query sequence name
qSize 364int(10) unsigned range Query sequence size
qStart 5int(10) unsigned range Alignment start position in query
qEnd 364int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 229590362int(10) unsigned range Target sequence size
tStart 61054int(10) unsigned range Alignment start position in target
tEnd 61413int(10) unsigned range Alignment end position in target
blockCount 1int(10) unsigned range Number of blocks in alignment
blockSizes 359,longblob   Size of each block
qStarts 0,longblob   Start of each block in query.
tStarts 61054,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via all_mrna.qName)
      hgFixed.gbMiscDiff.acc (via all_mrna.qName)
      hgFixed.gbSeq.acc (via all_mrna.qName)
      hgFixed.gbWarn.acc (via all_mrna.qName)
      hgFixed.imageClone.acc (via all_mrna.qName)
      rheMac3.all_est.qName (via all_mrna.qName)
      rheMac3.mrnaOrientInfo.name (via all_mrna.qName)
      rheMac3.refGene.name (via all_mrna.qName)
      rheMac3.refSeqAli.qName (via all_mrna.qName)
      rheMac3.xenoMrna.qName (via all_mrna.qName)
      rheMac3.xenoRefGene.name (via all_mrna.qName)
      rheMac3.xenoRefSeqAli.qName (via all_mrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5853590000000-JU3393753645364chr122959036261054614131359,0,61054,
5857533000000-JV707872940184940chr122959036261054618101756,0,61054,
5857513000000-JV607037864109863chr122959036261056618101754,1,61056,
5852260000000-JV4581492260226chr122959036261078613041226,0,61078,
5854660000000-JV4960684660466chr122959036261081615471466,0,61081,
5853660000000-JV0528793660366chr122959036261082614481366,0,61082,
5857165000000-JV643404854133854chr122959036261089618101721,0,61089,
5853380000000-JV6741833380338chr122959036261102614401338,0,61102,
5855641000000-JV5724715650565chr122959036261136617011565,0,61136,
5856214000000-JV53461170378703chr122959036261185618101625,0,61185,

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

Rhesus mRNAs (mrna) Track Description
 

Description

The mRNA track shows alignments between rhesus mRNAs in GenBank and the genome.

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 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. Multiple terms may be entered at once, separated by a space. 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. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank rhesus mRNAs were aligned against the genome using the blat program. When a single mRNA 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

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

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

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