Home     Genomes     Genome Browser     Blat     Tables     PCR     Session    FAQ     Help  
  Schema for Spliced ESTs - Cow ESTs That Have Been Spliced
  Database: bosTau4    Primary Table: intronEst    Row Count: 870,826
Format description: Summary info about a patSpace alignment
fieldexampleSQL type description
bin 886smallint unsigned Indexing field to speed chromosome range queries.
matches 429int unsigned Number of bases that match that aren't repeats
misMatches 0int unsigned Number of bases that don't match
repMatches 0int unsigned Number of bases that match but are part of repeats
nCount 1int unsigned Number of 'N' bases
qNumInsert 1int unsigned Number of inserts in query
qBaseInsert 1int unsigned Number of bases inserted in query
tNumInsert 3int unsigned Number of inserts in target
tBaseInsert 1120int unsigned Number of bases inserted in target
strand -char(2) + or - for strand. First character query, second target (optional)
qName AA961327varchar(255) Query sequence name
qSize 453int unsigned Query sequence size
qStart 16int unsigned Alignment start position in query
qEnd 447int unsigned Alignment end position in query
tName chr11varchar(255) Target sequence name
tSize 110171769int unsigned Target sequence size
tStart 39476297int unsigned Alignment start position in target
tEnd 39477847int unsigned Alignment end position in target
blockCount 5int unsigned Number of blocks in alignment
blockSizes 21,4,84,132,189,longblob Size of each block
qStarts 6,28,32,116,248,longblob Start of each block in query.
tStarts 39476297,39476318,39476672,...longblob Start of each block in target.

  Connected Tables and Joining Fields
        bosTau4.all_est.qName (via intronEst.qName)
      bosTau4.estOrientInfo.name (via intronEst.qName)
      bosTau4.gbCdnaInfo.acc (via intronEst.qName)
      bosTau4.gbSeq.acc (via intronEst.qName)
      bosTau4.gbStatus.acc (via intronEst.qName)
      bosTau4.imageClone.acc (via intronEst.qName)

  Sample Rows

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

  Spliced ESTs (intronEst) Track Description


This track shows alignments between cow expressed sequence tags (ESTs) in GenBank and the genome that show signs of splicing when aligned against the genome. ESTs are single-read sequences, typically about 500 bases in length, that usually represent fragments of transcribed genes.

To be considered spliced, an EST must show evidence of at least one canonical intron, i.e. the genomic sequence between EST alignment blocks must be at least 32 bases in length and have GT/AG ends. By requiring splicing, the level of contamination in the EST databases is drastically reduced at the expense of eliminating many genuine 3' ESTs. For a display of all ESTs (including unspliced), see the cow EST track.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, darker shading indicates a larger number of aligned ESTs.

The strand information (+/-) indicates the direction of the match between the EST and the matching genomic sequence. It bears no relationship to the direction of transcription of the RNA with which it might be associated.

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 EST display. For example, to apply the filter to all ESTs 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 ESTs that match all filter criteria will be highlighted. If "or" is selected, ESTs 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 ESTs that match the filter criteria. If "include" is selected, the browser will display only those ESTs that match the filter criteria.

This track may also be configured to display base labeling, a feature that allows the user to display all bases in the aligning sequence or only those that differ from the genomic sequence. For more information about this option, click here. Several types of alignment gap may also be colored; for more information, click here.


To make an EST, RNA is isolated from cells and reverse transcribed into cDNA. Typically, the cDNA is cloned into a plasmid vector and a read is taken from the 5' and/or 3' primer. For most — but not all — ESTs, the reverse transcription is primed by an oligo-dT, which hybridizes with the poly-A tail of mature mRNA. The reverse transcriptase may or may not make it to the 5' end of the mRNA, which may or may not be degraded.

In general, the 3' ESTs mark the end of transcription reasonably well, but the 5' ESTs may end at any point within the transcript. Some of the newer cap-selected libraries cover transcription start reasonably well. Before the cap-selection techniques emerged, some projects used random rather than poly-A priming in an attempt to retrieve sequence distant from the 3' end. These projects were successful at this, but as a side effect also deposited sequences from unprocessed mRNA and perhaps even genomic sequences into the EST databases. Even outside of the random-primed projects, there is a degree of non-mRNA contamination. Because of this, a single unspliced EST should be viewed with considerable skepticism.

To generate this track, cow ESTs from GenBank were aligned against the genome using blat. Note that the maximum intron length allowed by blat is 750,000 bases, which may eliminate some ESTs with very long introns that might otherwise align. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence are displayed in this track.


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


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

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