Information on mRNA DQ694904

Description: Mus musculus piRNA piR-110226, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2006-06-09
Version: 1
mRNA sequence: DQ694904
Position: chr12:56959399-56959425

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
browser |    27  100.0%         12     -  56959399  56959425              DQ694904     1    27    27
browser |    27  100.0%          1     +  30728026  30728052              DQ694904     1    27    27
browser |    27  100.0%         11     +  85331625  85331651              DQ694904     1    27    27
browser |    27  100.0%         13     +   8318583   8318609              DQ694904     1    27    27
browser |    27  100.0%         13     -  39863826  39863852              DQ694904     1    27    27
browser |    27  100.0%         14     + 108886254 108886280              DQ694904     1    27    27
browser |    27  100.0%         17     +  27572509  27572535              DQ694904     1    27    27
browser |    27  100.0%          3     - 112492801 112492827              DQ694904     1    27    27
browser |    27  100.0%          9     +  33130089  33130115              DQ694904     1    27    27
browser |    27  100.0%          X     + 141962680 141962706              DQ694904     1    27    27

View details of parts of alignment within browser window
Data schema/format description and download

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18


The mRNA track shows alignments between mouse 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.


GenBank mouse 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.


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


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