AB350764
 

Information on mRNA AB350764

Description: Mus musculus non-coding RNA, oocyte_piRNA1580, complete sequence.
Gene: n/a
Product: n/a
Author: Watanabe,T., Totoki,Y., Toyoda,A., Kaneda,M., Kuramochi-Miyagawa,S., Obata,Y., Chiba,H., Kohara,Y., Kono,T., Nakano,T., Surani,M.A., Sakaki,Y. and Sasaki,H.
Organism: Mus musculus
Tissue: ovary
Development stage: p8
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB350764
Position: chr12:56798655-56798680

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    26  100.0%         12     -  56798655  56798680              AB350764     1    26    27
browser |    27  100.0%          1     +   6238629   6238655              AB350764     1    27    27
browser |    27  100.0%          1     +   6242980   6243006              AB350764     1    27    27
browser |    27  100.0%          1     -   6500636   6500662              AB350764     1    27    27
browser |    27  100.0%          1     -   6507404   6507430              AB350764     1    27    27
browser |    27  100.0%          1     +   8226709   8226735              AB350764     1    27    27
browser |    27  100.0%          1     +   8233413   8233439              AB350764     1    27    27
browser |    27  100.0%          1     -  11957371  11957397              AB350764     1    27    27
browser |    27  100.0%          1     -  11961582  11961608              AB350764     1    27    27
browser |    27  100.0%          1     +  14069079  14069105              AB350764     1    27    27
browser |    27  100.0%          1     +  18587358  18587384              AB350764     1    27    27
browser |    27  100.0%          1     +  18591379  18591405              AB350764     1    27    27
browser |    27  100.0%          1     +  19692894  19692920              AB350764     1    27    27
browser |    27  100.0%          1     +  19699739  19699765              AB350764     1    27    27
browser |    27  100.0%          1     -  26388297  26388323              AB350764     1    27    27
browser |    27  100.0%          1     -  26393149  26393175              AB350764     1    27    27
browser |    27  100.0%          1     +  26453365  26453391              AB350764     1    27    27
browser |    27  100.0%          1     +  26460106  26460132              AB350764     1    27    27
browser |    27  100.0%          1     +  27219527  27219553              AB350764     1    27    27
browser |    27  100.0%          1     +  27226284  27226310              AB350764     1    27    27
browser |    27  100.0%          1     +  34386833  34386859              AB350764     1    27    27
browser |    27  100.0%          1     +  34390393  34390419              AB350764     1    27    27
browser |    27  100.0%          1     +  34954440  34954466              AB350764     1    27    27
browser |    27  100.0%          1     -  53168777  53168803              AB350764     1    27    27
browser |    27  100.0%          1     -  53173606  53173632              AB350764     1    27    27
browser |    27  100.0%          1     -  54658150  54658176              AB350764     1    27    27
browser |    27  100.0%          1     -  58362538  58362564              AB350764     1    27    27
browser |    27  100.0%          1     -  58369293  58369319              AB350764     1    27    27
browser |    27  100.0%          1     -  58850878  58850904              AB350764     1    27    27
browser |    27  100.0%          1     -  58857712  58857738              AB350764     1    27    27
browser |    27  100.0%          1     -  62573233  62573259              AB350764     1    27    27
browser |    27  100.0%          1     -  62580057  62580083              AB350764     1    27    27
browser |    27  100.0%          1     -  64999502  64999528              AB350764     1    27    27
browser |    27  100.0%          1     -  81541915  81541941              AB350764     1    27    27
browser |    27  100.0%          1     -  81548642  81548668              AB350764     1    27    27
browser |    27  100.0%          1     +  89127126  89127152              AB350764     1    27    27
browser |    27  100.0%          1     +  89130924  89130950              AB350764     1    27    27
browser |    27  100.0%          1     +  97100707  97100733              AB350764     1    27    27
browser |    27  100.0%          1     +  97108880  97108906              AB350764     1    27    27
browser |    27  100.0%          1     + 102959703 102959729              AB350764     1    27    27
browser |    27  100.0%          1     + 102966461 102966487              AB350764     1    27    27
browser |    27  100.0%          1     - 103132922 103132948              AB350764     1    27    27
browser |    27  100.0%          1     - 103139675 103139701              AB350764     1    27    27
browser |    27  100.0%          1     + 103516766 103516792              AB350764     1    27    27
browser |    27  100.0%          1     + 103521735 103521761              AB350764     1    27    27
browser |    27  100.0%          1     - 104217334 104217360              AB350764     1    27    27
browser |    27  100.0%          1     - 104222223 104222249              AB350764     1    27    27
browser |    27  100.0%          1     - 107966564 107966590              AB350764     1    27    27
browser |    27  100.0%          1     - 107968300 107968326              AB350764     1    27    27
browser |    27  100.0%          1     - 109056437 109056463              AB350764     1    27    27
browser |    27  100.0%          1     - 109061341 109061367              AB350764     1    27    27
browser |    27  100.0%          1     + 109541447 109541473              AB350764     1    27    27
browser |    27  100.0%          1     + 109548205 109548231              AB350764     1    27    27
browser |    27  100.0%          1     + 110257125 110257151              AB350764     1    27    27
browser |    27  100.0%          1     + 110261933 110261959              AB350764     1    27    27
browser |    27  100.0%          1     - 110865370 110865396              AB350764     1    27    27
browser |    27  100.0%          1     - 110869848 110869874              AB350764     1    27    27
browser |    27  100.0%          1     + 114113311 114113337              AB350764     1    27    27
browser |    27  100.0%          1     + 114118230 114118256              AB350764     1    27    27
browser |    27  100.0%          1     - 115813019 115813045              AB350764     1    27    27
browser |    27  100.0%          1     - 115817997 115818023              AB350764     1    27    27
browser |    27  100.0%          1     - 116576027 116576053              AB350764     1    27    27
browser |    27  100.0%          1     - 116582789 116582815              AB350764     1    27    27
browser |    27  100.0%          1     + 126352091 126352117              AB350764     1    27    27
browser |    27  100.0%          1     + 126357374 126357400              AB350764     1    27    27
browser |    27  100.0%          1     - 159797372 159797398              AB350764     1    27    27
browser |    27  100.0%          1     - 159804101 159804127              AB350764     1    27    27
browser |    27  100.0%          1     - 160643499 160643525              AB350764     1    27    27
browser |    27  100.0%          1     - 160648291 160648317              AB350764     1    27    27
browser |    27  100.0%          1     - 163520568 163520594              AB350764     1    27    27
browser |    27  100.0%          1     + 178001955 178001981              AB350764     1    27    27
browser |    27  100.0%          1     + 178008706 178008732              AB350764     1    27    27
browser |    27  100.0%          1     - 181091122 181091148              AB350764     1    27    27
browser |    27  100.0%          1     - 181097851 181097877              AB350764     1    27    27
browser |    27  100.0%          1     + 191840020 191840046              AB350764     1    27    27
browser |    27  100.0%          1     + 194336441 194336467              AB350764     1    27    27
browser |    27  100.0%         10     -   3550975   3551001              AB350764     1    27    27
browser |    27  100.0%         10     +  21087398  21087424              AB350764     1    27    27
browser |    27  100.0%         10     +  21092398  21092424              AB350764     1    27    27
browser |    27  100.0%         10     -  21518217  21518243              AB350764     1    27    27
browser |    27  100.0%         10     -  21525068  21525094              AB350764     1    27    27
browser |    27  100.0%         10     -  22559151  22559177              AB350764     1    27    27
browser |    27  100.0%         10     -  22566079  22566105              AB350764     1    27    27
browser |    27  100.0%         10     +  24562654  24562680              AB350764     1    27    27
browser |    27  100.0%         10     +  24567455  24567481              AB350764     1    27    27
browser |    27  100.0%         10     -  24977495  24977521              AB350764     1    27    27
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browser |    27  100.0%         10     -  34617852  34617878              AB350764     1    27    27
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browser |    27  100.0%         10     +  80812166  80812192              AB350764     1    27    27
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browser |    27  100.0%         10     -  83506817  83506843              AB350764     1    27    27
browser |    27  100.0%         10     -  83513542  83513568              AB350764     1    27    27
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browser |    27  100.0%         10     -  90160522  90160548              AB350764     1    27    27
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browser |    27  100.0%         10     -  96028429  96028455              AB350764     1    27    27
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browser |    27  100.0%         10     -  98934086  98934112              AB350764     1    27    27
browser |    27  100.0%         10     -  98938968  98938994              AB350764     1    27    27
browser |    27  100.0%         10     - 104655343 104655369              AB350764     1    27    27
browser |    27  100.0%         10     - 104660345 104660371              AB350764     1    27    27
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browser |    27  100.0%         10     - 105508494 105508520              AB350764     1    27    27
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browser |    27  100.0%         10     + 121005106 121005132              AB350764     1    27    27
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View details of parts of alignment within browser window
.
View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

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.

Methods

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.

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