AB351587
 

Information on mRNA AB351587

Description: Mus musculus non-coding RNA, oocyte_piRNA2403, 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: AB351587
Position: chr12:56795441-56795462

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 |    22  100.0%         12     +  56795441  56795462              AB351587     1    22    22
browser |    22  100.0%          1     +   5875375   5875396              AB351587     1    22    22
browser |    22  100.0%          1     -   6242199   6242220              AB351587     1    22    22
browser |    22  100.0%          1     +   6501404   6501425              AB351587     1    22    22
browser |    22  100.0%          1     -   8070220   8070241              AB351587     1    22    22
browser |    22  100.0%          1     -   8232655   8232676              AB351587     1    22    22
browser |    22  100.0%          1     +  10800895  10800916              AB351587     1    22    22
browser |    22  100.0%          1     -  16814733  16814754              AB351587     1    22    22
browser |    22  100.0%          1     -  18590607  18590628              AB351587     1    22    22
browser |    22  100.0%          1     -  19698941  19698962              AB351587     1    22    22
browser |    22  100.0%          1     -  21654312  21654333              AB351587     1    22    22
browser |    22  100.0%          1     -  23344603  23344624              AB351587     1    22    22
browser |    22  100.0%          1     +  26389060  26389081              AB351587     1    22    22
browser |    22  100.0%          1     -  26459348  26459369              AB351587     1    22    22
browser |    22  100.0%          1     +  26510260  26510281              AB351587     1    22    22
browser |    22  100.0%          1     -  27225497  27225518              AB351587     1    22    22
browser |    22  100.0%          1     +  29982614  29982635              AB351587     1    22    22
browser |    22  100.0%          1     -  34389613  34389634              AB351587     1    22    22
browser |    22  100.0%          1     -  34957446  34957467              AB351587     1    22    22
browser |    22  100.0%          1     -  35833827  35833848              AB351587     1    22    22
browser |    22  100.0%          1     +  37318695  37318716              AB351587     1    22    22
browser |    22  100.0%          1     -  38747208  38747229              AB351587     1    22    22
browser |    22  100.0%          1     -  45777683  45777704              AB351587     1    22    22
browser |    22  100.0%          1     +  47263403  47263424              AB351587     1    22    22
browser |    22  100.0%          1     -  48132618  48132639              AB351587     1    22    22
browser |    22  100.0%          1     +  48394302  48394323              AB351587     1    22    22
browser |    22  100.0%          1     +  53169592  53169613              AB351587     1    22    22
browser |    22  100.0%          1     +  58363331  58363352              AB351587     1    22    22
browser |    22  100.0%          1     +  58851641  58851662              AB351587     1    22    22
browser |    22  100.0%          1     +  60764825  60764846              AB351587     1    22    22
browser |    22  100.0%          1     +  62574087  62574108              AB351587     1    22    22
browser |    22  100.0%          1     +  64218154  64218175              AB351587     1    22    22
browser |    22  100.0%          1     +  65000287  65000308              AB351587     1    22    22
browser |    22  100.0%          1     +  81542700  81542721              AB351587     1    22    22
browser |    22  100.0%          1     -  82482888  82482909              AB351587     1    22    22
browser |    22  100.0%          1     +  84974418  84974439              AB351587     1    22    22
browser |    22  100.0%          1     +  87062181  87062202              AB351587     1    22    22
browser |    22  100.0%          1     -  87394154  87394175              AB351587     1    22    22
browser |    22  100.0%          1     -  89130110  89130131              AB351587     1    22    22
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browser |    22  100.0%          1     +  93036025  93036046              AB351587     1    22    22
browser |    22  100.0%          1     -  93888197  93888218              AB351587     1    22    22
browser |    22  100.0%          1     -  97108122  97108143              AB351587     1    22    22
browser |    22  100.0%          1     + 101906687 101906708              AB351587     1    22    22
browser |    22  100.0%          1     - 102965665 102965686              AB351587     1    22    22
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browser |    22  100.0%          1     - 103520923 103520944              AB351587     1    22    22
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browser |    22  100.0%          1     - 109547403 109547424              AB351587     1    22    22
browser |    22  100.0%          1     - 110261175 110261196              AB351587     1    22    22
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browser |    22  100.0%          1     + 111182179 111182200              AB351587     1    22    22
browser |    22  100.0%          1     - 111637373 111637394              AB351587     1    22    22
browser |    22  100.0%          1     + 112492844 112492865              AB351587     1    22    22
browser |    22  100.0%          1     - 112862366 112862387              AB351587     1    22    22
browser |    22  100.0%          1     - 112950082 112950103              AB351587     1    22    22
browser |    22  100.0%          1     - 114117391 114117412              AB351587     1    22    22
browser |    22  100.0%          1     + 115813914 115813935              AB351587     1    22    22
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browser |    22  100.0%          1     - 125250866 125250887              AB351587     1    22    22
browser |    22  100.0%          1     - 126356560 126356581              AB351587     1    22    22
browser |    22  100.0%          1     - 126871287 126871308              AB351587     1    22    22
browser |    22  100.0%          1     + 159798149 159798170              AB351587     1    22    22
browser |    22  100.0%          1     + 160644262 160644283              AB351587     1    22    22
browser |    22  100.0%          1     - 162674395 162674416              AB351587     1    22    22
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browser |    22  100.0%          1     - 169375638 169375659              AB351587     1    22    22
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browser |    22  100.0%          1     - 177891864 177891885              AB351587     1    22    22
browser |    22  100.0%          1     - 178007947 178007968              AB351587     1    22    22
browser |    22  100.0%          1     + 181091905 181091926              AB351587     1    22    22
browser |    22  100.0%          1     - 181326232 181326253              AB351587     1    22    22
browser |    22  100.0%          1     - 191844056 191844077              AB351587     1    22    22
browser |    22  100.0%          1     - 195008927 195008948              AB351587     1    22    22
browser |    22  100.0%         10     +   3267152   3267173              AB351587     1    22    22
browser |    22  100.0%         10     +   3551744   3551765              AB351587     1    22    22
browser |    22  100.0%         10     -   9726702   9726723              AB351587     1    22    22
browser |    22  100.0%         10     -  11576297  11576318              AB351587     1    22    22
browser |    22  100.0%         10     +  19415459  19415480              AB351587     1    22    22
browser |    22  100.0%         10     -  21091621  21091642              AB351587     1    22    22
browser |    22  100.0%         10     +  21519032  21519053              AB351587     1    22    22
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browser |    22  100.0%         10     -  24566651  24566672              AB351587     1    22    22
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browser |    22  100.0%         10     -  30970946  30970967              AB351587     1    22    22
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browser |    22  100.0%         10     -  31630033  31630054              AB351587     1    22    22
browser |    22  100.0%         10     -  33766205  33766226              AB351587     1    22    22
browser |    22  100.0%         10     +  34618636  34618657              AB351587     1    22    22
browser |    22  100.0%         10     -  41722811  41722832              AB351587     1    22    22
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browser |    22  100.0%         10     -  50370738  50370759              AB351587     1    22    22
browser |    22  100.0%         10     -  51763182  51763203              AB351587     1    22    22
browser |    22  100.0%         10     -  54468768  54468789              AB351587     1    22    22
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browser |    22  100.0%         10     -  56603119  56603140              AB351587     1    22    22
browser |    22  100.0%         10     -  57020039  57020060              AB351587     1    22    22
browser |    22  100.0%         10     +  65475507  65475528              AB351587     1    22    22
browser |    22  100.0%         10     +  65787411  65787432              AB351587     1    22    22
browser |    22  100.0%         10     +  66559057  66559078              AB351587     1    22    22
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browser |    22  100.0%         10     -  80815850  80815871              AB351587     1    22    22
browser |    22  100.0%         10     -  81809999  81810020              AB351587     1    22    22
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browser |    22  100.0%         10     +  94199250  94199271              AB351587     1    22    22
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browser |    22  100.0%         10     - 104397487 104397508              AB351587     1    22    22
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View details of parts of alignment within browser window
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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