AB349982
 

Information on mRNA AB349982

Description: Mus musculus non-coding RNA, oocyte_piRNA798, 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: AB349982
Position: chr12:56796279-56796304

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     -  56796279  56796304              AB349982     1    26    26
browser |    26  100.0%          1     -   5878964   5878989              AB349982     1    26    26
browser |    26  100.0%          1     -   6504993   6505018              AB349982     1    26    26
browser |    26  100.0%          1     +   8066630   8066655              AB349982     1    26    26
browser |    26  100.0%          1     +   8229071   8229096              AB349982     1    26    26
browser |    26  100.0%          1     +  13623495  13623520              AB349982     1    26    26
browser |    26  100.0%          1     +  16811141  16811166              AB349982     1    26    26
browser |    26  100.0%          1     +  18029735  18029760              AB349982     1    26    26
browser |    26  100.0%          1     +  18589765  18589790              AB349982     1    26    26
browser |    26  100.0%          1     +  19695349  19695374              AB349982     1    26    26
browser |    26  100.0%          1     -  22069857  22069882              AB349982     1    26    26
browser |    26  100.0%          1     +  26455757  26455782              AB349982     1    26    26
browser |    26  100.0%          1     -  26512569  26512594              AB349982     1    26    26
browser |    26  100.0%          1     +  27221905  27221930              AB349982     1    26    26
browser |    26  100.0%          1     +  29696529  29696554              AB349982     1    26    26
browser |    26  100.0%          1     -  29985699  29985724              AB349982     1    26    26
browser |    26  100.0%          1     +  34389238  34389263              AB349982     1    26    26
browser |    26  100.0%          1     +  35830234  35830259              AB349982     1    26    26
browser |    26  100.0%          1     -  47264413  47264438              AB349982     1    26    26
browser |    26  100.0%          1     -  48399754  48399779              AB349982     1    26    26
browser |    26  100.0%          1     -  53171244  53171269              AB349982     1    26    26
browser |    26  100.0%          1     -  58366919  58366944              AB349982     1    26    26
browser |    26  100.0%          1     -  58855227  58855252              AB349982     1    26    26
browser |    26  100.0%          1     -  60768413  60768438              AB349982     1    26    26
browser |    26  100.0%          1     -  66061182  66061207              AB349982     1    26    26
browser |    26  100.0%          1     -  67794987  67795012              AB349982     1    26    26
browser |    26  100.0%          1     -  72169099  72169124              AB349982     1    26    26
browser |    26  100.0%          1     -  74696995  74697020              AB349982     1    26    26
browser |    26  100.0%          1     +  76594037  76594062              AB349982     1    26    26
browser |    26  100.0%          1     +  78999220  78999245              AB349982     1    26    26
browser |    26  100.0%          1     +  79917448  79917473              AB349982     1    26    26
browser |    26  100.0%          1     -  81546288  81546313              AB349982     1    26    26
browser |    26  100.0%          1     +  82481484  82481509              AB349982     1    26    26
browser |    26  100.0%          1     -  87065770  87065795              AB349982     1    26    26
browser |    26  100.0%          1     +  87390561  87390586              AB349982     1    26    26
browser |    26  100.0%          1     -  91403343  91403368              AB349982     1    26    26
browser |    26  100.0%          1     +  93886971  93886996              AB349982     1    26    26
browser |    26  100.0%          1     +  95625559  95625584              AB349982     1    26    26
browser |    26  100.0%          1     +  97103170  97103195              AB349982     1    26    26
browser |    26  100.0%          1     - 101910278 101910303              AB349982     1    26    26
browser |    26  100.0%          1     + 102962072 102962097              AB349982     1    26    26
browser |    26  100.0%          1     - 103137307 103137332              AB349982     1    26    26
browser |    26  100.0%          1     - 108340995 108341020              AB349982     1    26    26
browser |    26  100.0%          1     + 109543814 109543839              AB349982     1    26    26
browser |    26  100.0%          1     - 111185764 111185789              AB349982     1    26    26
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browser |    26  100.0%          1     - 112196473 112196498              AB349982     1    26    26
browser |    26  100.0%          1     + 112859891 112859916              AB349982     1    26    26
browser |    26  100.0%          1     - 116580412 116580437              AB349982     1    26    26
browser |    26  100.0%          1     - 117634070 117634095              AB349982     1    26    26
browser |    26  100.0%          1     - 125275513 125275538              AB349982     1    26    26
browser |    26  100.0%          1     - 127490406 127490431              AB349982     1    26    26
browser |    26  100.0%          1     - 127807205 127807230              AB349982     1    26    26
browser |    26  100.0%          1     + 130464736 130464761              AB349982     1    26    26
browser |    26  100.0%          1     - 137203312 137203337              AB349982     1    26    26
browser |    26  100.0%          1     + 140747232 140747257              AB349982     1    26    26
browser |    26  100.0%          1     + 140965830 140965855              AB349982     1    26    26
browser |    26  100.0%          1     + 144262589 144262614              AB349982     1    26    26
browser |    26  100.0%          1     - 144734835 144734860              AB349982     1    26    26
browser |    26  100.0%          1     + 145999356 145999381              AB349982     1    26    26
browser |    26  100.0%          1     + 149271679 149271704              AB349982     1    26    26
browser |    26  100.0%          1     + 149459990 149460015              AB349982     1    26    26
browser |    26  100.0%          1     - 159801738 159801763              AB349982     1    26    26
browser |    26  100.0%          1     + 162670802 162670827              AB349982     1    26    26
browser |    26  100.0%          1     + 166182440 166182465              AB349982     1    26    26
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browser |    26  100.0%          1     - 174873143 174873168              AB349982     1    26    26
browser |    26  100.0%          1     - 176375037 176375062              AB349982     1    26    26
browser |    26  100.0%          1     + 177888301 177888326              AB349982     1    26    26
browser |    26  100.0%          1     + 178004354 178004379              AB349982     1    26    26
browser |    26  100.0%          1     + 179724249 179724274              AB349982     1    26    26
browser |    26  100.0%          1     - 181095494 181095519              AB349982     1    26    26
browser |    26  100.0%          1     + 181323143 181323168              AB349982     1    26    26
browser |    26  100.0%          1     + 195005338 195005363              AB349982     1    26    26
browser |    26  100.0%         10     -   3555334   3555359              AB349982     1    26    26
browser |    26  100.0%         10     +   8477727   8477752              AB349982     1    26    26
browser |    26  100.0%         10     +  11572706  11572731              AB349982     1    26    26
browser |    26  100.0%         10     -  19419047  19419072              AB349982     1    26    26
browser |    26  100.0%         10     +  19675578  19675603              AB349982     1    26    26
browser |    26  100.0%         10     -  19890774  19890799              AB349982     1    26    26
browser |    26  100.0%         10     -  21522620  21522645              AB349982     1    26    26
browser |    26  100.0%         10     -  22403511  22403536              AB349982     1    26    26
browser |    26  100.0%         10     -  22563566  22563591              AB349982     1    26    26
browser |    26  100.0%         10     -  23751621  23751646              AB349982     1    26    26
browser |    26  100.0%         10     -  24979693  24979718              AB349982     1    26    26
browser |    26  100.0%         10     +  25846999  25847024              AB349982     1    26    26
browser |    26  100.0%         10     +  30692667  30692692              AB349982     1    26    26
browser |    26  100.0%         10     +  30967352  30967377              AB349982     1    26    26
browser |    26  100.0%         10     +  31361295  31361320              AB349982     1    26    26
browser |    26  100.0%         10     -  34622224  34622249              AB349982     1    26    26
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browser |    26  100.0%         10     -  43647496  43647521              AB349982     1    26    26
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browser |    26  100.0%         10     +  62942449  62942474              AB349982     1    26    26
browser |    26  100.0%         10     -  65478027  65478052              AB349982     1    26    26
browser |    26  100.0%         10     -  66562642  66562667              AB349982     1    26    26
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browser |    26  100.0%         10     +  71529933  71529958              AB349982     1    26    26
browser |    26  100.0%         10     +  77789291  77789316              AB349982     1    26    26
browser |    26  100.0%         10     -  78656191  78656216              AB349982     1    26    26
browser |    26  100.0%         10     -  81510776  81510801              AB349982     1    26    26
browser |    26  100.0%         10     -  81669904  81669929              AB349982     1    26    26
browser |    26  100.0%         10     +  81806411  81806436              AB349982     1    26    26
browser |    26  100.0%         10     -  83306132  83306157              AB349982     1    26    26
browser |    26  100.0%         10     -  83511187  83511212              AB349982     1    26    26
browser |    26  100.0%         10     +  85553745  85553770              AB349982     1    26    26
browser |    26  100.0%         10     +  88489532  88489557              AB349982     1    26    26
browser |    26  100.0%         10     -  94202335  94202360              AB349982     1    26    26
browser |    26  100.0%         10     -  96032795  96032820              AB349982     1    26    26
browser |    26  100.0%         10     -  97162714  97162739              AB349982     1    26    26
browser |    26  100.0%         10     +  99177671  99177696              AB349982     1    26    26
browser |    26  100.0%         10     + 104393898 104393923              AB349982     1    26    26
browser |    26  100.0%         10     + 104674115 104674140              AB349982     1    26    26
browser |    26  100.0%         10     + 105015634 105015659              AB349982     1    26    26
browser |    26  100.0%         10     + 107838044 107838069              AB349982     1    26    26
browser |    26  100.0%         10     - 109155481 109155506              AB349982     1    26    26
browser |    26  100.0%         10     + 110534815 110534840              AB349982     1    26    26
browser |    26  100.0%         10     - 113563007 113563032              AB349982     1    26    26
browser |    26  100.0%         10     - 116446568 116446593              AB349982     1    26    26
browser |    26  100.0%         10     + 117909238 117909263              AB349982     1    26    26
browser |    26  100.0%         10     + 121003323 121003348              AB349982     1    26    26
browser |    26  100.0%         10     - 122204177 122204202              AB349982     1    26    26
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browser |    26  100.0%         10     - 129229093 129229118              AB349982     1    26    26
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browser |    26  100.0%         10     - 130399302 130399327              AB349982     1    26    26
browser |    26  100.0%         11     -   6095895   6095920              AB349982     1    26    26
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browser |    26  100.0%         11     -   9662386   9662411              AB349982     1    26    26
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browser |    26  100.0%         11     -  18760859  18760884              AB349982     1    26    26
browser |    26  100.0%         11     -  19517828  19517853              AB349982     1    26    26
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View details of parts of alignment within browser window
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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