AB349956
 

Information on mRNA AB349956

Description: Mus musculus non-coding RNA, oocyte_piRNA772, 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: AB349956
Position: chr12:56796463-56796487

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 |    25  100.0%         12     -  56796463  56796487              AB349956     1    25    25
browser |    25  100.0%          1     -   5879148   5879172              AB349956     1    25    25
browser |    25  100.0%          1     -   6505177   6505201              AB349956     1    25    25
browser |    25  100.0%          1     +   8066447   8066471              AB349956     1    25    25
browser |    25  100.0%          1     +   8228888   8228912              AB349956     1    25    25
browser |    25  100.0%          1     -  10804664  10804688              AB349956     1    25    25
browser |    25  100.0%          1     -  11101415  11101439              AB349956     1    25    25
browser |    25  100.0%          1     +  13623312  13623336              AB349956     1    25    25
browser |    25  100.0%          1     +  16810958  16810982              AB349956     1    25    25
browser |    25  100.0%          1     +  18029552  18029576              AB349956     1    25    25
browser |    25  100.0%          1     +  18589582  18589606              AB349956     1    25    25
browser |    25  100.0%          1     +  19695166  19695190              AB349956     1    25    25
browser |    25  100.0%          1     -  22070041  22070065              AB349956     1    25    25
browser |    25  100.0%          1     +  26455574  26455598              AB349956     1    25    25
browser |    25  100.0%          1     -  26512753  26512777              AB349956     1    25    25
browser |    25  100.0%          1     +  27221722  27221746              AB349956     1    25    25
browser |    25  100.0%          1     +  29696346  29696370              AB349956     1    25    25
browser |    25  100.0%          1     -  29985883  29985907              AB349956     1    25    25
browser |    25  100.0%          1     +  34389055  34389079              AB349956     1    25    25
browser |    25  100.0%          1     -  47264597  47264621              AB349956     1    25    25
browser |    25  100.0%          1     -  48399938  48399962              AB349956     1    25    25
browser |    25  100.0%          1     -  53171428  53171452              AB349956     1    25    25
browser |    25  100.0%          1     +  56813858  56813882              AB349956     1    25    25
browser |    25  100.0%          1     -  58367103  58367127              AB349956     1    25    25
browser |    25  100.0%          1     -  58855411  58855435              AB349956     1    25    25
browser |    25  100.0%          1     +  64424758  64424782              AB349956     1    25    25
browser |    25  100.0%          1     -  67795171  67795195              AB349956     1    25    25
browser |    25  100.0%          1     +  70278740  70278764              AB349956     1    25    25
browser |    25  100.0%          1     -  72169283  72169307              AB349956     1    25    25
browser |    25  100.0%          1     -  74697179  74697203              AB349956     1    25    25
browser |    25  100.0%          1     +  79917265  79917289              AB349956     1    25    25
browser |    25  100.0%          1     -  81546472  81546496              AB349956     1    25    25
browser |    25  100.0%          1     +  82481301  82481325              AB349956     1    25    25
browser |    25  100.0%          1     -  87065954  87065978              AB349956     1    25    25
browser |    25  100.0%          1     +  87390378  87390402              AB349956     1    25    25
browser |    25  100.0%          1     -  91403527  91403551              AB349956     1    25    25
browser |    25  100.0%          1     +  93886788  93886812              AB349956     1    25    25
browser |    25  100.0%          1     +  95625376  95625400              AB349956     1    25    25
browser |    25  100.0%          1     +  97102987  97103011              AB349956     1    25    25
browser |    25  100.0%          1     - 101910462 101910486              AB349956     1    25    25
browser |    25  100.0%          1     + 102961889 102961913              AB349956     1    25    25
browser |    25  100.0%          1     - 103137491 103137515              AB349956     1    25    25
browser |    25  100.0%          1     - 108341179 108341203              AB349956     1    25    25
browser |    25  100.0%          1     + 109543631 109543655              AB349956     1    25    25
browser |    25  100.0%          1     + 111633599 111633623              AB349956     1    25    25
browser |    25  100.0%          1     - 112196657 112196681              AB349956     1    25    25
browser |    25  100.0%          1     + 112859708 112859732              AB349956     1    25    25
browser |    25  100.0%          1     - 116580596 116580620              AB349956     1    25    25
browser |    25  100.0%          1     - 117634254 117634278              AB349956     1    25    25
browser |    25  100.0%          1     - 125275697 125275721              AB349956     1    25    25
browser |    25  100.0%          1     - 127490590 127490614              AB349956     1    25    25
browser |    25  100.0%          1     - 127807389 127807413              AB349956     1    25    25
browser |    25  100.0%          1     + 130464553 130464577              AB349956     1    25    25
browser |    25  100.0%          1     - 137203496 137203520              AB349956     1    25    25
browser |    25  100.0%          1     + 140747049 140747073              AB349956     1    25    25
browser |    25  100.0%          1     + 140965647 140965671              AB349956     1    25    25
browser |    25  100.0%          1     + 144262406 144262430              AB349956     1    25    25
browser |    25  100.0%          1     + 145999173 145999197              AB349956     1    25    25
browser |    25  100.0%          1     + 149271496 149271520              AB349956     1    25    25
browser |    25  100.0%          1     - 149394628 149394652              AB349956     1    25    25
browser |    25  100.0%          1     + 149459807 149459831              AB349956     1    25    25
browser |    25  100.0%          1     - 154779289 154779313              AB349956     1    25    25
browser |    25  100.0%          1     - 159801922 159801946              AB349956     1    25    25
browser |    25  100.0%          1     + 162670619 162670643              AB349956     1    25    25
browser |    25  100.0%          1     - 166594795 166594819              AB349956     1    25    25
browser |    25  100.0%          1     + 169371866 169371890              AB349956     1    25    25
browser |    25  100.0%          1     + 169945853 169945877              AB349956     1    25    25
browser |    25  100.0%          1     - 174873327 174873351              AB349956     1    25    25
browser |    25  100.0%          1     - 176375221 176375245              AB349956     1    25    25
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browser |    25  100.0%          1     + 178004171 178004195              AB349956     1    25    25
browser |    25  100.0%          1     + 179724066 179724090              AB349956     1    25    25
browser |    25  100.0%          1     - 181095678 181095702              AB349956     1    25    25
browser |    25  100.0%          1     + 183298778 183298802              AB349956     1    25    25
browser |    25  100.0%          1     + 195005155 195005179              AB349956     1    25    25
browser |    25  100.0%         10     -   3555518   3555542              AB349956     1    25    25
browser |    25  100.0%         10     +   8477544   8477568              AB349956     1    25    25
browser |    25  100.0%         10     +  11572523  11572547              AB349956     1    25    25
browser |    25  100.0%         10     -  19419231  19419255              AB349956     1    25    25
browser |    25  100.0%         10     +  19675395  19675419              AB349956     1    25    25
browser |    25  100.0%         10     -  19890958  19890982              AB349956     1    25    25
browser |    25  100.0%         10     -  21522804  21522828              AB349956     1    25    25
browser |    25  100.0%         10     -  22403695  22403719              AB349956     1    25    25
browser |    25  100.0%         10     -  22563750  22563774              AB349956     1    25    25
browser |    25  100.0%         10     -  23751805  23751829              AB349956     1    25    25
browser |    25  100.0%         10     -  24979877  24979901              AB349956     1    25    25
browser |    25  100.0%         10     +  25846816  25846840              AB349956     1    25    25
browser |    25  100.0%         10     +  30692484  30692508              AB349956     1    25    25
browser |    25  100.0%         10     +  30967169  30967193              AB349956     1    25    25
browser |    25  100.0%         10     +  31361112  31361136              AB349956     1    25    25
browser |    25  100.0%         10     +  41719038  41719062              AB349956     1    25    25
browser |    25  100.0%         10     -  43647680  43647704              AB349956     1    25    25
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browser |    25  100.0%         10     +  62942266  62942290              AB349956     1    25    25
browser |    25  100.0%         10     -  65478211  65478235              AB349956     1    25    25
browser |    25  100.0%         10     -  66562826  66562850              AB349956     1    25    25
browser |    25  100.0%         10     +  70629757  70629781              AB349956     1    25    25
browser |    25  100.0%         10     +  71529750  71529774              AB349956     1    25    25
browser |    25  100.0%         10     +  77789108  77789132              AB349956     1    25    25
browser |    25  100.0%         10     -  78656375  78656399              AB349956     1    25    25
browser |    25  100.0%         10     -  81510960  81510984              AB349956     1    25    25
browser |    25  100.0%         10     -  81670088  81670112              AB349956     1    25    25
browser |    25  100.0%         10     +  81806228  81806252              AB349956     1    25    25
browser |    25  100.0%         10     -  83306316  83306340              AB349956     1    25    25
browser |    25  100.0%         10     -  83511371  83511395              AB349956     1    25    25
browser |    25  100.0%         10     +  85553562  85553586              AB349956     1    25    25
browser |    25  100.0%         10     +  88489349  88489373              AB349956     1    25    25
browser |    25  100.0%         10     -  94202519  94202543              AB349956     1    25    25
browser |    25  100.0%         10     -  96032979  96033003              AB349956     1    25    25
browser |    25  100.0%         10     -  97162898  97162922              AB349956     1    25    25
browser |    25  100.0%         10     +  99177488  99177512              AB349956     1    25    25
browser |    25  100.0%         10     + 104393715 104393739              AB349956     1    25    25
browser |    25  100.0%         10     + 104673932 104673956              AB349956     1    25    25
browser |    25  100.0%         10     + 105015451 105015475              AB349956     1    25    25
browser |    25  100.0%         10     + 107837861 107837885              AB349956     1    25    25
browser |    25  100.0%         10     - 109155665 109155689              AB349956     1    25    25
browser |    25  100.0%         10     + 110534632 110534656              AB349956     1    25    25
browser |    25  100.0%         10     - 113563191 113563215              AB349956     1    25    25
browser |    25  100.0%         10     - 116446752 116446776              AB349956     1    25    25
browser |    25  100.0%         10     + 117909055 117909079              AB349956     1    25    25
browser |    25  100.0%         10     + 121003140 121003164              AB349956     1    25    25
browser |    25  100.0%         10     - 122204361 122204385              AB349956     1    25    25
browser |    25  100.0%         10     + 122344175 122344199              AB349956     1    25    25
browser |    25  100.0%         10     - 122673238 122673262              AB349956     1    25    25
browser |    25  100.0%         10     + 123697752 123697776              AB349956     1    25    25
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browser |    25  100.0%         10     - 124519432 124519456              AB349956     1    25    25
browser |    25  100.0%         10     - 129229277 129229301              AB349956     1    25    25
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browser |    25  100.0%         10     - 130399486 130399510              AB349956     1    25    25
browser |    25  100.0%         11     -   6096079   6096103              AB349956     1    25    25
browser |    25  100.0%         11     -   7530271   7530295              AB349956     1    25    25
browser |    25  100.0%         11     -   9662570   9662594              AB349956     1    25    25
browser |    25  100.0%         11     +  10712828  10712852              AB349956     1    25    25
browser |    25  100.0%         11     +  12514438  12514462              AB349956     1    25    25
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browser |    25  100.0%         11     +  15180208  15180232              AB349956     1    25    25
browser |    25  100.0%         11     -  18761043  18761067              AB349956     1    25    25
browser |    25  100.0%         11     -  19518012  19518036              AB349956     1    25    25
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browser |    25  100.0%         11     -  23173170  23173194              AB349956     1    25    25
browser |    25  100.0%         11     -  23194783  23194807              AB349956     1    25    25
browser |    25  100.0%         11     -  27904556  27904580              AB349956     1    25    25
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browser |    25  100.0%         11     -  39959139  39959163              AB349956     1    25    25
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browser |    25  100.0%         11     -  54471987  54472011              AB349956     1    25    25
browser |    25  100.0%         11     -  55136350  55136374              AB349956     1    25    25
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browser |    25  100.0%         11     -  65347197  65347221              AB349956     1    25    25
browser |    25  100.0%         11     -  66842656  66842680              AB349956     1    25    25
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browser |    25  100.0%         11     -  79634316  79634340              AB349956     1    25    25
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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