AB346088
 

Information on mRNA AB346088

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA11289, 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: n/a
Development stage: growing stage
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB346088
Position: chrX:15589625-15589650

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%          X     +  15589625  15589650              AB346088     1    26    27
browser |    26  100.0%          1     +   3683828   3683853              AB346088     1    26    27
browser |    26  100.0%          1     -   4887523   4887548              AB346088     1    26    27
browser |    26  100.0%          1     +   6396493   6396518              AB346088     1    26    27
browser |    26  100.0%          1     +   6733945   6733970              AB346088     1    26    27
browser |    26  100.0%          1     -   7149214   7149239              AB346088     1    26    27
browser |    26  100.0%          1     -   7351520   7351545              AB346088     1    26    27
browser |    26  100.0%          1     -   7523805   7523830              AB346088     1    26    27
browser |    26  100.0%          1     +   7676391   7676416              AB346088     1    26    27
browser |    26  100.0%          1     -   8783448   8783473              AB346088     1    26    27
browser |    26  100.0%          1     -   8868733   8868758              AB346088     1    26    27
browser |    26  100.0%          1     -   9597758   9597783              AB346088     1    26    27
browser |    26  100.0%          1     +  11777650  11777675              AB346088     1    26    27
browser |    26  100.0%          1     -  11887492  11887517              AB346088     1    26    27
browser |    26  100.0%          1     +  12552255  12552280              AB346088     1    26    27
browser |    26  100.0%          1     +  12997573  12997598              AB346088     1    26    27
browser |    26  100.0%          1     +  13523799  13523824              AB346088     1    26    27
browser |    26  100.0%          1     -  13793238  13793263              AB346088     1    26    27
browser |    26  100.0%          1     -  14153939  14153964              AB346088     1    26    27
browser |    26  100.0%          1     +  14347736  14347761              AB346088     1    26    27
browser |    26  100.0%          1     +  15282317  15282342              AB346088     1    26    27
browser |    26  100.0%          1     -  16088066  16088091              AB346088     1    26    27
browser |    26  100.0%          1     -  17681925  17681950              AB346088     1    26    27
browser |    26  100.0%          1     +  18227319  18227344              AB346088     1    26    27
browser |    26  100.0%          1     -  18850938  18850963              AB346088     1    26    27
browser |    26  100.0%          1     +  19254751  19254776              AB346088     1    26    27
browser |    26  100.0%          1     +  19395343  19395368              AB346088     1    26    27
browser |    26  100.0%          1     -  19888493  19888518              AB346088     1    26    27
browser |    26  100.0%          1     -  20197261  20197286              AB346088     1    26    27
browser |    26  100.0%          1     +  20463978  20464003              AB346088     1    26    27
browser |    26  100.0%          1     -  20773481  20773506              AB346088     1    26    27
browser |    26  100.0%          1     +  22225261  22225286              AB346088     1    26    27
browser |    26  100.0%          1     +  29533945  29533970              AB346088     1    26    27
browser |    26  100.0%          1     -  80959519  80959544              AB346088     1    26    27
browser |    26  100.0%          1     -  83708520  83708545              AB346088     1    26    27
browser |    26  100.0%          1     +  84314707  84314732              AB346088     1    26    27
browser |    26  100.0%          1     -  85137371  85137396              AB346088     1    26    27
browser |    26  100.0%          1     -  85414804  85414829              AB346088     1    26    27
browser |    26  100.0%          1     -  87545776  87545801              AB346088     1    26    27
browser |    26  100.0%          1     +  88450728  88450753              AB346088     1    26    27
browser |    26  100.0%          1     -  88542615  88542640              AB346088     1    26    27
browser |    26  100.0%          1     -  90913894  90913919              AB346088     1    26    27
browser |    26  100.0%          1     +  91161345  91161370              AB346088     1    26    27
browser |    26  100.0%          1     -  92280828  92280853              AB346088     1    26    27
browser |    26  100.0%          1     -  92428752  92428777              AB346088     1    26    27
browser |    26  100.0%          1     -  92883657  92883682              AB346088     1    26    27
browser |    26  100.0%          1     -  94840474  94840499              AB346088     1    26    27
browser |    26  100.0%          1     +  97107186  97107211              AB346088     1    26    27
browser |    26  100.0%          1     -  97119925  97119950              AB346088     1    26    27
browser |    26  100.0%          1     -  98570805  98570830              AB346088     1    26    27
browser |    26  100.0%          1     -  99028307  99028332              AB346088     1    26    27
browser |    26  100.0%          1     - 103083547 103083572              AB346088     1    26    27
browser |    26  100.0%          1     - 104085324 104085349              AB346088     1    26    27
browser |    26  100.0%          1     + 105862600 105862625              AB346088     1    26    27
browser |    26  100.0%          1     + 106992548 106992573              AB346088     1    26    27
browser |    26  100.0%          1     + 107382471 107382496              AB346088     1    26    27
browser |    26  100.0%          1     + 107471343 107471368              AB346088     1    26    27
browser |    26  100.0%          1     + 113699200 113699225              AB346088     1    26    27
browser |    26  100.0%          1     + 125584036 125584061              AB346088     1    26    27
browser |    26  100.0%          1     + 125710652 125710677              AB346088     1    26    27
browser |    26  100.0%          1     + 127210178 127210203              AB346088     1    26    27
browser |    26  100.0%          1     + 129113177 129113202              AB346088     1    26    27
browser |    26  100.0%          1     + 129768156 129768181              AB346088     1    26    27
browser |    26  100.0%          1     + 130158791 130158816              AB346088     1    26    27
browser |    26  100.0%          1     + 130842650 130842675              AB346088     1    26    27
browser |    26  100.0%          1     - 158634191 158634216              AB346088     1    26    27
browser |    26  100.0%          1     + 158970379 158970404              AB346088     1    26    27
browser |    26  100.0%          1     + 162359185 162359210              AB346088     1    26    27
browser |    26  100.0%          1     - 162490814 162490839              AB346088     1    26    27
browser |    26  100.0%          1     - 164346463 164346488              AB346088     1    26    27
browser |    26  100.0%          1     + 166283200 166283225              AB346088     1    26    27
browser |    26  100.0%          1     + 169925770 169925795              AB346088     1    26    27
browser |    26  100.0%          1     - 171391946 171391972              AB346088     1    26    27
browser |    26  100.0%          1     + 172733704 172733729              AB346088     1    26    27
browser |    26  100.0%          1     + 174015966 174015991              AB346088     1    26    27
browser |    25  100.0%          1     - 175718174 175718198              AB346088     2    26    27
browser |    26  100.0%          1     + 176173852 176173877              AB346088     1    26    27
browser |    26  100.0%          1     - 177414999 177415024              AB346088     1    26    27
browser |    26  100.0%          1     + 177712572 177712597              AB346088     1    26    27
browser |    26  100.0%          1     + 178300022 178300047              AB346088     1    26    27
browser |    26  100.0%          1     + 181114712 181114737              AB346088     1    26    27
browser |    25  100.0%          1     - 182070026 182070050              AB346088     1    25    27
browser |    26  100.0%          1     - 182598167 182598192              AB346088     1    26    27
browser |    26  100.0%          1     - 185251030 185251055              AB346088     1    26    27
browser |    26  100.0%          1     + 186812116 186812141              AB346088     1    26    27
browser |    26  100.0%          1     - 188972844 188972869              AB346088     1    26    27
browser |    26  100.0%          1     - 191386648 191386673              AB346088     1    26    27
browser |    26  100.0%          1     + 191603235 191603260              AB346088     1    26    27
browser |    26  100.0%          1     - 191993100 191993125              AB346088     1    26    27
browser |    26  100.0%         10     +   3407015   3407040              AB346088     1    26    27
browser |    26  100.0%         10     +   3535663   3535688              AB346088     1    26    27
browser |    26  100.0%         10     -   5525633   5525658              AB346088     1    26    27
browser |    26  100.0%         10     +   5883517   5883542              AB346088     1    26    27
browser |    26  100.0%         10     +   6916481   6916506              AB346088     1    26    27
browser |    26  100.0%         10     +   9233892   9233917              AB346088     1    26    27
browser |    26  100.0%         10     -  10354962  10354987              AB346088     1    26    27
browser |    26  100.0%         10     +  10440640  10440665              AB346088     1    26    27
browser |    26  100.0%         10     +  12010014  12010039              AB346088     1    26    27
browser |    26  100.0%         10     -  13353727  13353752              AB346088     1    26    27
browser |    26  100.0%         10     -  14081569  14081594              AB346088     1    26    27
browser |    26  100.0%         10     -  14539164  14539189              AB346088     1    26    27
browser |    26  100.0%         10     -  15332090  15332115              AB346088     1    26    27
browser |    26  100.0%         10     +  15673047  15673072              AB346088     1    26    27
browser |    26  100.0%         10     -  17376333  17376358              AB346088     1    26    27
browser |    26  100.0%         10     +  17729459  17729484              AB346088     1    26    27
browser |    26  100.0%         10     -  18105180  18105205              AB346088     1    26    27
browser |    26  100.0%         10     +  18254436  18254461              AB346088     1    26    27
browser |    26  100.0%         10     +  18643429  18643454              AB346088     1    26    27
browser |    26  100.0%         10     -  19165954  19165979              AB346088     1    26    27
browser |    26  100.0%         10     +  19622697  19622722              AB346088     1    26    27
browser |    26  100.0%         10     +  22896896  22896921              AB346088     1    26    27
browser |    26  100.0%         10     +  23707280  23707305              AB346088     1    26    27
browser |    26  100.0%         10     +  24046917  24046942              AB346088     1    26    27
browser |    26  100.0%         10     -  26011802  26011827              AB346088     1    26    27
browser |    26  100.0%         10     -  27913473  27913498              AB346088     1    26    27
browser |    26  100.0%         10     +  28218555  28218580              AB346088     1    26    27
browser |    26  100.0%         10     -  29674014  29674039              AB346088     1    26    27
browser |    26  100.0%         10     -  30238007  30238032              AB346088     1    26    27
browser |    26  100.0%         10     -  31607323  31607348              AB346088     1    26    27
browser |    26  100.0%         10     -  32615471  32615496              AB346088     1    26    27
browser |    26  100.0%         10     -  36471908  36471933              AB346088     1    26    27
browser |    26  100.0%         10     +  83634681  83634706              AB346088     1    26    27
browser |    26  100.0%         10     +  84308568  84308593              AB346088     1    26    27
browser |    26  100.0%         10     +  85670391  85670416              AB346088     1    26    27
browser |    26  100.0%         10     -  85675191  85675216              AB346088     1    26    27
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browser |    26  100.0%         10     -  87611895  87611920              AB346088     1    26    27
browser |    26  100.0%         10     -  87817530  87817555              AB346088     1    26    27
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browser |    26  100.0%         10     +  87909016  87909041              AB346088     1    26    27
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browser |    26  100.0%         10     -  88704216  88704241              AB346088     1    26    27
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browser |    26  100.0%         10     + 101151205 101151230              AB346088     1    26    27
browser |    26  100.0%         10     + 104389474 104389499              AB346088     1    26    27
browser |    26  100.0%         10     - 104671093 104671118              AB346088     1    26    27
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browser |    26  100.0%         10     - 108832865 108832890              AB346088     1    26    27
browser |    26  100.0%         10     + 110504037 110504062              AB346088     1    26    27
browser |    26  100.0%         10     - 114008683 114008708              AB346088     1    26    27
browser |    26  100.0%         10     + 116173154 116173179              AB346088     1    26    27
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browser |    26  100.0%         10     - 119239349 119239374              AB346088     1    26    27
browser |    26  100.0%         10     - 121402918 121402943              AB346088     1    26    27
browser |    26  100.0%         10     - 124249751 124249776              AB346088     1    26    27
browser |    26  100.0%         10     - 124750066 124750091              AB346088     1    26    27
browser |    26  100.0%         10     - 125424513 125424538              AB346088     1    26    27
browser |    26  100.0%         10     - 126195477 126195502              AB346088     1    26    27
browser |    26  100.0%         10     - 126622370 126622395              AB346088     1    26    27
browser |    26  100.0%         11     +   3953455   3953480              AB346088     1    26    27
browser |    26  100.0%         11     -   5602059   5602084              AB346088     1    26    27
browser |    26  100.0%         11     -   7535058   7535083              AB346088     1    26    27
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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