AB346087
 

Information on mRNA AB346087

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA11288, 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: AB346087
Position: chrX:15589629-15589654

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%          X     +  15589629  15589654              AB346087     1    25    25
browser |    25  100.0%          1     +   3683832   3683857              AB346087     1    25    25
browser |    25  100.0%          1     -   4887519   4887544              AB346087     1    25    25
browser |    25  100.0%          1     +   6396497   6396522              AB346087     1    25    25
browser |    25  100.0%          1     +   6733949   6733974              AB346087     1    25    25
browser |    25  100.0%          1     -   7149210   7149235              AB346087     1    25    25
browser |    25  100.0%          1     -   7351516   7351541              AB346087     1    25    25
browser |    25  100.0%          1     -   7523801   7523826              AB346087     1    25    25
browser |    25  100.0%          1     +   7676395   7676420              AB346087     1    25    25
browser |    25  100.0%          1     -   8208717   8208742              AB346087     1    25    25
browser |    25  100.0%          1     -   8868729   8868754              AB346087     1    25    25
browser |    25  100.0%          1     +  11777654  11777679              AB346087     1    25    25
browser |    25  100.0%          1     -  11887488  11887513              AB346087     1    25    25
browser |    25  100.0%          1     +  12552259  12552284              AB346087     1    25    25
browser |    25  100.0%          1     +  13523803  13523828              AB346087     1    25    25
browser |    25  100.0%          1     -  13793234  13793259              AB346087     1    25    25
browser |    25  100.0%          1     -  14153935  14153960              AB346087     1    25    25
browser |    25  100.0%          1     +  14347740  14347765              AB346087     1    25    25
browser |    25  100.0%          1     +  15282321  15282346              AB346087     1    25    25
browser |    25  100.0%          1     -  16088062  16088087              AB346087     1    25    25
browser |    25  100.0%          1     -  17681921  17681946              AB346087     1    25    25
browser |    25  100.0%          1     +  18227323  18227348              AB346087     1    25    25
browser |    25  100.0%          1     -  18850934  18850959              AB346087     1    25    25
browser |    25  100.0%          1     +  19254755  19254780              AB346087     1    25    25
browser |    25  100.0%          1     +  19395347  19395372              AB346087     1    25    25
browser |    25  100.0%          1     -  20197257  20197282              AB346087     1    25    25
browser |    25  100.0%          1     +  20463982  20464007              AB346087     1    25    25
browser |    25  100.0%          1     -  20773477  20773502              AB346087     1    25    25
browser |    25  100.0%          1     -  21969512  21969537              AB346087     1    25    25
browser |    25  100.0%          1     +  22225265  22225290              AB346087     1    25    25
browser |    25  100.0%          1     -  27108545  27108570              AB346087     1    25    25
browser |    25  100.0%          1     +  29533949  29533974              AB346087     1    25    25
browser |    25  100.0%          1     +  30305682  30305707              AB346087     1    25    25
browser |    25  100.0%          1     -  80959515  80959540              AB346087     1    25    25
browser |    25  100.0%          1     -  83708516  83708541              AB346087     1    25    25
browser |    25  100.0%          1     +  84314711  84314736              AB346087     1    25    25
browser |    25  100.0%          1     -  85137367  85137392              AB346087     1    25    25
browser |    25  100.0%          1     -  85414800  85414825              AB346087     1    25    25
browser |    25  100.0%          1     +  86002224  86002249              AB346087     1    25    25
browser |    25  100.0%          1     -  87545772  87545797              AB346087     1    25    25
browser |    25  100.0%          1     +  88450732  88450757              AB346087     1    25    25
browser |    25  100.0%          1     -  88542611  88542636              AB346087     1    25    25
browser |    25  100.0%          1     -  90913890  90913915              AB346087     1    25    25
browser |    25  100.0%          1     +  91396951  91396976              AB346087     1    25    25
browser |    25  100.0%          1     -  92280824  92280849              AB346087     1    25    25
browser |    25  100.0%          1     -  92428748  92428773              AB346087     1    25    25
browser |    25  100.0%          1     -  92883653  92883678              AB346087     1    25    25
browser |    25  100.0%          1     -  94840470  94840495              AB346087     1    25    25
browser |    25  100.0%          1     +  97107190  97107215              AB346087     1    25    25
browser |    25  100.0%          1     -  97119921  97119946              AB346087     1    25    25
browser |    25  100.0%          1     -  98570801  98570826              AB346087     1    25    25
browser |    25  100.0%          1     -  99028303  99028328              AB346087     1    25    25
browser |    25  100.0%          1     - 102724321 102724346              AB346087     1    25    25
browser |    25  100.0%          1     - 103083543 103083568              AB346087     1    25    25
browser |    25  100.0%          1     + 105862604 105862629              AB346087     1    25    25
browser |    25  100.0%          1     + 106992552 106992577              AB346087     1    25    25
browser |    25  100.0%          1     + 107382475 107382500              AB346087     1    25    25
browser |    25  100.0%          1     + 107471347 107471372              AB346087     1    25    25
browser |    25  100.0%          1     + 125584040 125584065              AB346087     1    25    25
browser |    25  100.0%          1     + 125710656 125710681              AB346087     1    25    25
browser |    25  100.0%          1     + 127210182 127210207              AB346087     1    25    25
browser |    25  100.0%          1     + 129113181 129113206              AB346087     1    25    25
browser |    25  100.0%          1     + 129768160 129768185              AB346087     1    25    25
browser |    25  100.0%          1     + 130158795 130158820              AB346087     1    25    25
browser |    25  100.0%          1     + 130842654 130842679              AB346087     1    25    25
browser |    25  100.0%          1     - 158634187 158634212              AB346087     1    25    25
browser |    25  100.0%          1     + 158970383 158970408              AB346087     1    25    25
browser |    25  100.0%          1     - 162490810 162490835              AB346087     1    25    25
browser |    23  100.0%          1     - 162778565 162778588              AB346087     3    25    25
browser |    23  100.0%          1     + 163933697 163933720              AB346087     3    25    25
browser |    25  100.0%          1     + 166283204 166283229              AB346087     1    25    25
browser |    25  100.0%          1     + 169925774 169925799              AB346087     1    25    25
browser |    25  100.0%          1     + 174015970 174015995              AB346087     1    25    25
browser |    25  100.0%          1     - 175718170 175718195              AB346087     1    25    25
browser |    25  100.0%          1     + 176173856 176173881              AB346087     1    25    25
browser |    25  100.0%          1     - 177414995 177415020              AB346087     1    25    25
browser |    25  100.0%          1     + 178300026 178300051              AB346087     1    25    25
browser |    25  100.0%          1     + 179489210 179489235              AB346087     1    25    25
browser |    25  100.0%          1     + 181114716 181114741              AB346087     1    25    25
browser |    23  100.0%          1     + 182066753 182066776              AB346087     3    25    25
browser |    25  100.0%          1     - 182598163 182598188              AB346087     1    25    25
browser |    25  100.0%          1     - 185251026 185251051              AB346087     1    25    25
browser |    25  100.0%          1     + 186812120 186812145              AB346087     1    25    25
browser |    25  100.0%          1     - 188972840 188972865              AB346087     1    25    25
browser |    25  100.0%          1     - 191386644 191386669              AB346087     1    25    25
browser |    25  100.0%          1     + 191603239 191603264              AB346087     1    25    25
browser |    25  100.0%         10     +   3407019   3407044              AB346087     1    25    25
browser |    25  100.0%         10     +   3535667   3535692              AB346087     1    25    25
browser |    25  100.0%         10     -   5525629   5525654              AB346087     1    25    25
browser |    25  100.0%         10     +   6916485   6916510              AB346087     1    25    25
browser |    25  100.0%         10     +   9233896   9233921              AB346087     1    25    25
browser |    25  100.0%         10     +  10440644  10440669              AB346087     1    25    25
browser |    25  100.0%         10     +  12010018  12010043              AB346087     1    25    25
browser |    25  100.0%         10     -  13353723  13353748              AB346087     1    25    25
browser |    25  100.0%         10     -  14081565  14081590              AB346087     1    25    25
browser |    25  100.0%         10     -  14539160  14539185              AB346087     1    25    25
browser |    25  100.0%         10     +  14985546  14985571              AB346087     1    25    25
browser |    25  100.0%         10     -  15332086  15332111              AB346087     1    25    25
browser |    25  100.0%         10     +  15673051  15673076              AB346087     1    25    25
browser |    25  100.0%         10     -  17376329  17376354              AB346087     1    25    25
browser |    25  100.0%         10     +  17729463  17729488              AB346087     1    25    25
browser |    25  100.0%         10     -  18105176  18105201              AB346087     1    25    25
browser |    25  100.0%         10     -  18107638  18107663              AB346087     1    25    25
browser |    25  100.0%         10     +  18254440  18254465              AB346087     1    25    25
browser |    25  100.0%         10     +  18643433  18643458              AB346087     1    25    25
browser |    25  100.0%         10     -  19165950  19165975              AB346087     1    25    25
browser |    25  100.0%         10     +  19622701  19622726              AB346087     1    25    25
browser |    25  100.0%         10     +  22896900  22896925              AB346087     1    25    25
browser |    25  100.0%         10     +  23707284  23707309              AB346087     1    25    25
browser |    25  100.0%         10     +  24046921  24046946              AB346087     1    25    25
browser |    25  100.0%         10     -  26011798  26011823              AB346087     1    25    25
browser |    25  100.0%         10     +  28218559  28218584              AB346087     1    25    25
browser |    25  100.0%         10     -  29674010  29674035              AB346087     1    25    25
browser |    25  100.0%         10     -  31607319  31607344              AB346087     1    25    25
browser |    25  100.0%         10     -  36471904  36471929              AB346087     1    25    25
browser |    25  100.0%         10     -  37171409  37171434              AB346087     1    25    25
browser |    25  100.0%         10     -  37676724  37676749              AB346087     1    25    25
browser |    25  100.0%         10     -  38522326  38522351              AB346087     1    25    25
browser |    25  100.0%         10     +  83634685  83634710              AB346087     1    25    25
browser |    25  100.0%         10     +  84308572  84308597              AB346087     1    25    25
browser |    25  100.0%         10     +  85670395  85670420              AB346087     1    25    25
browser |    25  100.0%         10     -  85675187  85675212              AB346087     1    25    25
browser |    25  100.0%         10     +  86582767  86582792              AB346087     1    25    25
browser |    25  100.0%         10     -  87611891  87611916              AB346087     1    25    25
browser |    25  100.0%         10     -  87817526  87817551              AB346087     1    25    25
browser |    25  100.0%         10     -  87886554  87886579              AB346087     1    25    25
browser |    25  100.0%         10     +  87909020  87909045              AB346087     1    25    25
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browser |    25  100.0%         10     -  95577916  95577941              AB346087     1    25    25
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browser |    25  100.0%         10     +  98789236  98789261              AB346087     1    25    25
browser |    25  100.0%         10     + 101151209 101151234              AB346087     1    25    25
browser |    25  100.0%         10     + 104389478 104389503              AB346087     1    25    25
browser |    25  100.0%         10     - 104671089 104671114              AB346087     1    25    25
browser |    25  100.0%         10     + 104811455 104811480              AB346087     1    25    25
browser |    25  100.0%         10     + 106069115 106069140              AB346087     1    25    25
browser |    25  100.0%         10     - 108832861 108832886              AB346087     1    25    25
browser |    25  100.0%         10     + 110504041 110504066              AB346087     1    25    25
browser |    25  100.0%         10     - 110613116 110613141              AB346087     1    25    25
browser |    25  100.0%         10     - 114008679 114008704              AB346087     1    25    25
browser |    25  100.0%         10     - 114326706 114326731              AB346087     1    25    25
browser |    25  100.0%         10     + 116173158 116173183              AB346087     1    25    25
browser |    25  100.0%         10     - 116599000 116599025              AB346087     1    25    25
browser |    25  100.0%         10     - 118061021 118061046              AB346087     1    25    25
browser |    25  100.0%         10     - 119239345 119239370              AB346087     1    25    25
browser |    25  100.0%         10     - 121402914 121402939              AB346087     1    25    25
browser |    25  100.0%         10     - 124249747 124249772              AB346087     1    25    25
browser |    25  100.0%         11     +   3953459   3953484              AB346087     1    25    25
browser |    25  100.0%         11     -   5602055   5602080              AB346087     1    25    25
browser |    25  100.0%         11     -   7535054   7535079              AB346087     1    25    25
browser |    25  100.0%         11     -   9331940   9331965              AB346087     1    25    25
browser |    25  100.0%         11     -  13785816  13785841              AB346087     1    25    25
browser |    25  100.0%         11     -  13919346  13919371              AB346087     1    25    25
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browser |    25  100.0%         11     -  20000840  20000865              AB346087     1    25    25
browser |    25  100.0%         11     -  20670262  20670287              AB346087     1    25    25
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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