AB351266
 

Information on mRNA AB351266

Description: Mus musculus non-coding RNA, oocyte_piRNA2082, 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: AB351266
Position: chr12:56795816-56795841

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     -  56795816  56795841              AB351266     1    26    26
browser |    26  100.0%          1     -   4628510   4628535              AB351266     1    26    26
browser |    26  100.0%          1     +   6241820   6241845              AB351266     1    26    26
browser |    26  100.0%          1     -   6501780   6501805              AB351266     1    26    26
browser |    26  100.0%          1     +   8069840   8069865              AB351266     1    26    26
browser |    26  100.0%          1     +   8232285   8232310              AB351266     1    26    26
browser |    26  100.0%          1     -  10801270  10801295              AB351266     1    26    26
browser |    26  100.0%          1     -  11958528  11958553              AB351266     1    26    26
browser |    26  100.0%          1     +  16814354  16814379              AB351266     1    26    26
browser |    26  100.0%          1     +  18590228  18590253              AB351266     1    26    26
browser |    26  100.0%          1     +  19698562  19698587              AB351266     1    26    26
browser |    26  100.0%          1     +  23344222  23344247              AB351266     1    26    26
browser |    26  100.0%          1     -  26389437  26389462              AB351266     1    26    26
browser |    26  100.0%          1     -  29982989  29983014              AB351266     1    26    26
browser |    26  100.0%          1     +  35833447  35833472              AB351266     1    26    26
browser |    26  100.0%          1     +  38746829  38746854              AB351266     1    26    26
browser |    26  100.0%          1     +  45777303  45777328              AB351266     1    26    26
browser |    26  100.0%          1     +  48132237  48132262              AB351266     1    26    26
browser |    26  100.0%          1     -  48394677  48394702              AB351266     1    26    26
browser |    26  100.0%          1     +  52632087  52632112              AB351266     1    26    26
browser |    26  100.0%          1     -  53169968  53169993              AB351266     1    26    26
browser |    26  100.0%          1     +  55821212  55821237              AB351266     1    26    26
browser |    26  100.0%          1     +  56817254  56817279              AB351266     1    26    26
browser |    26  100.0%          1     -  58363706  58363731              AB351266     1    26    26
browser |    26  100.0%          1     -  60765200  60765225              AB351266     1    26    26
browser |    26  100.0%          1     -  62574464  62574489              AB351266     1    26    26
browser |    26  100.0%          1     +  64428154  64428179              AB351266     1    26    26
browser |    26  100.0%          1     -  65000662  65000687              AB351266     1    26    26
browser |    26  100.0%          1     -  66057973  66057998              AB351266     1    26    26
browser |    26  100.0%          1     -  67791779  67791804              AB351266     1    26    26
browser |    26  100.0%          1     -  69738416  69738441              AB351266     1    26    26
browser |    26  100.0%          1     +  79920661  79920686              AB351266     1    26    26
browser |    26  100.0%          1     -  81543075  81543100              AB351266     1    26    26
browser |    26  100.0%          1     -  84974793  84974818              AB351266     1    26    26
browser |    26  100.0%          1     -  87062557  87062582              AB351266     1    26    26
browser |    26  100.0%          1     +  87393774  87393799              AB351266     1    26    26
browser |    26  100.0%          1     -  91400133  91400158              AB351266     1    26    26
browser |    26  100.0%          1     +  93887817  93887842              AB351266     1    26    26
browser |    26  100.0%          1     +  97105883  97105908              AB351266     1    26    26
browser |    26  100.0%          1     - 101907062 101907087              AB351266     1    26    26
browser |    26  100.0%          1     + 102965285 102965310              AB351266     1    26    26
browser |    26  100.0%          1     - 103134094 103134119              AB351266     1    26    26
browser |    26  100.0%          1     - 104218487 104218512              AB351266     1    26    26
browser |    26  100.0%          1     - 108337782 108337807              AB351266     1    26    26
browser |    26  100.0%          1     - 109057598 109057623              AB351266     1    26    26
browser |    26  100.0%          1     + 110260795 110260820              AB351266     1    26    26
browser |    26  100.0%          1     - 110866529 110866554              AB351266     1    26    26
browser |    26  100.0%          1     - 111182554 111182579              AB351266     1    26    26
browser |    26  100.0%          1     + 112861987 112862012              AB351266     1    26    26
browser |    26  100.0%          1     + 112949702 112949727              AB351266     1    26    26
browser |    26  100.0%          1     + 114117012 114117037              AB351266     1    26    26
browser |    26  100.0%          1     - 115814289 115814314              AB351266     1    26    26
browser |    26  100.0%          1     - 116577199 116577224              AB351266     1    26    26
browser |    26  100.0%          1     - 117630856 117630881              AB351266     1    26    26
browser |    26  100.0%          1     - 120499772 120499797              AB351266     1    26    26
browser |    26  100.0%          1     + 125250487 125250512              AB351266     1    26    26
browser |    26  100.0%          1     - 125275050 125275075              AB351266     1    26    26
browser |    26  100.0%          1     + 126356181 126356206              AB351266     1    26    26
browser |    26  100.0%          1     + 130465760 130465785              AB351266     1    26    26
browser |    26  100.0%          1     + 139656600 139656625              AB351266     1    26    26
browser |    26  100.0%          1     + 140750444 140750469              AB351266     1    26    26
browser |    26  100.0%          1     + 149274892 149274917              AB351266     1    26    26
browser |    26  100.0%          1     + 149463206 149463231              AB351266     1    26    26
browser |    26  100.0%          1     + 152542650 152542675              AB351266     1    26    26
browser |    26  100.0%          1     - 159798525 159798550              AB351266     1    26    26
browser |    26  100.0%          1     - 160644639 160644664              AB351266     1    26    26
browser |    26  100.0%          1     + 162674015 162674040              AB351266     1    26    26
browser |    26  100.0%          1     - 163297255 163297280              AB351266     1    26    26
browser |    26  100.0%          1     - 166591897 166591922              AB351266     1    26    26
browser |    26  100.0%          1     + 169375259 169375284              AB351266     1    26    26
browser |    26  100.0%          1     - 174870742 174870767              AB351266     1    26    26
browser |    26  100.0%          1     - 176371824 176371849              AB351266     1    26    26
browser |    26  100.0%          1     + 177891514 177891539              AB351266     1    26    26
browser |    26  100.0%          1     + 178007567 178007592              AB351266     1    26    26
browser |    26  100.0%          1     - 181092280 181092305              AB351266     1    26    26
browser |    26  100.0%          1     + 191843675 191843700              AB351266     1    26    26
browser |    26  100.0%         10     -   3267527   3267552              AB351266     1    26    26
browser |    26  100.0%         10     -   3552120   3552145              AB351266     1    26    26
browser |    26  100.0%         10     +   9726323   9726348              AB351266     1    26    26
browser |    26  100.0%         10     +  19676041  19676066              AB351266     1    26    26
browser |    26  100.0%         10     +  21091242  21091267              AB351266     1    26    26
browser |    26  100.0%         10     -  21519407  21519432              AB351266     1    26    26
browser |    26  100.0%         10     -  22560353  22560378              AB351266     1    26    26
browser |    26  100.0%         10     -  23748408  23748433              AB351266     1    26    26
browser |    26  100.0%         10     +  24566270  24566295              AB351266     1    26    26
browser |    26  100.0%         10     -  24978632  24978657              AB351266     1    26    26
browser |    26  100.0%         10     +  30695880  30695905              AB351266     1    26    26
browser |    26  100.0%         10     +  30970565  30970590              AB351266     1    26    26
browser |    26  100.0%         10     +  31364510  31364535              AB351266     1    26    26
browser |    26  100.0%         10     +  33765826  33765851              AB351266     1    26    26
browser |    26  100.0%         10     -  34619011  34619036              AB351266     1    26    26
browser |    26  100.0%         10     +  41722432  41722457              AB351266     1    26    26
browser |    26  100.0%         10     -  45432189  45432214              AB351266     1    26    26
browser |    26  100.0%         10     +  50370359  50370384              AB351266     1    26    26
browser |    26  100.0%         10     +  51762803  51762828              AB351266     1    26    26
browser |    26  100.0%         10     -  55592816  55592841              AB351266     1    26    26
browser |    26  100.0%         10     +  56602740  56602765              AB351266     1    26    26
browser |    26  100.0%         10     -  65787788  65787813              AB351266     1    26    26
browser |    26  100.0%         10     +  71533145  71533170              AB351266     1    26    26
browser |    26  100.0%         10     +  77792504  77792529              AB351266     1    26    26
browser |    26  100.0%         10     +  77860194  77860219              AB351266     1    26    26
browser |    26  100.0%         10     +  80815471  80815496              AB351266     1    26    26
browser |    26  100.0%         10     -  83507974  83507999              AB351266     1    26    26
browser |    26  100.0%         10     +  83627251  83627276              AB351266     1    26    26
browser |    26  100.0%         10     +  85555345  85555370              AB351266     1    26    26
browser |    26  100.0%         10     +  88802847  88802872              AB351266     1    26    26
browser |    26  100.0%         10     -  90161660  90161685              AB351266     1    26    26
browser |    26  100.0%         10     -  94199626  94199651              AB351266     1    26    26
browser |    26  100.0%         10     -  96029582  96029607              AB351266     1    26    26
browser |    26  100.0%         10     -  97157610  97157635              AB351266     1    26    26
browser |    26  100.0%         10     + 100418417 100418442              AB351266     1    26    26
browser |    26  100.0%         10     - 104656542 104656567              AB351266     1    26    26
browser |    26  100.0%         10     - 105509701 105509726              AB351266     1    26    26
browser |    26  100.0%         10     + 107841257 107841282              AB351266     1    26    26
browser |    26  100.0%         10     - 109152267 109152292              AB351266     1    26    26
browser |    26  100.0%         10     - 113559797 113559822              AB351266     1    26    26
browser |    26  100.0%         10     - 116443355 116443380              AB351266     1    26    26
browser |    26  100.0%         10     - 122203153 122203178              AB351266     1    26    26
browser |    26  100.0%         10     + 124418124 124418149              AB351266     1    26    26
browser |    26  100.0%         10     + 124445629 124445654              AB351266     1    26    26
browser |    26  100.0%         10     - 124517544 124517569              AB351266     1    26    26
browser |    26  100.0%         10     - 129225880 129225905              AB351266     1    26    26
browser |    26  100.0%         10     - 130397199 130397224              AB351266     1    26    26
browser |    26  100.0%         11     -   6092681   6092706              AB351266     1    26    26
browser |    26  100.0%         11     +   6484577   6484602              AB351266     1    26    26
browser |    26  100.0%         11     -   9659176   9659201              AB351266     1    26    26
browser |    26  100.0%         11     -  12458480  12458505              AB351266     1    26    26
browser |    26  100.0%         11     +  12517834  12517859              AB351266     1    26    26
browser |    26  100.0%         11     -  12905207  12905232              AB351266     1    26    26
browser |    26  100.0%         11     +  15183604  15183629              AB351266     1    26    26
browser |    26  100.0%         11     +  15836606  15836631              AB351266     1    26    26
browser |    26  100.0%         11     +  16181459  16181484              AB351266     1    26    26
browser |    26  100.0%         11     -  18757646  18757671              AB351266     1    26    26
browser |    26  100.0%         11     -  19517365  19517390              AB351266     1    26    26
browser |    26  100.0%         11     -  19739915  19739940              AB351266     1    26    26
browser |    26  100.0%         11     -  22286444  22286469              AB351266     1    26    26
browser |    26  100.0%         11     +  22531795  22531820              AB351266     1    26    26
browser |    26  100.0%         11     -  23169773  23169798              AB351266     1    26    26
browser |    26  100.0%         11     +  26509537  26509562              AB351266     1    26    26
browser |    26  100.0%         11     -  27902269  27902294              AB351266     1    26    26
browser |    26  100.0%         11     +  28053204  28053229              AB351266     1    26    26
browser |    26  100.0%         11     -  31398756  31398781              AB351266     1    26    26
browser |    26  100.0%         11     +  43553452  43553477              AB351266     1    26    26
browser |    26  100.0%         11     -  51557044  51557069              AB351266     1    26    26
browser |    26  100.0%         11     +  61317175  61317200              AB351266     1    26    26
browser |    26  100.0%         11     +  64686993  64687018              AB351266     1    26    26
browser |    26  100.0%         11     -  73627981  73628006              AB351266     1    26    26
browser |    26  100.0%         11     +  74025669  74025694              AB351266     1    26    26
browser |    26  100.0%         11     -  74111709  74111734              AB351266     1    26    26
browser |    26  100.0%         11     +  74434970  74434995              AB351266     1    26    26
browser |    26  100.0%         11     +  74781134  74781159              AB351266     1    26    26
browser |    26  100.0%         11     -  79124809  79124834              AB351266     1    26    26
browser |    26  100.0%         11     +  81442278  81442303              AB351266     1    26    26
browser |    26  100.0%         11     -  82226013  82226038              AB351266     1    26    26
browser |    26  100.0%         11     -  85177586  85177611              AB351266     1    26    26
browser |    26  100.0%         11     -  88802978  88803003              AB351266     1    26    26
browser |    26  100.0%         11     +  90797870  90797895              AB351266     1    26    26
browser |    26  100.0%         11     +  91995797  91995822              AB351266     1    26    26
browser |    26  100.0%         11     +  98510001  98510026              AB351266     1    26    26
browser |    26  100.0%         11     + 100559154 100559179              AB351266     1    26    26
browser |    26  100.0%         11     - 105920272 105920297              AB351266     1    26    26
browser |    26  100.0%         11     - 106184706 106184731              AB351266     1    26    26
browser |    26  100.0%         11     + 108544798 108544823              AB351266     1    26    26
browser |    26  100.0%         11     + 111079243 111079268              AB351266     1    26    26
browser |    26  100.0%         11     - 111107662 111107687              AB351266     1    26    26
browser |    26  100.0%         11     + 113808933 113808958              AB351266     1    26    26
browser |    26  100.0%         11     - 115646916 115646941              AB351266     1    26    26
browser |    26  100.0%         11     + 116284287 116284312              AB351266     1    26    26
browser |    26  100.0%         11     + 116682300 116682325              AB351266     1    26    26
browser |    26  100.0%         12     +   3058278   3058303              AB351266     1    26    26
browser |    26  100.0%         12     +   6572450   6572475              AB351266     1    26    26
browser |    26  100.0%         12     -  11154846  11154871              AB351266     1    26    26
browser |    26  100.0%         12     +  17178128  17178153              AB351266     1    26    26
browser |    26  100.0%         12     -  19309430  19309455              AB351266     1    26    26
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browser |    26  100.0%         12     -  31409341  31409366              AB351266     1    26    26
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browser |    26  100.0%         13     -  31418525  31418550              AB351266     1    26    26
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browser |    26  100.0%         13     -  46530846  46530871              AB351266     1    26    26
browser |    26  100.0%         13     -  51420987  51421012              AB351266     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