AB351466
 

Information on mRNA AB351466

Description: Mus musculus non-coding RNA, oocyte_piRNA2282, 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: AB351466
Position: chr12:56796212-56796236

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     -  56796212  56796236              AB351466     1    25    26
browser |    26  100.0%          1     +   8066698   8066723              AB351466     1    26    26
browser |    26  100.0%          1     -  10804412  10804437              AB351466     1    26    26
browser |    25  100.0%          1     +  18029803  18029827              AB351466     1    25    26
browser |    25  100.0%          1     +  18589833  18589857              AB351466     1    25    26
browser |    26  100.0%          1     +  19695417  19695442              AB351466     1    26    26
browser |    26  100.0%          1     +  26455825  26455850              AB351466     1    26    26
browser |    26  100.0%          1     -  26512501  26512526              AB351466     1    26    26
browser |    26  100.0%          1     +  27221973  27221998              AB351466     1    26    26
browser |    26  100.0%          1     -  29985631  29985656              AB351466     1    26    26
browser |    26  100.0%          1     +  34389306  34389331              AB351466     1    26    26
browser |    26  100.0%          1     +  35830302  35830327              AB351466     1    26    26
browser |    26  100.0%          1     +  40739819  40739844              AB351466     1    26    26
browser |    26  100.0%          1     -  47264345  47264370              AB351466     1    26    26
browser |    26  100.0%          1     -  48399686  48399711              AB351466     1    26    26
browser |    26  100.0%          1     -  53171176  53171201              AB351466     1    26    26
browser |    26  100.0%          1     +  55820256  55820281              AB351466     1    26    26
browser |    26  100.0%          1     +  56814109  56814134              AB351466     1    26    26
browser |    26  100.0%          1     -  58855159  58855184              AB351466     1    26    26
browser |    26  100.0%          1     -  60768345  60768370              AB351466     1    26    26
browser |    26  100.0%          1     -  62577609  62577634              AB351466     1    26    26
browser |    26  100.0%          1     -  64221671  64221696              AB351466     1    26    26
browser |    26  100.0%          1     +  64425009  64425034              AB351466     1    26    26
browser |    25  100.0%          1     -  65003808  65003832              AB351466     1    25    26
browser |    26  100.0%          1     -  66061114  66061139              AB351466     1    26    26
browser |    26  100.0%          1     -  67794919  67794944              AB351466     1    26    26
browser |    26  100.0%          1     +  70278991  70279016              AB351466     1    26    26
browser |    25  100.0%          1     -  72169032  72169056              AB351466     1    25    26
browser |    26  100.0%          1     -  74696927  74696952              AB351466     1    26    26
browser |    26  100.0%          1     +  78999288  78999313              AB351466     1    26    26
browser |    26  100.0%          1     +  79917516  79917541              AB351466     1    26    26
browser |    26  100.0%          1     -  81546220  81546245              AB351466     1    26    26
browser |    26  100.0%          1     +  82481552  82481577              AB351466     1    26    26
browser |    26  100.0%          1     -  87065702  87065727              AB351466     1    26    26
browser |    26  100.0%          1     +  87390629  87390654              AB351466     1    26    26
browser |    26  100.0%          1     -  91403275  91403300              AB351466     1    26    26
browser |    26  100.0%          1     +  93887039  93887064              AB351466     1    26    26
browser |    26  100.0%          1     - 101910210 101910235              AB351466     1    26    26
browser |    26  100.0%          1     + 102962140 102962165              AB351466     1    26    26
browser |    26  100.0%          1     - 103137239 103137264              AB351466     1    26    26
browser |    26  100.0%          1     - 108340927 108340952              AB351466     1    26    26
browser |    25  100.0%          1     + 109543882 109543906              AB351466     1    25    26
browser |    26  100.0%          1     - 111185696 111185721              AB351466     1    26    26
browser |    25  100.0%          1     + 111633850 111633874              AB351466     1    25    26
browser |    26  100.0%          1     + 112859959 112859984              AB351466     1    26    26
browser |    26  100.0%          1     + 112946557 112946582              AB351466     1    26    26
browser |    26  100.0%          1     - 116580344 116580369              AB351466     1    26    26
browser |    26  100.0%          1     - 117634002 117634027              AB351466     1    26    26
browser |    26  100.0%          1     + 125247345 125247370              AB351466     1    26    26
browser |    26  100.0%          1     - 125275445 125275470              AB351466     1    26    26
browser |    26  100.0%          1     - 127490338 127490363              AB351466     1    26    26
browser |    26  100.0%          1     - 127807137 127807162              AB351466     1    26    26
browser |    26  100.0%          1     + 130464804 130464829              AB351466     1    26    26
browser |    26  100.0%          1     + 140747300 140747325              AB351466     1    26    26
browser |    26  100.0%          1     + 140965898 140965923              AB351466     1    26    26
browser |    25  100.0%          1     + 144262657 144262681              AB351466     1    25    26
browser |    26  100.0%          1     - 144734767 144734792              AB351466     1    26    26
browser |    25  100.0%          1     + 145999424 145999448              AB351466     1    25    26
browser |    26  100.0%          1     + 149271747 149271772              AB351466     1    26    26
browser |    26  100.0%          1     - 149386376 149386401              AB351466     1    26    26
browser |    26  100.0%          1     - 149394376 149394401              AB351466     1    26    26
browser |    26  100.0%          1     + 149460058 149460083              AB351466     1    26    26
browser |    26  100.0%          1     - 159801670 159801695              AB351466     1    26    26
browser |    26  100.0%          1     + 162670870 162670895              AB351466     1    26    26
browser |    25  100.0%          1     + 166182508 166182532              AB351466     1    25    26
browser |    25  100.0%          1     - 166594544 166594568              AB351466     1    25    26
browser |    25  100.0%          1     + 169372117 169372141              AB351466     1    25    26
browser |    25  100.0%          1     + 169946104 169946128              AB351466     1    25    26
browser |    25  100.0%          1     - 174873076 174873100              AB351466     1    25    26
browser |    25  100.0%          1     - 176374970 176374994              AB351466     1    25    26
browser |    26  100.0%          1     + 177888369 177888394              AB351466     1    26    26
browser |    26  100.0%          1     + 178004422 178004447              AB351466     1    26    26
browser |    25  100.0%          1     + 179724317 179724341              AB351466     1    25    26
browser |    26  100.0%          1     - 181095426 181095451              AB351466     1    26    26
browser |    25  100.0%          1     + 181323211 181323235              AB351466     1    25    26
browser |    25  100.0%          1     + 183299030 183299054              AB351466     1    25    26
browser |    25  100.0%          1     + 195005406 195005430              AB351466     1    25    26
browser |    26  100.0%         10     -   3555266   3555291              AB351466     1    26    26
browser |    25  100.0%         10     +   8477795   8477819              AB351466     1    25    26
browser |    25  100.0%         10     +  11572774  11572798              AB351466     1    25    26
browser |    26  100.0%         10     -  19418979  19419004              AB351466     1    26    26
browser |    26  100.0%         10     +  19675646  19675671              AB351466     1    26    26
browser |    25  100.0%         10     -  19890707  19890731              AB351466     1    25    26
browser |    25  100.0%         10     -  21522553  21522577              AB351466     1    25    26
browser |    25  100.0%         10     -  22403444  22403468              AB351466     1    25    26
browser |    26  100.0%         10     -  22563498  22563523              AB351466     1    26    26
browser |    25  100.0%         10     -  23751554  23751578              AB351466     1    25    26
browser |    26  100.0%         10     -  24979625  24979650              AB351466     1    26    26
browser |    26  100.0%         10     +  25847067  25847092              AB351466     1    26    26
browser |    25  100.0%         10     +  30692735  30692759              AB351466     1    25    26
browser |    26  100.0%         10     +  30967420  30967445              AB351466     1    26    26
browser |    26  100.0%         10     +  31361363  31361388              AB351466     1    26    26
browser |    25  100.0%         10     -  34622157  34622181              AB351466     1    25    26
browser |    26  100.0%         10     +  41719289  41719314              AB351466     1    26    26
browser |    26  100.0%         10     -  43647428  43647453              AB351466     1    26    26
browser |    26  100.0%         10     +  51761847  51761872              AB351466     1    26    26
browser |    26  100.0%         10     +  56599595  56599620              AB351466     1    26    26
browser |    26  100.0%         10     +  57016515  57016540              AB351466     1    26    26
browser |    26  100.0%         10     +  62942517  62942542              AB351466     1    26    26
browser |    26  100.0%         10     -  65477959  65477984              AB351466     1    26    26
browser |    26  100.0%         10     -  66562574  66562599              AB351466     1    26    26
browser |    26  100.0%         10     +  70630008  70630033              AB351466     1    26    26
browser |    26  100.0%         10     +  71530001  71530026              AB351466     1    26    26
browser |    26  100.0%         10     +  77789359  77789384              AB351466     1    26    26
browser |    26  100.0%         10     -  78656123  78656148              AB351466     1    26    26
browser |    25  100.0%         10     -  81510709  81510733              AB351466     1    25    26
browser |    25  100.0%         10     -  81669837  81669861              AB351466     1    25    26
browser |    26  100.0%         10     +  81806479  81806504              AB351466     1    26    26
browser |    25  100.0%         10     -  83306065  83306089              AB351466     1    25    26
browser |    26  100.0%         10     -  83511119  83511144              AB351466     1    26    26
browser |    26  100.0%         10     +  85553813  85553838              AB351466     1    26    26
browser |    25  100.0%         10     +  88489600  88489624              AB351466     1    25    26
browser |    26  100.0%         10     -  94202267  94202292              AB351466     1    26    26
browser |    25  100.0%         10     -  96032728  96032752              AB351466     1    25    26
browser |    25  100.0%         10     -  97162647  97162671              AB351466     1    25    26
browser |    26  100.0%         10     +  99177739  99177764              AB351466     1    26    26
browser |    26  100.0%         10     + 104393966 104393991              AB351466     1    26    26
browser |    26  100.0%         10     + 104674183 104674208              AB351466     1    26    26
browser |    26  100.0%         10     + 105015702 105015727              AB351466     1    26    26
browser |    26  100.0%         10     + 107838112 107838137              AB351466     1    26    26
browser |    26  100.0%         10     - 109155413 109155438              AB351466     1    26    26
browser |    26  100.0%         10     + 110534883 110534908              AB351466     1    26    26
browser |    26  100.0%         10     - 113562939 113562964              AB351466     1    26    26
browser |    25  100.0%         10     - 116446501 116446525              AB351466     1    25    26
browser |    26  100.0%         10     + 117909306 117909331              AB351466     1    26    26
browser |    26  100.0%         10     + 121003391 121003416              AB351466     1    26    26
browser |    26  100.0%         10     - 122204109 122204134              AB351466     1    26    26
browser |    26  100.0%         10     + 122344426 122344451              AB351466     1    26    26
browser |    25  100.0%         10     - 122672987 122673011              AB351466     1    25    26
browser |    25  100.0%         10     + 123698003 123698027              AB351466     1    25    26
browser |    26  100.0%         10     + 124414978 124415003              AB351466     1    26    26
browser |    26  100.0%         10     - 124519180 124519205              AB351466     1    26    26
browser |    26  100.0%         10     - 129229025 129229050              AB351466     1    26    26
browser |    26  100.0%         10     + 129763926 129763951              AB351466     1    26    26
browser |    26  100.0%         10     - 130399234 130399259              AB351466     1    26    26
browser |    26  100.0%         11     -   6095827   6095852              AB351466     1    26    26
browser |    26  100.0%         11     -   9662318   9662343              AB351466     1    26    26
browser |    26  100.0%         11     +  10713079  10713104              AB351466     1    26    26
browser |    26  100.0%         11     +  12514689  12514714              AB351466     1    26    26
browser |    25  100.0%         11     +  12748361  12748385              AB351466     1    25    26
browser |    26  100.0%         11     +  15180459  15180484              AB351466     1    26    26
browser |    25  100.0%         11     -  18760792  18760816              AB351466     1    25    26
browser |    26  100.0%         11     -  19517760  19517785              AB351466     1    26    26
browser |    26  100.0%         11     +  20469145  20469170              AB351466     1    26    26
browser |    26  100.0%         11     -  23172918  23172943              AB351466     1    26    26
browser |    25  100.0%         11     -  23194532  23194556              AB351466     1    25    26
browser |    26  100.0%         11     -  27904304  27904329              AB351466     1    26    26
browser |    26  100.0%         11     +  28050062  28050087              AB351466     1    26    26
browser |    25  100.0%         11     -  31401899  31401923              AB351466     1    25    26
browser |    25  100.0%         11     +  38375091  38375115              AB351466     1    25    26
browser |    26  100.0%         11     -  39958887  39958912              AB351466     1    26    26
browser |    26  100.0%         11     +  51331277  51331302              AB351466     1    26    26
browser |    25  100.0%         11     -  54471736  54471760              AB351466     1    25    26
browser |    26  100.0%         11     -  55136098  55136123              AB351466     1    26    26
browser |    26  100.0%         11     +  61314030  61314055              AB351466     1    26    26
browser |    26  100.0%         11     +  63361319  63361344              AB351466     1    26    26
browser |    26  100.0%         11     -  65346945  65346970              AB351466     1    26    26
browser |    26  100.0%         11     -  66842404  66842429              AB351466     1    26    26
browser |    26  100.0%         11     +  74022527  74022552              AB351466     1    26    26
browser |    25  100.0%         11     -  74114855  74114879              AB351466     1    25    26
browser |    26  100.0%         11     +  74777989  74778014              AB351466     1    26    26
browser |    26  100.0%         11     -  79634064  79634089              AB351466     1    26    26
browser |    26  100.0%         11     +  81439133  81439158              AB351466     1    26    26
browser |    26  100.0%         11     -  82226408  82226433              AB351466     1    26    26
browser |    25  100.0%         11     +  84954295  84954319              AB351466     1    25    26
browser |    26  100.0%         11     -  85180731  85180756              AB351466     1    26    26
browser |    26  100.0%         11     +  86739205  86739230              AB351466     1    26    26
browser |    25  100.0%         11     -  88806119  88806143              AB351466     1    25    26
browser |    26  100.0%         11     +  90795282  90795307              AB351466     1    26    26
browser |    26  100.0%         11     -  90855335  90855360              AB351466     1    26    26
browser |    26  100.0%         11     +  91992652  91992677              AB351466     1    26    26
browser |    26  100.0%         11     +  98506856  98506881              AB351466     1    26    26
browser |    26  100.0%         11     -  99605281  99605306              AB351466     1    26    26
browser |    25  100.0%         11     + 100556512 100556536              AB351466     1    25    26
browser |    26  100.0%         11     - 106185662 106185687              AB351466     1    26    26
browser |    26  100.0%         11     + 111076098 111076123              AB351466     1    26    26
browser |    25  100.0%         11     - 111110808 111110832              AB351466     1    25    26
browser |    26  100.0%         11     + 113805788 113805813              AB351466     1    26    26
browser |    26  100.0%         11     - 115650061 115650086              AB351466     1    26    26
browser |    26  100.0%         11     + 116679155 116679180              AB351466     1    26    26
browser |    26  100.0%         11     + 117393450 117393475              AB351466     1    26    26
browser |    25  100.0%         11     + 120214749 120214773              AB351466     1    25    26
browser |    26  100.0%         11     + 120963501 120963526              AB351466     1    26    26
browser |    26  100.0%         12     +   3055136   3055161              AB351466     1    26    26
browser |    26  100.0%         12     -   3385144   3385169              AB351466     1    26    26
browser |    26  100.0%         12     +   6569304   6569329              AB351466     1    26    26
browser |    26  100.0%         12     +   6855795   6855820              AB351466     1    26    26
browser |    26  100.0%         12     -  11157992  11158017              AB351466     1    26    26
browser |    26  100.0%         12     +  17174983  17175008              AB351466     1    26    26
browser |    26  100.0%         12     +  18012572  18012597              AB351466     1    26    26
browser |    26  100.0%         12     -  18329423  18329448              AB351466     1    26    26
browser |    26  100.0%         12     +  19827273  19827298              AB351466     1    26    26
browser |    26  100.0%         12     -  19849810  19849835              AB351466     1    26    26
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browser |    26  100.0%         12     +  24448239  24448264              AB351466     1    26    26
browser |    26  100.0%         12     -  31412483  31412508              AB351466     1    26    26
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browser |    26  100.0%         12     +  40454853  40454878              AB351466     1    26    26
browser |    26  100.0%         12     +  41416270  41416295              AB351466     1    26    26
browser |    26  100.0%         12     -  44816261  44816286              AB351466     1    26    26
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browser |    26  100.0%         12     +  49044335  49044360              AB351466     1    26    26
browser |    25  100.0%         12     -  60758017  60758041              AB351466     1    25    26
browser |    25  100.0%         12     -  61337677  61337701              AB351466     1    25    26
browser |    26  100.0%         12     +  62584382  62584407              AB351466     1    26    26
browser |    26  100.0%         12     -  65078279  65078304              AB351466     1    26    26
browser |    26  100.0%         12     -  65852337  65852362              AB351466     1    26    26
browser |    26  100.0%         12     -  66458137  66458162              AB351466     1    26    26
browser |    25  100.0%         12     -  68672891  68672915              AB351466     1    25    26
browser |    26  100.0%         12     -  70712270  70712295              AB351466     1    26    26
browser |    25  100.0%         12     -  70969120  70969144              AB351466     1    25    26
browser |    26  100.0%         12     +  76794132  76794157              AB351466     1    26    26
browser |    26  100.0%         12     -  79612949  79612974              AB351466     1    26    26
browser |    25  100.0%         12     +  80466832  80466856              AB351466     1    25    26
browser |    26  100.0%         12     -  85452131  85452156              AB351466     1    26    26
browser |    25  100.0%         12     +  93479094  93479118              AB351466     1    25    26
browser |    26  100.0%         12     -  94007618  94007643              AB351466     1    26    26
browser |    25  100.0%         12     -  94239141  94239165              AB351466     1    25    26
browser |    26  100.0%         12     -  96198541  96198566              AB351466     1    26    26
browser |    25  100.0%         12     +  98324255  98324279              AB351466     1    25    26
browser |    25  100.0%         12     - 105270818 105270842              AB351466     1    25    26
browser |    26  100.0%         12     + 109871116 109871141              AB351466     1    26    26
browser |    25  100.0%         12     + 114599806 114599830              AB351466     1    25    26
browser |    26  100.0%         12     + 115524614 115524639              AB351466     1    26    26
browser |    26  100.0%         12     + 118320869 118320894              AB351466     1    26    26
browser |    26  100.0%         12     + 119557288 119557313              AB351466     1    26    26
browser |    26  100.0%         13     +   3667113   3667138              AB351466     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