AB352442
 

Information on mRNA AB352442

Description: Mus musculus non-coding RNA, oocyte_piRNA3258, 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: AB352442
Position: chr12:56796260-56796284

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     -  56796260  56796284              AB352442     1    25    25
browser |    25  100.0%          1     -   5878945   5878969              AB352442     1    25    25
browser |    25  100.0%          1     -   6504974   6504998              AB352442     1    25    25
browser |    25  100.0%          1     +  13623515  13623539              AB352442     1    25    25
browser |    25  100.0%          1     +  16811161  16811185              AB352442     1    25    25
browser |    25  100.0%          1     +  18029755  18029779              AB352442     1    25    25
browser |    25  100.0%          1     +  19695369  19695393              AB352442     1    25    25
browser |    25  100.0%          1     -  22069838  22069862              AB352442     1    25    25
browser |    25  100.0%          1     +  26455777  26455801              AB352442     1    25    25
browser |    25  100.0%          1     +  35830254  35830278              AB352442     1    25    25
browser |    25  100.0%          1     +  40739771  40739795              AB352442     1    25    25
browser |    25  100.0%          1     -  48399735  48399759              AB352442     1    25    25
browser |    25  100.0%          1     +  55820208  55820232              AB352442     1    25    25
browser |    25  100.0%          1     +  56814061  56814085              AB352442     1    25    25
browser |    25  100.0%          1     -  60768394  60768418              AB352442     1    25    25
browser |    25  100.0%          1     +  64424961  64424985              AB352442     1    25    25
browser |    25  100.0%          1     -  66061163  66061187              AB352442     1    25    25
browser |    25  100.0%          1     -  67794968  67794992              AB352442     1    25    25
browser |    25  100.0%          1     +  70278943  70278967              AB352442     1    25    25
browser |    25  100.0%          1     -  72169080  72169104              AB352442     1    25    25
browser |    25  100.0%          1     -  81546269  81546293              AB352442     1    25    25
browser |    25  100.0%          1     -  87065751  87065775              AB352442     1    25    25
browser |    25  100.0%          1     +  87390581  87390605              AB352442     1    25    25
browser |    25  100.0%          1     -  91403324  91403348              AB352442     1    25    25
browser |    25  100.0%          1     +  93886991  93887015              AB352442     1    25    25
browser |    25  100.0%          1     +  95625579  95625603              AB352442     1    25    25
browser |    25  100.0%          1     +  97103190  97103214              AB352442     1    25    25
browser |    25  100.0%          1     + 102962092 102962116              AB352442     1    25    25
browser |    25  100.0%          1     - 108340976 108341000              AB352442     1    25    25
browser |    25  100.0%          1     - 111185745 111185769              AB352442     1    25    25
browser |    25  100.0%          1     + 111633802 111633826              AB352442     1    25    25
browser |    25  100.0%          1     - 112196454 112196478              AB352442     1    25    25
browser |    25  100.0%          1     - 116580393 116580417              AB352442     1    25    25
browser |    25  100.0%          1     + 125247297 125247321              AB352442     1    25    25
browser |    25  100.0%          1     - 125275494 125275518              AB352442     1    25    25
browser |    25  100.0%          1     - 127490387 127490411              AB352442     1    25    25
browser |    25  100.0%          1     - 137203293 137203317              AB352442     1    25    25
browser |    25  100.0%          1     + 140747252 140747276              AB352442     1    25    25
browser |    25  100.0%          1     + 144262609 144262633              AB352442     1    25    25
browser |    25  100.0%          1     + 145999376 145999400              AB352442     1    25    25
browser |    25  100.0%          1     - 146162026 146162050              AB352442     1    25    25
browser |    25  100.0%          1     - 146277329 146277353              AB352442     1    25    25
browser |    25  100.0%          1     - 149386425 149386449              AB352442     1    25    25
browser |    25  100.0%          1     - 149394425 149394449              AB352442     1    25    25
browser |    25  100.0%          1     - 154779086 154779110              AB352442     1    25    25
browser |    25  100.0%          1     - 159801719 159801743              AB352442     1    25    25
browser |    25  100.0%          1     + 162670822 162670846              AB352442     1    25    25
browser |    25  100.0%          1     - 166594592 166594616              AB352442     1    25    25
browser |    25  100.0%          1     + 169372069 169372093              AB352442     1    25    25
browser |    25  100.0%          1     + 169946056 169946080              AB352442     1    25    25
browser |    25  100.0%          1     - 174873124 174873148              AB352442     1    25    25
browser |    25  100.0%          1     + 178004374 178004398              AB352442     1    25    25
browser |    25  100.0%          1     + 179724269 179724293              AB352442     1    25    25
browser |    25  100.0%          1     + 181323163 181323187              AB352442     1    25    25
browser |    25  100.0%          1     + 183298982 183299006              AB352442     1    25    25
browser |    25  100.0%          1     + 195005358 195005382              AB352442     1    25    25
browser |    25  100.0%         10     -   3555315   3555339              AB352442     1    25    25
browser |    25  100.0%         10     +   8477747   8477771              AB352442     1    25    25
browser |    25  100.0%         10     +  11572726  11572750              AB352442     1    25    25
browser |    25  100.0%         10     +  19675598  19675622              AB352442     1    25    25
browser |    25  100.0%         10     -  19890755  19890779              AB352442     1    25    25
browser |    25  100.0%         10     -  22403492  22403516              AB352442     1    25    25
browser |    25  100.0%         10     -  22563547  22563571              AB352442     1    25    25
browser |    25  100.0%         10     -  23751602  23751626              AB352442     1    25    25
browser |    25  100.0%         10     -  24979674  24979698              AB352442     1    25    25
browser |    25  100.0%         10     +  41719241  41719265              AB352442     1    25    25
browser |    25  100.0%         10     +  56599547  56599571              AB352442     1    25    25
browser |    25  100.0%         10     +  57016467  57016491              AB352442     1    25    25
browser |    25  100.0%         10     -  65478008  65478032              AB352442     1    25    25
browser |    25  100.0%         10     +  70629960  70629984              AB352442     1    25    25
browser |    25  100.0%         10     +  71529953  71529977              AB352442     1    25    25
browser |    25  100.0%         10     +  77789311  77789335              AB352442     1    25    25
browser |    25  100.0%         10     -  81510757  81510781              AB352442     1    25    25
browser |    25  100.0%         10     -  83306113  83306137              AB352442     1    25    25
browser |    25  100.0%         10     -  83511168  83511192              AB352442     1    25    25
browser |    25  100.0%         10     +  88489552  88489576              AB352442     1    25    25
browser |    25  100.0%         10     -  94202316  94202340              AB352442     1    25    25
browser |    25  100.0%         10     -  97162695  97162719              AB352442     1    25    25
browser |    25  100.0%         10     +  99177691  99177715              AB352442     1    25    25
browser |    25  100.0%         10     + 107838064 107838088              AB352442     1    25    25
browser |    25  100.0%         10     - 109155462 109155486              AB352442     1    25    25
browser |    25  100.0%         10     + 110534835 110534859              AB352442     1    25    25
browser |    25  100.0%         10     + 121003343 121003367              AB352442     1    25    25
browser |    25  100.0%         10     - 122673035 122673059              AB352442     1    25    25
browser |    25  100.0%         10     + 123697955 123697979              AB352442     1    25    25
browser |    25  100.0%         10     + 124414930 124414954              AB352442     1    25    25
browser |    25  100.0%         10     - 124519229 124519253              AB352442     1    25    25
browser |    25  100.0%         10     - 129229074 129229098              AB352442     1    25    25
browser |    25  100.0%         11     -   6095876   6095900              AB352442     1    25    25
browser |    25  100.0%         11     -   7530068   7530092              AB352442     1    25    25
browser |    25  100.0%         11     +  12748313  12748337              AB352442     1    25    25
browser |    25  100.0%         11     +  15180411  15180435              AB352442     1    25    25
browser |    25  100.0%         11     -  18760840  18760864              AB352442     1    25    25
browser |    25  100.0%         11     -  19517809  19517833              AB352442     1    25    25
browser |    25  100.0%         11     -  23172967  23172991              AB352442     1    25    25
browser |    25  100.0%         11     -  23194580  23194604              AB352442     1    25    25
browser |    25  100.0%         11     +  27086318  27086342              AB352442     1    25    25
browser |    25  100.0%         11     -  31401947  31401971              AB352442     1    25    25
browser |    25  100.0%         11     +  38375043  38375067              AB352442     1    25    25
browser |    25  100.0%         11     -  39958936  39958960              AB352442     1    25    25
browser |    25  100.0%         11     +  51331229  51331253              AB352442     1    25    25
browser |    25  100.0%         11     -  54471784  54471808              AB352442     1    25    25
browser |    25  100.0%         11     -  55136147  55136171              AB352442     1    25    25
browser |    25  100.0%         11     +  61313982  61314006              AB352442     1    25    25
browser |    25  100.0%         11     +  63361271  63361295              AB352442     1    25    25
browser |    25  100.0%         11     -  65346994  65347018              AB352442     1    25    25
browser |    25  100.0%         11     -  66842453  66842477              AB352442     1    25    25
browser |    25  100.0%         11     +  74777941  74777965              AB352442     1    25    25
browser |    25  100.0%         11     +  81439085  81439109              AB352442     1    25    25
browser |    25  100.0%         11     -  82226457  82226481              AB352442     1    25    25
browser |    25  100.0%         11     +  84954247  84954271              AB352442     1    25    25
browser |    25  100.0%         11     -  85180780  85180804              AB352442     1    25    25
browser |    25  100.0%         11     +  86739157  86739181              AB352442     1    25    25
browser |    25  100.0%         11     -  88806167  88806191              AB352442     1    25    25
browser |    25  100.0%         11     -  90855384  90855408              AB352442     1    25    25
browser |    25  100.0%         11     +  91992604  91992628              AB352442     1    25    25
browser |    25  100.0%         11     -  99605330  99605354              AB352442     1    25    25
browser |    25  100.0%         11     - 106185711 106185735              AB352442     1    25    25
browser |    25  100.0%         11     + 111076050 111076074              AB352442     1    25    25
browser |    25  100.0%         11     - 111110856 111110880              AB352442     1    25    25
browser |    25  100.0%         11     + 113805740 113805764              AB352442     1    25    25
browser |    25  100.0%         11     - 115650110 115650134              AB352442     1    25    25
browser |    25  100.0%         11     + 116679107 116679131              AB352442     1    25    25
browser |    25  100.0%         11     + 117393402 117393426              AB352442     1    25    25
browser |    25  100.0%         11     + 120963453 120963477              AB352442     1    25    25
browser |    23  100.0%         12     -   3085549   3085571              AB352442     3    25    25
browser |    25  100.0%         12     -   3385193   3385217              AB352442     1    25    25
browser |    25  100.0%         12     -  14648542  14648566              AB352442     1    25    25
browser |    25  100.0%         12     +  17174935  17174959              AB352442     1    25    25
browser |    25  100.0%         12     -  19312624  19312648              AB352442     1    25    25
browser |    25  100.0%         12     +  24448191  24448215              AB352442     1    25    25
browser |    25  100.0%         12     -  31412532  31412556              AB352442     1    25    25
browser |    25  100.0%         12     +  40454805  40454829              AB352442     1    25    25
browser |    25  100.0%         12     +  41416222  41416246              AB352442     1    25    25
browser |    25  100.0%         12     +  48581677  48581701              AB352442     1    25    25
browser |    25  100.0%         12     +  49044287  49044311              AB352442     1    25    25
browser |    25  100.0%         12     +  59489879  59489903              AB352442     1    25    25
browser |    25  100.0%         12     -  60758065  60758089              AB352442     1    25    25
browser |    25  100.0%         12     -  61337725  61337749              AB352442     1    25    25
browser |    25  100.0%         12     -  65078328  65078352              AB352442     1    25    25
browser |    25  100.0%         12     -  70712319  70712343              AB352442     1    25    25
browser |    25  100.0%         12     -  70969168  70969192              AB352442     1    25    25
browser |    25  100.0%         12     -  79612998  79613022              AB352442     1    25    25
browser |    25  100.0%         12     +  80466784  80466808              AB352442     1    25    25
browser |    25  100.0%         12     +  93479046  93479070              AB352442     1    25    25
browser |    25  100.0%         12     -  94007667  94007691              AB352442     1    25    25
browser |    25  100.0%         12     -  94239189  94239213              AB352442     1    25    25
browser |    25  100.0%         12     +  98324207  98324231              AB352442     1    25    25
browser |    25  100.0%         12     - 105270866 105270890              AB352442     1    25    25
browser |    25  100.0%         12     + 109871068 109871092              AB352442     1    25    25
browser |    25  100.0%         12     + 119557240 119557264              AB352442     1    25    25
browser |    25  100.0%         13     +   5330744   5330768              AB352442     1    25    25
browser |    25  100.0%         13     -   8003561   8003585              AB352442     1    25    25
browser |    25  100.0%         13     -  10943591  10943615              AB352442     1    25    25
browser |    25  100.0%         13     +  11518677  11518701              AB352442     1    25    25
browser |    25  100.0%         13     +  15608862  15608886              AB352442     1    25    25
browser |    25  100.0%         13     -  19182420  19182444              AB352442     1    25    25
browser |    25  100.0%         13     -  21818363  21818387              AB352442     1    25    25
browser |    25  100.0%         13     +  22301880  22301904              AB352442     1    25    25
browser |    25  100.0%         13     -  23827318  23827342              AB352442     1    25    25
browser |    25  100.0%         13     +  30556827  30556851              AB352442     1    25    25
browser |    25  100.0%         13     +  32537250  32537274              AB352442     1    25    25
browser |    25  100.0%         13     +  33624339  33624363              AB352442     1    25    25
browser |    25  100.0%         13     +  34048700  34048724              AB352442     1    25    25
browser |    25  100.0%         13     -  34355171  34355195              AB352442     1    25    25
browser |    25  100.0%         13     +  37223432  37223456              AB352442     1    25    25
browser |    25  100.0%         13     +  43433750  43433774              AB352442     1    25    25
browser |    25  100.0%         13     +  45167306  45167330              AB352442     1    25    25
browser |    25  100.0%         13     -  46534040  46534064              AB352442     1    25    25
browser |    25  100.0%         13     -  50887112  50887136              AB352442     1    25    25
browser |    25  100.0%         13     -  52540496  52540520              AB352442     1    25    25
browser |    25  100.0%         13     -  56865072  56865096              AB352442     1    25    25
browser |    25  100.0%         13     -  60173802  60173826              AB352442     1    25    25
browser |    25  100.0%         13     -  60348892  60348916              AB352442     1    25    25
browser |    25  100.0%         13     -  62625218  62625242              AB352442     1    25    25
browser |    25  100.0%         13     -  63308782  63308806              AB352442     1    25    25
browser |    25  100.0%         13     +  65028783  65028807              AB352442     1    25    25
browser |    25  100.0%         13     +  66162816  66162840              AB352442     1    25    25
browser |    25  100.0%         13     +  66379743  66379767              AB352442     1    25    25
browser |    25  100.0%         13     -  77380544  77380568              AB352442     1    25    25
browser |    25  100.0%         13     -  77820629  77820653              AB352442     1    25    25
browser |    25  100.0%         13     +  79714349  79714373              AB352442     1    25    25
browser |    25  100.0%         13     +  83569830  83569854              AB352442     1    25    25
browser |    25  100.0%         13     -  87216378  87216402              AB352442     1    25    25
browser |    25  100.0%         13     +  98222183  98222207              AB352442     1    25    25
browser |    25  100.0%         13     -  99271702  99271726              AB352442     1    25    25
browser |    25  100.0%         13     + 102966358 102966382              AB352442     1    25    25
browser |    25  100.0%         13     + 104069336 104069360              AB352442     1    25    25
browser |    25  100.0%         13     - 111835167 111835191              AB352442     1    25    25
browser |    25  100.0%         13     + 116028522 116028546              AB352442     1    25    25
browser |    25  100.0%         13     + 116104417 116104441              AB352442     1    25    25
browser |    25  100.0%         13     + 117435100 117435124              AB352442     1    25    25
browser |    25  100.0%         13     - 119269226 119269250              AB352442     1    25    25
browser |    25  100.0%         13     + 120688877 120688901              AB352442     1    25    25
browser |    25  100.0%         14     +   3459425   3459449              AB352442     1    25    25
browser |    25  100.0%         14     -   6649528   6649552              AB352442     1    25    25
browser |    25  100.0%         14     -   8133889   8133913              AB352442     1    25    25
browser |    25  100.0%         14     -  12738266  12738290              AB352442     1    25    25
browser |    25  100.0%         14     +  13340946  13340970              AB352442     1    25    25
browser |    25  100.0%         14     +  14770252  14770276              AB352442     1    25    25
browser |    25  100.0%         14     +  19593958  19593982              AB352442     1    25    25
browser |    25  100.0%         14     +  20332736  20332760              AB352442     1    25    25
browser |    25  100.0%         14     +  21413313  21413337              AB352442     1    25    25
browser |    25  100.0%         14     -  32119612  32119636              AB352442     1    25    25
browser |    25  100.0%         14     +  35616544  35616568              AB352442     1    25    25
browser |    25  100.0%         14     +  35923400  35923424              AB352442     1    25    25
browser |    25  100.0%         14     -  37345865  37345889              AB352442     1    25    25
browser |    25  100.0%         14     +  38179747  38179771              AB352442     1    25    25
browser |    25  100.0%         14     -  41183941  41183965              AB352442     1    25    25
browser |    25  100.0%         14     -  42140411  42140435              AB352442     1    25    25
browser |    25  100.0%         14     +  42600244  42600268              AB352442     1    25    25
browser |    25  100.0%         14     -  52999729  52999753              AB352442     1    25    25
browser |    25  100.0%         14     +  58292718  58292742              AB352442     1    25    25
browser |    25  100.0%         14     -  62881862  62881886              AB352442     1    25    25
browser |    25  100.0%         14     -  63884188  63884212              AB352442     1    25    25
browser |    25  100.0%         14     -  68248668  68248692              AB352442     1    25    25
browser |    25  100.0%         14     -  80034541  80034565              AB352442     1    25    25
browser |    25  100.0%         14     +  82418348  82418372              AB352442     1    25    25
browser |    25  100.0%         14     -  85096960  85096984              AB352442     1    25    25
browser |    25  100.0%         14     -  85760247  85760271              AB352442     1    25    25
browser |    25  100.0%         14     +  86830648  86830672              AB352442     1    25    25
browser |    25  100.0%         14     -  88275531  88275555              AB352442     1    25    25
browser |    25  100.0%         14     +  90534879  90534903              AB352442     1    25    25
browser |    25  100.0%         14     -  90924999  90925023              AB352442     1    25    25
browser |    25  100.0%         14     -  95803315  95803339              AB352442     1    25    25
browser |    25  100.0%         14     +  96524041  96524065              AB352442     1    25    25
browser |    25  100.0%         14     + 100488751 100488775              AB352442     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