AB350022
 

Information on mRNA AB350022

Description: Mus musculus non-coding RNA, oocyte_piRNA838, 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: AB350022
Position: chr12:56797707-56797731

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     -  56797707  56797731              AB350022     1    25    25
browser |    25  100.0%          1     -   5880392   5880416              AB350022     1    25    25
browser |    25  100.0%          1     +   8065203   8065227              AB350022     1    25    25
browser |    25  100.0%          1     +  18028308  18028332              AB350022     1    25    25
browser |    25  100.0%          1     +  18588338  18588362              AB350022     1    25    25
browser |    25  100.0%          1     +  23341479  23341503              AB350022     1    25    25
browser |    25  100.0%          1     -  26392181  26392205              AB350022     1    25    25
browser |    25  100.0%          1     +  26454330  26454354              AB350022     1    25    25
browser |    25  100.0%          1     +  29695202  29695226              AB350022     1    25    25
browser |    25  100.0%          1     +  34387811  34387835              AB350022     1    25    25
browser |    25  100.0%          1     +  45774560  45774584              AB350022     1    25    25
browser |    25  100.0%          1     +  48129518  48129542              AB350022     1    25    25
browser |    25  100.0%          1     -  48401182  48401206              AB350022     1    25    25
browser |    25  100.0%          1     -  58856655  58856679              AB350022     1    25    25
browser |    25  100.0%          1     -  60769841  60769865              AB350022     1    25    25
browser |    25  100.0%          1     -  62579105  62579129              AB350022     1    25    25
browser |    25  100.0%          1     +  64423514  64423538              AB350022     1    25    25
browser |    25  100.0%          1     -  65005303  65005327              AB350022     1    25    25
browser |    25  100.0%          1     -  66062610  66062634              AB350022     1    25    25
browser |    25  100.0%          1     -  69741161  69741185              AB350022     1    25    25
browser |    25  100.0%          1     -  76753256  76753280              AB350022     1    25    25
browser |    25  100.0%          1     -  81547716  81547740              AB350022     1    25    25
browser |    25  100.0%          1     -  87067198  87067222              AB350022     1    25    25
browser |    25  100.0%          1     + 103517807 103517831              AB350022     1    25    25
browser |    25  100.0%          1     - 104221231 104221255              AB350022     1    25    25
browser |    25  100.0%          1     - 108342423 108342447              AB350022     1    25    25
browser |    25  100.0%          1     + 110258052 110258076              AB350022     1    25    25
browser |    25  100.0%          1     + 112858464 112858488              AB350022     1    25    25
browser |    25  100.0%          1     + 114114293 114114317              AB350022     1    25    25
browser |    25  100.0%          1     - 120502492 120502516              AB350022     1    25    25
browser |    25  100.0%          1     + 126868170 126868194              AB350022     1    25    25
browser |    25  100.0%          1     - 127491834 127491858              AB350022     1    25    25
browser |    25  100.0%          1     - 127823657 127823681              AB350022     1    25    25
browser |    25  100.0%          1     + 130463309 130463333              AB350022     1    25    25
browser |    25  100.0%          1     + 139653857 139653881              AB350022     1    25    25
browser |    25  100.0%          1     + 140964403 140964427              AB350022     1    25    25
browser |    25  100.0%          1     - 141300521 141300545              AB350022     1    25    25
browser |    25  100.0%          1     - 142287741 142287765              AB350022     1    25    25
browser |    25  100.0%          1     - 142516535 142516559              AB350022     1    25    25
browser |    25  100.0%          1     + 148151277 148151301              AB350022     1    25    25
browser |    25  100.0%          1     - 148338312 148338336              AB350022     1    25    25
browser |    25  100.0%          1     - 149387872 149387896              AB350022     1    25    25
browser |    25  100.0%          1     + 152539907 152539931              AB350022     1    25    25
browser |    25  100.0%          1     - 160647359 160647383              AB350022     1    25    25
browser |    25  100.0%          1     + 162669375 162669399              AB350022     1    25    25
browser |    25  100.0%          1     + 169944609 169944633              AB350022     1    25    25
browser |    25  100.0%          1     + 177886874 177886898              AB350022     1    25    25
browser |    25  100.0%          1     + 191840956 191840980              AB350022     1    25    25
browser |    25  100.0%          1     + 195003911 195003935              AB350022     1    25    25
browser |    25  100.0%         10     +  11571279  11571303              AB350022     1    25    25
browser |    25  100.0%         10     -  23753049  23753073              AB350022     1    25    25
browser |    25  100.0%         10     +  25845572  25845596              AB350022     1    25    25
browser |    25  100.0%         10     +  30965925  30965949              AB350022     1    25    25
browser |    25  100.0%         10     +  33764218  33764242              AB350022     1    25    25
browser |    25  100.0%         10     -  55595560  55595584              AB350022     1    25    25
browser |    25  100.0%         10     +  59218914  59218938              AB350022     1    25    25
browser |    25  100.0%         10     -  65790529  65790553              AB350022     1    25    25
browser |    25  100.0%         10     -  66564070  66564094              AB350022     1    25    25
browser |    25  100.0%         10     +  70628513  70628537              AB350022     1    25    25
browser |    25  100.0%         10     +  71528510  71528534              AB350022     1    25    25
browser |    25  100.0%         10     +  77787864  77787888              AB350022     1    25    25
browser |    25  100.0%         10     +  77857475  77857499              AB350022     1    25    25
browser |    25  100.0%         10     -  78657619  78657643              AB350022     1    25    25
browser |    25  100.0%         10     +  84581823  84581847              AB350022     1    25    25
browser |    25  100.0%         10     +  85552318  85552342              AB350022     1    25    25
browser |    25  100.0%         10     +  88488105  88488129              AB350022     1    25    25
browser |    25  100.0%         10     -  90164326  90164350              AB350022     1    25    25
browser |    25  100.0%         10     -  96034223  96034247              AB350022     1    25    25
browser |    25  100.0%         10     -  97164142  97164166              AB350022     1    25    25
browser |    25  100.0%         10     -  99385915  99385939              AB350022     1    25    25
browser |    25  100.0%         10     + 104392471 104392495              AB350022     1    25    25
browser |    25  100.0%         10     - 104659262 104659286              AB350022     1    25    25
browser |    25  100.0%         10     - 105512445 105512469              AB350022     1    25    25
browser |    25  100.0%         10     + 117907811 117907835              AB350022     1    25    25
browser |    25  100.0%         10     - 122674482 122674506              AB350022     1    25    25
browser |    25  100.0%         10     + 124442928 124442952              AB350022     1    25    25
browser |    25  100.0%         10     - 129230521 129230545              AB350022     1    25    25
browser |    25  100.0%         10     - 130400730 130400754              AB350022     1    25    25
browser |    25  100.0%         11     -   6097323   6097347              AB350022     1    25    25
browser |    25  100.0%         11     -  12461200  12461224              AB350022     1    25    25
browser |    25  100.0%         11     +  12513194  12513218              AB350022     1    25    25
browser |    25  100.0%         11     -  12907927  12907951              AB350022     1    25    25
browser |    25  100.0%         11     -  19519256  19519280              AB350022     1    25    25
browser |    25  100.0%         11     -  23174414  23174438              AB350022     1    25    25
browser |    25  100.0%         11     +  28048567  28048591              AB350022     1    25    25
browser |    25  100.0%         11     +  29075832  29075856              AB350022     1    25    25
browser |    25  100.0%         11     -  51559788  51559812              AB350022     1    25    25
browser |    25  100.0%         11     -  54473231  54473255              AB350022     1    25    25
browser |    25  100.0%         11     +  61312535  61312559              AB350022     1    25    25
browser |    25  100.0%         11     +  64684250  64684274              AB350022     1    25    25
browser |    25  100.0%         11     -  65348441  65348465              AB350022     1    25    25
browser |    25  100.0%         11     +  74432251  74432275              AB350022     1    25    25
browser |    25  100.0%         11     +  74776494  74776518              AB350022     1    25    25
browser |    25  100.0%         11     -  88807614  88807638              AB350022     1    25    25
browser |    25  100.0%         11     -  90724358  90724382              AB350022     1    25    25
browser |    25  100.0%         11     + 100555017 100555041              AB350022     1    25    25
browser |    25  100.0%         11     - 105923016 105923040              AB350022     1    25    25
browser |    25  100.0%         11     - 108293868 108293892              AB350022     1    25    25
browser |    25  100.0%         11     + 113804293 113804317              AB350022     1    25    25
browser |    25  100.0%         11     + 116281544 116281568              AB350022     1    25    25
browser |    25  100.0%         11     + 116677660 116677684              AB350022     1    25    25
browser |    25  100.0%         11     + 120213254 120213278              AB350022     1    25    25
browser |    25  100.0%         12     +   3053649   3053673              AB350022     1    25    25
browser |    25  100.0%         12     -   3386640   3386664              AB350022     1    25    25
browser |    25  100.0%         12     +   8454594   8454618              AB350022     1    25    25
browser |    25  100.0%         12     -  44817758  44817782              AB350022     1    25    25
browser |    25  100.0%         12     -  52780819  52780843              AB350022     1    25    25
browser |    24  100.0%         12     -  61339174  61339197              AB350022     1    24    25
browser |    25  100.0%         12     +  62582887  62582911              AB350022     1    25    25
browser |    25  100.0%         12     -  65079775  65079799              AB350022     1    25    25
browser |    25  100.0%         12     +  65681321  65681345              AB350022     1    25    25
browser |    25  100.0%         12     +  68793318  68793342              AB350022     1    25    25
browser |    25  100.0%         12     -  70713766  70713790              AB350022     1    25    25
browser |    25  100.0%         12     -  79614445  79614469              AB350022     1    25    25
browser |    25  100.0%         12     -  82511772  82511796              AB350022     1    25    25
browser |    25  100.0%         12     -  85453627  85453651              AB350022     1    25    25
browser |    25  100.0%         12     +  93477599  93477623              AB350022     1    25    25
browser |    25  100.0%         12     -  94009114  94009138              AB350022     1    25    25
browser |    25  100.0%         12     - 108049469 108049493              AB350022     1    25    25
browser |    25  100.0%         12     + 114598311 114598335              AB350022     1    25    25
browser |    25  100.0%         13     -   4953567   4953591              AB350022     1    25    25
browser |    25  100.0%         13     -   8523585   8523609              AB350022     1    25    25
browser |    25  100.0%         13     +  15607415  15607439              AB350022     1    25    25
browser |    25  100.0%         13     +  26552403  26552427              AB350022     1    25    25
browser |    25  100.0%         13     -  28314216  28314240              AB350022     1    25    25
browser |    25  100.0%         13     +  30555380  30555404              AB350022     1    25    25
browser |    25  100.0%         13     -  31423164  31423188              AB350022     1    25    25
browser |    25  100.0%         13     +  38294991  38295015              AB350022     1    25    25
browser |    25  100.0%         13     +  43432303  43432327              AB350022     1    25    25
browser |    25  100.0%         13     +  44419097  44419121              AB350022     1    25    25
browser |    25  100.0%         13     -  51423731  51423755              AB350022     1    25    25
browser |    25  100.0%         13     +  52140796  52140820              AB350022     1    25    25
browser |    25  100.0%         13     -  52447505  52447529              AB350022     1    25    25
browser |    25  100.0%         13     -  56866519  56866543              AB350022     1    25    25
browser |    25  100.0%         13     -  63310228  63310252              AB350022     1    25    25
browser |    25  100.0%         13     -  63369738  63369762              AB350022     1    25    25
browser |    25  100.0%         13     +  65027336  65027360              AB350022     1    25    25
browser |    25  100.0%         13     +  79712902  79712926              AB350022     1    25    25
browser |    25  100.0%         13     +  86922169  86922193              AB350022     1    25    25
browser |    25  100.0%         13     -  87500951  87500975              AB350022     1    25    25
browser |    25  100.0%         13     +  87705670  87705694              AB350022     1    25    25
browser |    25  100.0%         13     +  94873313  94873337              AB350022     1    25    25
browser |    25  100.0%         13     +  97985850  97985874              AB350022     1    25    25
browser |    25  100.0%         13     +  98220736  98220760              AB350022     1    25    25
browser |    25  100.0%         13     - 100729399 100729423              AB350022     1    25    25
browser |    25  100.0%         13     + 111205717 111205741              AB350022     1    25    25
browser |    25  100.0%         13     + 111637624 111637648              AB350022     1    25    25
browser |    25  100.0%         13     + 113410760 113410784              AB350022     1    25    25
browser |    25  100.0%         13     - 114762691 114762715              AB350022     1    25    25
browser |    25  100.0%         13     + 116027075 116027099              AB350022     1    25    25
browser |    25  100.0%         13     - 116720397 116720421              AB350022     1    25    25
browser |    25  100.0%         13     - 119270673 119270697              AB350022     1    25    25
browser |    25  100.0%         14     +   3457978   3458002              AB350022     1    25    25
browser |    25  100.0%         14     -   6650975   6650999              AB350022     1    25    25
browser |    25  100.0%         14     +  35921953  35921977              AB350022     1    25    25
browser |    25  100.0%         14     -  36956967  36956991              AB350022     1    25    25
browser |    25  100.0%         14     -  42141858  42141882              AB350022     1    25    25
browser |    25  100.0%         14     -  53001176  53001200              AB350022     1    25    25
browser |    25  100.0%         14     -  63885635  63885659              AB350022     1    25    25
browser |    25  100.0%         14     -  64704716  64704740              AB350022     1    25    25
browser |    25  100.0%         14     +  66852510  66852534              AB350022     1    25    25
browser |    25  100.0%         14     +  75664005  75664029              AB350022     1    25    25
browser |    25  100.0%         14     +  78573531  78573555              AB350022     1    25    25
browser |    25  100.0%         14     -  79025926  79025950              AB350022     1    25    25
browser |    25  100.0%         14     -  80035988  80036012              AB350022     1    25    25
browser |    25  100.0%         14     -  80863916  80863940              AB350022     1    25    25
browser |    25  100.0%         14     -  85098407  85098431              AB350022     1    25    25
browser |    25  100.0%         14     +  86829201  86829225              AB350022     1    25    25
browser |    25  100.0%         14     -  88276978  88277002              AB350022     1    25    25
browser |    25  100.0%         14     +  90533432  90533456              AB350022     1    25    25
browser |    25  100.0%         14     +  96522594  96522618              AB350022     1    25    25
browser |    25  100.0%         14     + 100487304 100487328              AB350022     1    25    25
browser |    25  100.0%         14     - 104348093 104348117              AB350022     1    25    25
browser |    25  100.0%         14     + 108408278 108408302              AB350022     1    25    25
browser |    25  100.0%         14     - 112576063 112576087              AB350022     1    25    25
browser |    25  100.0%         14     - 112871006 112871030              AB350022     1    25    25
browser |    25  100.0%         14     + 113257255 113257279              AB350022     1    25    25
browser |    25  100.0%         14     + 113526832 113526856              AB350022     1    25    25
browser |    25  100.0%         14     + 114744563 114744587              AB350022     1    25    25
browser |    25  100.0%         14     + 117417654 117417678              AB350022     1    25    25
browser |    25  100.0%         14     - 118099428 118099452              AB350022     1    25    25
browser |    25  100.0%         14     - 120199407 120199431              AB350022     1    25    25
browser |    25  100.0%         15     -  12061917  12061941              AB350022     1    25    25
browser |    25  100.0%         15     +  17573918  17573942              AB350022     1    25    25
browser |    25  100.0%         15     -  20976848  20976872              AB350022     1    25    25
browser |    25  100.0%         15     -  27292069  27292093              AB350022     1    25    25
browser |    25  100.0%         15     -  27388922  27388946              AB350022     1    25    25
browser |    25  100.0%         15     +  38480319  38480343              AB350022     1    25    25
browser |    25  100.0%         15     +  39037725  39037749              AB350022     1    25    25
browser |    25  100.0%         15     +  43195359  43195383              AB350022     1    25    25
browser |    25  100.0%         15     +  47221266  47221290              AB350022     1    25    25
browser |    25  100.0%         15     +  56040561  56040585              AB350022     1    25    25
browser |    25  100.0%         15     -  74238436  74238460              AB350022     1    25    25
browser |    25  100.0%         15     -  75083327  75083351              AB350022     1    25    25
browser |    25  100.0%         15     -  77785235  77785259              AB350022     1    25    25
browser |    25  100.0%         15     -  82480806  82480830              AB350022     1    25    25
browser |    25  100.0%         15     -  86200399  86200423              AB350022     1    25    25
browser |    25  100.0%         15     -  90526501  90526525              AB350022     1    25    25
browser |    25  100.0%         15     -  92626528  92626552              AB350022     1    25    25
browser |    25  100.0%         15     +  96877251  96877275              AB350022     1    25    25
browser |    25  100.0%         15     -  97453935  97453959              AB350022     1    25    25
browser |    25  100.0%         16     -   4567082   4567106              AB350022     1    25    25
browser |    25  100.0%         16     -   7857707   7857731              AB350022     1    25    25
browser |    25  100.0%         16     +  11499296  11499320              AB350022     1    25    25
browser |    25  100.0%         16     +  12795491  12795515              AB350022     1    25    25
browser |    25  100.0%         16     -  12923439  12923463              AB350022     1    25    25
browser |    25  100.0%         16     -  19861152  19861176              AB350022     1    25    25
browser |    25  100.0%         16     -  20397445  20397469              AB350022     1    25    25
browser |    25  100.0%         16     +  31968188  31968212              AB350022     1    25    25
browser |    25  100.0%         16     +  32399349  32399373              AB350022     1    25    25
browser |    25  100.0%         16     -  33671575  33671599              AB350022     1    25    25
browser |    25  100.0%         16     +  34404005  34404029              AB350022     1    25    25
browser |    25  100.0%         16     -  36119232  36119256              AB350022     1    25    25
browser |    25  100.0%         16     -  36589368  36589392              AB350022     1    25    25
browser |    25  100.0%         16     -  38540545  38540569              AB350022     1    25    25
browser |    25  100.0%         16     +  50731468  50731492              AB350022     1    25    25
browser |    25  100.0%         16     -  52837043  52837067              AB350022     1    25    25
browser |    25  100.0%         16     +  53393092  53393116              AB350022     1    25    25
browser |    25  100.0%         16     -  55500596  55500620              AB350022     1    25    25
browser |    25  100.0%         16     -  58474572  58474596              AB350022     1    25    25
browser |    25  100.0%         16     -  58948098  58948122              AB350022     1    25    25
browser |    25  100.0%         16     -  60751935  60751959              AB350022     1    25    25
browser |    25  100.0%         16     +  66040189  66040213              AB350022     1    25    25
browser |    25  100.0%         16     +  70340673  70340697              AB350022     1    25    25
browser |    25  100.0%         16     -  74574578  74574602              AB350022     1    25    25
browser |    25  100.0%         16     -  78244717  78244741              AB350022     1    25    25
browser |    25  100.0%         16     +  79741361  79741385              AB350022     1    25    25
browser |    25  100.0%         16     -  80562591  80562615              AB350022     1    25    25
browser |    25  100.0%         16     +  80870023  80870047              AB350022     1    25    25
browser |    25  100.0%         16     -  82038694  82038718              AB350022     1    25    25
browser |    25  100.0%         16     +  82381655  82381679              AB350022     1    25    25
browser |    25  100.0%         16     +  83158922  83158946              AB350022     1    25    25
browser |    25  100.0%         16     -  88593362  88593386              AB350022     1    25    25
browser |    25  100.0%         16     +  89241124  89241148              AB350022     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