AB350211
 

Information on mRNA AB350211

Description: Mus musculus non-coding RNA, oocyte_piRNA1027, 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: AB350211
Position: chr12:56795380-56795399

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 |    20  100.0%         12     +  56795380  56795399              AB350211     1    20    20
browser |    20  100.0%          1     -   6242262   6242281              AB350211     1    20    20
browser |    20  100.0%          1     -   8070283   8070302              AB350211     1    20    20
browser |    20  100.0%          1     -   8232718   8232737              AB350211     1    20    20
browser |    20  100.0%          1     +  10800834  10800853              AB350211     1    20    20
browser |    20  100.0%          1     +  11958092  11958111              AB350211     1    20    20
browser |    20  100.0%          1     +  12017592  12017611              AB350211     1    20    20
browser |    20  100.0%          1     -  16814796  16814815              AB350211     1    20    20
browser |    20  100.0%          1     -  18590670  18590689              AB350211     1    20    20
browser |    20  100.0%          1     -  21654375  21654394              AB350211     1    20    20
browser |    20  100.0%          1     -  23344666  23344685              AB350211     1    20    20
browser |    20  100.0%          1     +  26388999  26389018              AB350211     1    20    20
browser |    20  100.0%          1     -  26459411  26459430              AB350211     1    20    20
browser |    20  100.0%          1     +  26510199  26510218              AB350211     1    20    20
browser |    20  100.0%          1     -  27225560  27225579              AB350211     1    20    20
browser |    20  100.0%          1     +  29982553  29982572              AB350211     1    20    20
browser |    20  100.0%          1     -  34389676  34389695              AB350211     1    20    20
browser |    20  100.0%          1     -  34957509  34957528              AB350211     1    20    20
browser |    20  100.0%          1     -  35833890  35833909              AB350211     1    20    20
browser |    20  100.0%          1     +  37318634  37318653              AB350211     1    20    20
browser |    20  100.0%          1     -  38747271  38747290              AB350211     1    20    20
browser |    20  100.0%          1     -  40740849  40740868              AB350211     1    20    20
browser |    20  100.0%          1     -  45777746  45777765              AB350211     1    20    20
browser |    20  100.0%          1     +  47263342  47263361              AB350211     1    20    20
browser |    20  100.0%          1     -  48132681  48132700              AB350211     1    20    20
browser |    20  100.0%          1     +  48394241  48394260              AB350211     1    20    20
browser |    20  100.0%          1     +  53169531  53169550              AB350211     1    20    20
browser |    20  100.0%          1     +  58363270  58363289              AB350211     1    20    20
browser |    20  100.0%          1     +  64218093  64218112              AB350211     1    20    20
browser |    20  100.0%          1     +  67791343  67791362              AB350211     1    20    20
browser |    20  100.0%          1     +  74693349  74693368              AB350211     1    20    20
browser |    20  100.0%          1     +  76750748  76750767              AB350211     1    20    20
browser |    20  100.0%          1     +  81542639  81542658              AB350211     1    20    20
browser |    20  100.0%          1     -  82482951  82482970              AB350211     1    20    20
browser |    20  100.0%          1     +  84974357  84974376              AB350211     1    20    20
browser |    20  100.0%          1     +  87062120  87062139              AB350211     1    20    20
browser |    20  100.0%          1     -  87394217  87394236              AB350211     1    20    20
browser |    20  100.0%          1     -  89130173  89130192              AB350211     1    20    20
browser |    20  100.0%          1     +  91399696  91399715              AB350211     1    20    20
browser |    20  100.0%          1     -  97108185  97108204              AB350211     1    20    20
browser |    20  100.0%          1     + 101906626 101906645              AB350211     1    20    20
browser |    20  100.0%          1     - 102965728 102965747              AB350211     1    20    20
browser |    20  100.0%          1     + 103133658 103133677              AB350211     1    20    20
browser |    20  100.0%          1     - 103520986 103521005              AB350211     1    20    20
browser |    20  100.0%          1     + 104218048 104218067              AB350211     1    20    20
browser |    20  100.0%          1     + 107967287 107967306              AB350211     1    20    20
browser |    20  100.0%          1     + 108337345 108337364              AB350211     1    20    20
browser |    20  100.0%          1     + 109057160 109057179              AB350211     1    20    20
browser |    20  100.0%          1     - 109547466 109547485              AB350211     1    20    20
browser |    20  100.0%          1     - 110261238 110261257              AB350211     1    20    20
browser |    20  100.0%          1     + 110866093 110866112              AB350211     1    20    20
browser |    20  100.0%          1     + 111182118 111182137              AB350211     1    20    20
browser |    20  100.0%          1     - 111637436 111637455              AB350211     1    20    20
browser |    20  100.0%          1     + 112192831 112192850              AB350211     1    20    20
browser |    20  100.0%          1     + 112492783 112492802              AB350211     1    20    20
browser |    20  100.0%          1     - 112862429 112862448              AB350211     1    20    20
browser |    20  100.0%          1     - 112950145 112950164              AB350211     1    20    20
browser |    20  100.0%          1     - 114117454 114117473              AB350211     1    20    20
browser |    20  100.0%          1     + 115813853 115813872              AB350211     1    20    20
browser |    20  100.0%          1     + 116576763 116576782              AB350211     1    20    20
browser |    20  100.0%          1     - 125250929 125250948              AB350211     1    20    20
browser |    20  100.0%          1     - 148365676 148365695              AB350211     1    20    20
browser |    20  100.0%          1     - 149463648 149463667              AB350211     1    20    20
browser |    20  100.0%          1     - 152543094 152543113              AB350211     1    20    20
browser |    20  100.0%          1     + 159798088 159798107              AB350211     1    20    20
browser |    20  100.0%          1     + 160644201 160644220              AB350211     1    20    20
browser |    20  100.0%          1     - 162674458 162674477              AB350211     1    20    20
browser |    20  100.0%          1     + 163296818 163296837              AB350211     1    20    20
browser |    20  100.0%          1     + 166591461 166591480              AB350211     1    20    20
browser |    20  100.0%          1     - 169375701 169375720              AB350211     1    20    20
browser |    20  100.0%          1     - 172096531 172096550              AB350211     1    20    20
browser |    20  100.0%          1     + 174870306 174870325              AB350211     1    20    20
browser |    20  100.0%          1     + 176371388 176371407              AB350211     1    20    20
browser |    20  100.0%          1     - 177891927 177891946              AB350211     1    20    20
browser |    20  100.0%          1     - 181326295 181326314              AB350211     1    20    20
browser |    20  100.0%          1     - 191844119 191844138              AB350211     1    20    20
browser |    20  100.0%          1     - 195008990 195009009              AB350211     1    20    20
browser |    20  100.0%         10     +   3267091   3267110              AB350211     1    20    20
browser |    20  100.0%         10     +   3551683   3551702              AB350211     1    20    20
browser |    20  100.0%         10     -   8481382   8481401              AB350211     1    20    20
browser |    20  100.0%         10     -   9726765   9726784              AB350211     1    20    20
browser |    20  100.0%         10     -  11576360  11576379              AB350211     1    20    20
browser |    20  100.0%         10     +  19415398  19415417              AB350211     1    20    20
browser |    20  100.0%         10     -  19676492  19676511              AB350211     1    20    20
browser |    20  100.0%         10     -  21091684  21091703              AB350211     1    20    20
browser |    20  100.0%         10     +  21518971  21518990              AB350211     1    20    20
browser |    20  100.0%         10     +  22399874  22399893              AB350211     1    20    20
browser |    20  100.0%         10     +  22559917  22559936              AB350211     1    20    20
browser |    20  100.0%         10     +  23747972  23747991              AB350211     1    20    20
browser |    20  100.0%         10     -  24566714  24566733              AB350211     1    20    20
browser |    20  100.0%         10     +  24978196  24978215              AB350211     1    20    20
browser |    20  100.0%         10     -  25848425  25848444              AB350211     1    20    20
browser |    20  100.0%         10     -  30696323  30696342              AB350211     1    20    20
browser |    20  100.0%         10     -  30971009  30971028              AB350211     1    20    20
browser |    20  100.0%         10     -  31630096  31630115              AB350211     1    20    20
browser |    20  100.0%         10     -  32814397  32814416              AB350211     1    20    20
browser |    20  100.0%         10     +  34618575  34618594              AB350211     1    20    20
browser |    20  100.0%         10     -  41722874  41722893              AB350211     1    20    20
browser |    20  100.0%         10     -  50370801  50370820              AB350211     1    20    20
browser |    20  100.0%         10     -  51763245  51763264              AB350211     1    20    20
browser |    20  100.0%         10     -  54468831  54468850              AB350211     1    20    20
browser |    20  100.0%         10     +  55592379  55592398              AB350211     1    20    20
browser |    20  100.0%         10     -  56603182  56603201              AB350211     1    20    20
browser |    20  100.0%         10     +  65475446  65475465              AB350211     1    20    20
browser |    20  100.0%         10     +  65787350  65787369              AB350211     1    20    20
browser |    20  100.0%         10     +  66558996  66559015              AB350211     1    20    20
browser |    20  100.0%         10     +  78653045  78653064              AB350211     1    20    20
browser |    20  100.0%         10     -  80815913  80815932              AB350211     1    20    20
browser |    20  100.0%         10     +  83302488  83302507              AB350211     1    20    20
browser |    20  100.0%         10     -  83627695  83627714              AB350211     1    20    20
browser |    20  100.0%         10     -  84584986  84585005              AB350211     1    20    20
browser |    20  100.0%         10     -  85555787  85555806              AB350211     1    20    20
browser |    20  100.0%         10     +  85605044  85605063              AB350211     1    20    20
browser |    20  100.0%         10     -  88493168  88493187              AB350211     1    20    20
browser |    20  100.0%         10     -  88803289  88803308              AB350211     1    20    20
browser |    20  100.0%         10     +  90161222  90161241              AB350211     1    20    20
browser |    20  100.0%         10     +  94199189  94199208              AB350211     1    20    20
browser |    20  100.0%         10     +  95993860  95993879              AB350211     1    20    20
browser |    20  100.0%         10     +  96029146  96029165              AB350211     1    20    20
browser |    20  100.0%         10     +  97157174  97157193              AB350211     1    20    20
browser |    20  100.0%         10     -  99181323  99181342              AB350211     1    20    20
browser |    20  100.0%         10     - 100418859 100418878              AB350211     1    20    20
browser |    20  100.0%         10     - 104397550 104397569              AB350211     1    20    20
browser |    20  100.0%         10     + 104656104 104656123              AB350211     1    20    20
browser |    20  100.0%         10     - 104677771 104677790              AB350211     1    20    20
browser |    20  100.0%         10     + 105509263 105509282              AB350211     1    20    20
browser |    20  100.0%         10     + 109151830 109151849              AB350211     1    20    20
browser |    20  100.0%         10     - 111893495 111893514              AB350211     1    20    20
browser |    20  100.0%         10     - 117911615 117911634              AB350211     1    20    20
browser |    20  100.0%         10     - 121004412 121004431              AB350211     1    20    20
browser |    20  100.0%         10     + 122140290 122140309              AB350211     1    20    20
browser |    20  100.0%         10     + 122202716 122202735              AB350211     1    20    20
browser |    20  100.0%         10     + 122669516 122669535              AB350211     1    20    20
browser |    20  100.0%         10     - 124418567 124418586              AB350211     1    20    20
browser |    20  100.0%         10     - 124446073 124446092              AB350211     1    20    20
browser |    20  100.0%         10     + 124517106 124517125              AB350211     1    20    20
browser |    20  100.0%         10     + 129225444 129225463              AB350211     1    20    20
browser |    20  100.0%         10     - 129764763 129764782              AB350211     1    20    20
browser |    20  100.0%         10     + 130396763 130396782              AB350211     1    20    20
browser |    20  100.0%         11     +   6092244   6092263              AB350211     1    20    20
browser |    20  100.0%         11     -   6485020   6485039              AB350211     1    20    20
browser |    20  100.0%         11     +   7526441   7526460              AB350211     1    20    20
browser |    20  100.0%         11     +   9658739   9658758              AB350211     1    20    20
browser |    20  100.0%         11     -  10716665  10716684              AB350211     1    20    20
browser |    20  100.0%         11     +  12458042  12458061              AB350211     1    20    20
browser |    20  100.0%         11     -  12518277  12518296              AB350211     1    20    20
browser |    20  100.0%         11     +  12904769  12904788              AB350211     1    20    20
browser |    20  100.0%         11     -  15184046  15184065              AB350211     1    20    20
browser |    20  100.0%         11     -  15837049  15837068              AB350211     1    20    20
browser |    20  100.0%         11     +  18757210  18757229              AB350211     1    20    20
browser |    20  100.0%         11     +  19516929  19516948              AB350211     1    20    20
browser |    20  100.0%         11     +  19739479  19739498              AB350211     1    20    20
browser |    20  100.0%         11     +  22286006  22286025              AB350211     1    20    20
browser |    20  100.0%         11     -  22532237  22532256              AB350211     1    20    20
browser |    20  100.0%         11     +  23169336  23169355              AB350211     1    20    20
browser |    20  100.0%         11     +  27901832  27901851              AB350211     1    20    20
browser |    20  100.0%         11     -  28053646  28053665              AB350211     1    20    20
browser |    20  100.0%         11     -  29079019  29079038              AB350211     1    20    20
browser |    20  100.0%         11     -  43553895  43553914              AB350211     1    20    20
browser |    20  100.0%         11     -  51332115  51332134              AB350211     1    20    20
browser |    20  100.0%         11     +  51556606  51556625              AB350211     1    20    20
browser |    20  100.0%         11     +  54468154  54468173              AB350211     1    20    20
browser |    20  100.0%         11     -  63364906  63364925              AB350211     1    20    20
browser |    20  100.0%         11     -  64687435  64687454              AB350211     1    20    20
browser |    20  100.0%         11     -  74026111  74026130              AB350211     1    20    20
browser |    20  100.0%         11     +  74111273  74111292              AB350211     1    20    20
browser |    20  100.0%         11     -  74435414  74435433              AB350211     1    20    20
browser |    20  100.0%         11     -  74781577  74781596              AB350211     1    20    20
browser |    20  100.0%         11     +  79124373  79124392              AB350211     1    20    20
browser |    20  100.0%         11     -  81442721  81442740              AB350211     1    20    20
browser |    20  100.0%         11     +  82225577  82225596              AB350211     1    20    20
browser |    20  100.0%         11     +  85177150  85177169              AB350211     1    20    20
browser |    20  100.0%         11     -  86740226  86740245              AB350211     1    20    20
browser |    20  100.0%         11     +  88802542  88802561              AB350211     1    20    20
browser |    20  100.0%         11     +  90721201  90721220              AB350211     1    20    20
browser |    20  100.0%         11     -  90798312  90798331              AB350211     1    20    20
browser |    20  100.0%         11     +  90851754  90851773              AB350211     1    20    20
browser |    20  100.0%         11     -  91996239  91996258              AB350211     1    20    20
browser |    20  100.0%         11     -  98510444  98510463              AB350211     1    20    20
browser |    20  100.0%         11     +  99604284  99604303              AB350211     1    20    20
browser |    20  100.0%         11     - 100559596 100559615              AB350211     1    20    20
browser |    20  100.0%         11     + 105919835 105919854              AB350211     1    20    20
browser |    20  100.0%         11     + 106184270 106184289              AB350211     1    20    20
browser |    20  100.0%         11     + 108290833 108290852              AB350211     1    20    20
browser |    20  100.0%         11     - 108545240 108545259              AB350211     1    20    20
browser |    20  100.0%         11     - 109914448 109914467              AB350211     1    20    20
browser |    20  100.0%         11     - 111079686 111079705              AB350211     1    20    20
browser |    20  100.0%         11     + 111107226 111107245              AB350211     1    20    20
browser |    20  100.0%         11     - 113809376 113809395              AB350211     1    20    20
browser |    20  100.0%         11     + 115646479 115646498              AB350211     1    20    20
browser |    20  100.0%         11     - 116284732 116284751              AB350211     1    20    20
browser |    20  100.0%         11     - 116682742 116682761              AB350211     1    20    20
browser |    20  100.0%         11     - 117395028 117395047              AB350211     1    20    20
browser |    20  100.0%         11     - 120218336 120218355              AB350211     1    20    20
browser |    20  100.0%         11     - 120964899 120964918              AB350211     1    20    20
browser |    20  100.0%         12     -   3058721   3058740              AB350211     1    20    20
browser |    20  100.0%         12     +   3084476   3084495              AB350211     1    20    20
browser |    20  100.0%         12     -   3112494   3112513              AB350211     1    20    20
browser |    20  100.0%         12     +   3381561   3381580              AB350211     1    20    20
browser |    20  100.0%         12     -   6572892   6572911              AB350211     1    20    20
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browser |    20  100.0%         12     -  17178570  17178589              AB350211     1    20    20
browser |    20  100.0%         12     +  19308994  19309013              AB350211     1    20    20
browser |    20  100.0%         12     -  19830854  19830873              AB350211     1    20    20
browser |    20  100.0%         12     -  24451823  24451842              AB350211     1    20    20
browser |    20  100.0%         12     -  24745331  24745350              AB350211     1    20    20
browser |    20  100.0%         12     -  25644330  25644349              AB350211     1    20    20
browser |    20  100.0%         12     +  31408904  31408923              AB350211     1    20    20
browser |    20  100.0%         12     -  32081601  32081620              AB350211     1    20    20
browser |    20  100.0%         12     -  32649801  32649820              AB350211     1    20    20
browser |    20  100.0%         12     -  32955679  32955698              AB350211     1    20    20
browser |    20  100.0%         12     -  39485474  39485493              AB350211     1    20    20
browser |    20  100.0%         12     -  40458442  40458461              AB350211     1    20    20
browser |    20  100.0%         12     -  41419858  41419877              AB350211     1    20    20
browser |    20  100.0%         12     -  48585313  48585332              AB350211     1    20    20
browser |    20  100.0%         12     +  49267879  49267898              AB350211     1    20    20
browser |    20  100.0%         12     +  52777638  52777657              AB350211     1    20    20
browser |    20  100.0%         12     +  60754441  60754460              AB350211     1    20    20
browser |    20  100.0%         12     +  61336660  61336679              AB350211     1    20    20
browser |    20  100.0%         12     +  68669309  68669328              AB350211     1    20    20
browser |    20  100.0%         12     +  70708688  70708707              AB350211     1    20    20
browser |    20  100.0%         12     +  70965538  70965557              AB350211     1    20    20
browser |    20  100.0%         12     +  73358545  73358564              AB350211     1    20    20
browser |    20  100.0%         12     +  79609367  79609386              AB350211     1    20    20
browser |    20  100.0%         12     -  80470419  80470438              AB350211     1    20    20
browser |    20  100.0%         12     -  81633849  81633868              AB350211     1    20    20
browser |    20  100.0%         12     +  85448553  85448572              AB350211     1    20    20
browser |    20  100.0%         12     -  88482631  88482650              AB350211     1    20    20
browser |    20  100.0%         12     -  90737719  90737738              AB350211     1    20    20
browser |    20  100.0%         12     -  93482679  93482698              AB350211     1    20    20
browser |    20  100.0%         12     +  94236062  94236081              AB350211     1    20    20
browser |    20  100.0%         12     +  96197710  96197729              AB350211     1    20    20
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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