AB349257
 

Information on mRNA AB349257

Description: Mus musculus non-coding RNA, oocyte_piRNA73, 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: AB349257
Position: chr12:56797602-56797626

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     -  56797602  56797626              AB349257     1    25    25
browser |    25  100.0%          1     -   5880287   5880311              AB349257     1    25    25
browser |    25  100.0%          1     -   6506316   6506340              AB349257     1    25    25
browser |    25  100.0%          1     +   8065308   8065332              AB349257     1    25    25
browser |    25  100.0%          1     +   8227749   8227773              AB349257     1    25    25
browser |    25  100.0%          1     -   8731327   8731351              AB349257     1    25    25
browser |    25  100.0%          1     +   8858783   8858807              AB349257     1    25    25
browser |    25  100.0%          1     -  10805803  10805827              AB349257     1    25    25
browser |    25  100.0%          1     -  12019627  12019651              AB349257     1    25    25
browser |    25  100.0%          1     +  13622173  13622197              AB349257     1    25    25
browser |    25  100.0%          1     +  16809819  16809843              AB349257     1    25    25
browser |    25  100.0%          1     +  18028413  18028437              AB349257     1    25    25
browser |    25  100.0%          1     +  18588443  18588467              AB349257     1    25    25
browser |    25  100.0%          1     +  19694027  19694051              AB349257     1    25    25
browser |    25  100.0%          1     -  22071180  22071204              AB349257     1    25    25
browser |    25  100.0%          1     -  26392076  26392100              AB349257     1    25    25
browser |    25  100.0%          1     +  26454435  26454459              AB349257     1    25    25
browser |    25  100.0%          1     -  26513892  26513916              AB349257     1    25    25
browser |    25  100.0%          1     +  29695307  29695331              AB349257     1    25    25
browser |    25  100.0%          1     -  29987022  29987046              AB349257     1    25    25
browser |    25  100.0%          1     +  34387916  34387940              AB349257     1    25    25
browser |    25  100.0%          1     +  35828912  35828936              AB349257     1    25    25
browser |    25  100.0%          1     +  38745301  38745325              AB349257     1    25    25
browser |    25  100.0%          1     +  40738592  40738616              AB349257     1    25    25
browser |    25  100.0%          1     -  48401077  48401101              AB349257     1    25    25
browser |    25  100.0%          1     -  53172567  53172591              AB349257     1    25    25
browser |    25  100.0%          1     -  58368242  58368266              AB349257     1    25    25
browser |    25  100.0%          1     -  58856550  58856574              AB349257     1    25    25
browser |    25  100.0%          1     -  72170423  72170447              AB349257     1    25    25
browser |    25  100.0%          1     -  74698318  74698342              AB349257     1    25    25
browser |    25  100.0%          1     +  79916126  79916150              AB349257     1    25    25
browser |    25  100.0%          1     -  81547611  81547635              AB349257     1    25    25
browser |    25  100.0%          1     +  82480162  82480186              AB349257     1    25    25
browser |    25  100.0%          1     -  83209215  83209239              AB349257     1    25    25
browser |    25  100.0%          1     -  87067093  87067117              AB349257     1    25    25
browser |    25  100.0%          1     +  89128167  89128191              AB349257     1    25    25
browser |    25  100.0%          1     -  91404666  91404690              AB349257     1    25    25
browser |    25  100.0%          1     +  93885649  93885673              AB349257     1    25    25
browser |    25  100.0%          1     +  95624237  95624261              AB349257     1    25    25
browser |    25  100.0%          1     +  97101848  97101872              AB349257     1    25    25
browser |    25  100.0%          1     -  98529863  98529887              AB349257     1    25    25
browser |    25  100.0%          1     - 101911601 101911625              AB349257     1    25    25
browser |    25  100.0%          1     + 102960750 102960774              AB349257     1    25    25
browser |    25  100.0%          1     - 103138630 103138654              AB349257     1    25    25
browser |    25  100.0%          1     + 103517912 103517936              AB349257     1    25    25
browser |    25  100.0%          1     - 109060177 109060201              AB349257     1    25    25
browser |    25  100.0%          1     + 109542492 109542516              AB349257     1    25    25
browser |    25  100.0%          1     - 111187087 111187111              AB349257     1    25    25
browser |    25  100.0%          1     + 111632460 111632484              AB349257     1    25    25
browser |    25  100.0%          1     - 112197807 112197831              AB349257     1    25    25
browser |    25  100.0%          1     + 112858569 112858593              AB349257     1    25    25
browser |    25  100.0%          1     + 112945167 112945191              AB349257     1    25    25
browser |    25  100.0%          1     + 114114374 114114398              AB349257     1    25    25
browser |    25  100.0%          1     - 115816928 115816952              AB349257     1    25    25
browser |    25  100.0%          1     - 116581735 116581759              AB349257     1    25    25
browser |    25  100.0%          1     - 117635393 117635417              AB349257     1    25    25
browser |    25  100.0%          1     - 120502411 120502435              AB349257     1    25    25
browser |    25  100.0%          1     + 125245955 125245979              AB349257     1    25    25
browser |    25  100.0%          1     - 125276836 125276860              AB349257     1    25    25
browser |    25  100.0%          1     + 126353133 126353157              AB349257     1    25    25
browser |    25  100.0%          1     - 127491729 127491753              AB349257     1    25    25
browser |    25  100.0%          1     + 130463414 130463438              AB349257     1    25    25
browser |    25  100.0%          1     + 139653962 139653986              AB349257     1    25    25
browser |    25  100.0%          1     - 159803061 159803085              AB349257     1    25    25
browser |    25  100.0%          1     - 160647278 160647302              AB349257     1    25    25
browser |    25  100.0%          1     - 166595934 166595958              AB349257     1    25    25
browser |    25  100.0%          1     + 169944714 169944738              AB349257     1    25    25
browser |    25  100.0%          1     - 174874466 174874490              AB349257     1    25    25
browser |    25  100.0%          1     - 176376360 176376384              AB349257     1    25    25
browser |    25  100.0%          1     + 178003032 178003056              AB349257     1    25    25
browser |    25  100.0%          1     + 179722927 179722951              AB349257     1    25    25
browser |    25  100.0%          1     - 181096817 181096841              AB349257     1    25    25
browser |    25  100.0%          1     + 181321821 181321845              AB349257     1    25    25
browser |    25  100.0%          1     + 183297639 183297663              AB349257     1    25    25
browser |    25  100.0%          1     + 191841037 191841061              AB349257     1    25    25
browser |    25  100.0%          1     + 195004016 195004040              AB349257     1    25    25
browser |    25  100.0%         10     -   3556657   3556681              AB349257     1    25    25
browser |    25  100.0%         10     +   8476405   8476429              AB349257     1    25    25
browser |    25  100.0%         10     +  11571384  11571408              AB349257     1    25    25
browser |    25  100.0%         10     -  19420370  19420394              AB349257     1    25    25
browser |    25  100.0%         10     -  19892097  19892121              AB349257     1    25    25
browser |    25  100.0%         10     +  21088604  21088628              AB349257     1    25    25
browser |    25  100.0%         10     -  21523943  21523967              AB349257     1    25    25
browser |    25  100.0%         10     -  22404835  22404859              AB349257     1    25    25
browser |    25  100.0%         10     -  22564889  22564913              AB349257     1    25    25
browser |    25  100.0%         10     -  23752944  23752968              AB349257     1    25    25
browser |    25  100.0%         10     -  24981016  24981040              AB349257     1    25    25
browser |    25  100.0%         10     +  25845677  25845701              AB349257     1    25    25
browser |    25  100.0%         10     +  30358749  30358773              AB349257     1    25    25
browser |    25  100.0%         10     +  30691345  30691369              AB349257     1    25    25
browser |    25  100.0%         10     +  31359972  31359996              AB349257     1    25    25
browser |    25  100.0%         10     +  33764299  33764323              AB349257     1    25    25
browser |    25  100.0%         10     -  34616769  34616793              AB349257     1    25    25
browser |    25  100.0%         10     -  34623547  34623571              AB349257     1    25    25
browser |    25  100.0%         10     +  41717899  41717923              AB349257     1    25    25
browser |    25  100.0%         10     -  45434828  45434852              AB349257     1    25    25
browser |    25  100.0%         10     +  51760457  51760481              AB349257     1    25    25
browser |    25  100.0%         10     +  56598205  56598229              AB349257     1    25    25
browser |    25  100.0%         10     +  57015125  57015149              AB349257     1    25    25
browser |    25  100.0%         10     +  62941127  62941151              AB349257     1    25    25
browser |    25  100.0%         10     -  65479350  65479374              AB349257     1    25    25
browser |    25  100.0%         10     -  66563965  66563989              AB349257     1    25    25
browser |    25  100.0%         10     +  71528615  71528639              AB349257     1    25    25
browser |    25  100.0%         10     +  77857556  77857580              AB349257     1    25    25
browser |    25  100.0%         10     -  78657514  78657538              AB349257     1    25    25
browser |    25  100.0%         10     -  81512098  81512122              AB349257     1    25    25
browser |    25  100.0%         10     -  81671226  81671250              AB349257     1    25    25
browser |    25  100.0%         10     +  81805089  81805113              AB349257     1    25    25
browser |    25  100.0%         10     -  83307455  83307479              AB349257     1    25    25
browser |    25  100.0%         10     -  83512510  83512534              AB349257     1    25    25
browser |    25  100.0%         10     +  83624667  83624691              AB349257     1    25    25
browser |    25  100.0%         10     +  84581904  84581928              AB349257     1    25    25
browser |    25  100.0%         10     +  85552423  85552447              AB349257     1    25    25
browser |    25  100.0%         10     +  86979843  86979867              AB349257     1    25    25
browser |    25  100.0%         10     +  88488210  88488234              AB349257     1    25    25
browser |    25  100.0%         10     -  90164245  90164269              AB349257     1    25    25
browser |    25  100.0%         10     -  94203658  94203682              AB349257     1    25    25
browser |    25  100.0%         10     -  96034118  96034142              AB349257     1    25    25
browser |    25  100.0%         10     -  97164037  97164061              AB349257     1    25    25
browser |    25  100.0%         10     +  99176349  99176373              AB349257     1    25    25
browser |    25  100.0%         10     -  99385810  99385834              AB349257     1    25    25
browser |    25  100.0%         10     + 104392576 104392600              AB349257     1    25    25
browser |    25  100.0%         10     + 104672793 104672817              AB349257     1    25    25
browser |    25  100.0%         10     + 105014312 105014336              AB349257     1    25    25
browser |    25  100.0%         10     - 113564330 113564354              AB349257     1    25    25
browser |    25  100.0%         10     - 116447891 116447915              AB349257     1    25    25
browser |    25  100.0%         10     - 122205500 122205524              AB349257     1    25    25
browser |    25  100.0%         10     + 122343047 122343071              AB349257     1    25    25
browser |    25  100.0%         10     - 122674377 122674401              AB349257     1    25    25
browser |    25  100.0%         10     + 123696614 123696638              AB349257     1    25    25
browser |    25  100.0%         10     + 124413588 124413612              AB349257     1    25    25
browser |    25  100.0%         10     + 124443009 124443033              AB349257     1    25    25
browser |    25  100.0%         10     - 124520571 124520595              AB349257     1    25    25
browser |    25  100.0%         10     + 129051028 129051052              AB349257     1    25    25
browser |    25  100.0%         10     - 129230416 129230440              AB349257     1    25    25
browser |    25  100.0%         10     + 129762536 129762560              AB349257     1    25    25
browser |    25  100.0%         10     - 130400625 130400649              AB349257     1    25    25
browser |    25  100.0%         11     -   7531410   7531434              AB349257     1    25    25
browser |    25  100.0%         11     -   9663709   9663733              AB349257     1    25    25
browser |    25  100.0%         11     +  10711689  10711713              AB349257     1    25    25
browser |    25  100.0%         11     -  12461119  12461143              AB349257     1    25    25
browser |    25  100.0%         11     +  12513299  12513323              AB349257     1    25    25
browser |    25  100.0%         11     +  12746970  12746994              AB349257     1    25    25
browser |    25  100.0%         11     -  12907846  12907870              AB349257     1    25    25
browser |    25  100.0%         11     -  14848428  14848452              AB349257     1    25    25
browser |    25  100.0%         11     +  15179069  15179093              AB349257     1    25    25
browser |    25  100.0%         11     -  15236584  15236608              AB349257     1    25    25
browser |    25  100.0%         11     -  18762182  18762206              AB349257     1    25    25
browser |    25  100.0%         11     -  19519151  19519175              AB349257     1    25    25
browser |    25  100.0%         11     +  20467755  20467779              AB349257     1    25    25
browser |    25  100.0%         11     -  22289083  22289107              AB349257     1    25    25
browser |    25  100.0%         11     +  22529157  22529181              AB349257     1    25    25
browser |    25  100.0%         11     -  23174309  23174333              AB349257     1    25    25
browser |    25  100.0%         11     +  26506899  26506923              AB349257     1    25    25
browser |    25  100.0%         11     +  28048672  28048696              AB349257     1    25    25
browser |    25  100.0%         11     +  38373701  38373725              AB349257     1    25    25
browser |    25  100.0%         11     +  51329887  51329911              AB349257     1    25    25
browser |    25  100.0%         11     -  54473126  54473150              AB349257     1    25    25
browser |    25  100.0%         11     -  55137489  55137513              AB349257     1    25    25
browser |    25  100.0%         11     +  61312640  61312664              AB349257     1    25    25
browser |    25  100.0%         11     +  63359929  63359953              AB349257     1    25    25
browser |    25  100.0%         11     +  64684355  64684379              AB349257     1    25    25
browser |    25  100.0%         11     -  65348336  65348360              AB349257     1    25    25
browser |    25  100.0%         11     -  66843795  66843819              AB349257     1    25    25
browser |    25  100.0%         11     +  74021137  74021161              AB349257     1    25    25
browser |    25  100.0%         11     -  74116205  74116229              AB349257     1    25    25
browser |    25  100.0%         11     +  74432332  74432356              AB349257     1    25    25
browser |    25  100.0%         11     +  81437743  81437767              AB349257     1    25    25
browser |    25  100.0%         11     -  82227799  82227823              AB349257     1    25    25
browser |    25  100.0%         11     +  84952905  84952929              AB349257     1    25    25
browser |    25  100.0%         11     -  85182122  85182146              AB349257     1    25    25
browser |    25  100.0%         11     +  86737815  86737839              AB349257     1    25    25
browser |    25  100.0%         11     -  88807509  88807533              AB349257     1    25    25
browser |    25  100.0%         11     -  90201893  90201917              AB349257     1    25    25
browser |    25  100.0%         11     -  90724277  90724301              AB349257     1    25    25
browser |    25  100.0%         11     +  90793892  90793916              AB349257     1    25    25
browser |    25  100.0%         11     -  90856726  90856750              AB349257     1    25    25
browser |    25  100.0%         11     +  91991262  91991286              AB349257     1    25    25
browser |    25  100.0%         11     +  98505466  98505490              AB349257     1    25    25
browser |    25  100.0%         11     -  99606672  99606696              AB349257     1    25    25
browser |    25  100.0%         11     + 100555122 100555146              AB349257     1    25    25
browser |    25  100.0%         11     - 106187053 106187077              AB349257     1    25    25
browser |    25  100.0%         11     - 108293787 108293811              AB349257     1    25    25
browser |    25  100.0%         11     + 108542160 108542184              AB349257     1    25    25
browser |    25  100.0%         11     + 111074708 111074732              AB349257     1    25    25
browser |    25  100.0%         11     - 111112198 111112222              AB349257     1    25    25
browser |    25  100.0%         11     + 113804398 113804422              AB349257     1    25    25
browser |    25  100.0%         11     - 115651452 115651476              AB349257     1    25    25
browser |    25  100.0%         11     + 116677765 116677789              AB349257     1    25    25
browser |    25  100.0%         11     + 117392060 117392084              AB349257     1    25    25
browser |    25  100.0%         11     + 120213359 120213383              AB349257     1    25    25
browser |    25  100.0%         11     + 120962111 120962135              AB349257     1    25    25
browser |    25  100.0%         12     +   3053754   3053778              AB349257     1    25    25
browser |    25  100.0%         12     -   3386535   3386559              AB349257     1    25    25
browser |    25  100.0%         12     +   6567914   6567938              AB349257     1    25    25
browser |    25  100.0%         12     +   6854405   6854429              AB349257     1    25    25
browser |    25  100.0%         12     +   8454699   8454723              AB349257     1    25    25
browser |    25  100.0%         12     -  11159383  11159407              AB349257     1    25    25
browser |    25  100.0%         12     +  14492245  14492269              AB349257     1    25    25
browser |    25  100.0%         12     -  14649883  14649907              AB349257     1    25    25
browser |    25  100.0%         12     +  17173593  17173617              AB349257     1    25    25
browser |    25  100.0%         12     +  18011182  18011206              AB349257     1    25    25
browser |    25  100.0%         12     +  18181620  18181644              AB349257     1    25    25
browser |    25  100.0%         12     -  18330815  18330839              AB349257     1    25    25
browser |    25  100.0%         12     -  19313966  19313990              AB349257     1    25    25
browser |    25  100.0%         12     +  24446849  24446873              AB349257     1    25    25
browser |    25  100.0%         12     -  31413874  31413898              AB349257     1    25    25
browser |    25  100.0%         12     +  32079373  32079397              AB349257     1    25    25
browser |    25  100.0%         12     +  39483199  39483223              AB349257     1    25    25
browser |    25  100.0%         12     +  40453463  40453487              AB349257     1    25    25
browser |    25  100.0%         12     +  41414880  41414904              AB349257     1    25    25
browser |    25  100.0%         12     -  44817653  44817677              AB349257     1    25    25
browser |    25  100.0%         12     +  48580335  48580359              AB349257     1    25    25
browser |    25  100.0%         12     +  49042945  49042969              AB349257     1    25    25
browser |    25  100.0%         12     -  60759408  60759432              AB349257     1    25    25
browser |    25  100.0%         12     -  65079670  65079694              AB349257     1    25    25
browser |    25  100.0%         12     -  65853728  65853752              AB349257     1    25    25
browser |    25  100.0%         12     -  66459528  66459552              AB349257     1    25    25
browser |    25  100.0%         12     -  68674281  68674305              AB349257     1    25    25
browser |    25  100.0%         12     -  70970510  70970534              AB349257     1    25    25
browser |    25  100.0%         12     -  79614340  79614364              AB349257     1    25    25
browser |    25  100.0%         12     +  80465442  80465466              AB349257     1    25    25
browser |    25  100.0%         12     -  82511691  82511715              AB349257     1    25    25
browser |    25  100.0%         12     -  85453522  85453546              AB349257     1    25    25
browser |    25  100.0%         12     +  93477704  93477728              AB349257     1    25    25
browser |    25  100.0%         12     -  94009009  94009033              AB349257     1    25    25
browser |    25  100.0%         12     -  94240531  94240555              AB349257     1    25    25
browser |    25  100.0%         12     -  96199932  96199956              AB349257     1    25    25
browser |    25  100.0%         12     +  98322865  98322889              AB349257     1    25    25
browser |    25  100.0%         12     - 105272208 105272232              AB349257     1    25    25
browser |    25  100.0%         12     - 108049388 108049412              AB349257     1    25    25
browser |    25  100.0%         12     + 109869726 109869750              AB349257     1    25    25
browser |    25  100.0%         12     + 111355983 111356007              AB349257     1    25    25
browser |    25  100.0%         12     - 113163267 113163291              AB349257     1    25    25
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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