AB352071
 

Information on mRNA AB352071

Description: Mus musculus non-coding RNA, oocyte_piRNA2887, 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: AB352071
Position: chrX:15597065-15597091

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 |    27  100.0%          X     -  15597065  15597091              AB352071     1    27    27
browser |    27  100.0%          1     +   5635219   5635245              AB352071     1    27    27
browser |    27  100.0%          1     +   5638026   5638052              AB352071     1    27    27
browser |    27  100.0%          1     -   5819129   5819155              AB352071     1    27    27
browser |    27  100.0%          1     +  11052263  11052289              AB352071     1    27    27
browser |    27  100.0%          1     +  16950010  16950036              AB352071     1    27    27
browser |    27  100.0%          1     -  22159253  22159279              AB352071     1    27    27
browser |    27  100.0%          1     +  27436650  27436676              AB352071     1    27    27
browser |    27  100.0%          1     -  27715674  27715700              AB352071     1    27    27
browser |    27  100.0%          1     -  28928144  28928170              AB352071     1    27    27
browser |    27  100.0%          1     -  28930481  28930507              AB352071     1    27    27
browser |    27  100.0%          1     +  32627627  32627653              AB352071     1    27    27
browser |    27  100.0%          1     +  43552814  43552840              AB352071     1    27    27
browser |    27  100.0%          1     +  47995303  47995329              AB352071     1    27    27
browser |    27  100.0%          1     +  47997550  47997576              AB352071     1    27    27
browser |    27  100.0%          1     -  65747321  65747347              AB352071     1    27    27
browser |    27  100.0%          1     -  65854256  65854282              AB352071     1    27    27
browser |    27  100.0%          1     -  71908891  71908917              AB352071     1    27    27
browser |    27  100.0%          1     -  75620055  75620081              AB352071     1    27    27
browser |    27  100.0%          1     -  75979589  75979615              AB352071     1    27    27
browser |    27  100.0%          1     -  75982102  75982128              AB352071     1    27    27
browser |    27  100.0%          1     -  96607745  96607771              AB352071     1    27    27
browser |    27  100.0%          1     +  96894986  96895012              AB352071     1    27    27
browser |    27  100.0%          1     +  96897482  96897508              AB352071     1    27    27
browser |    27  100.0%          1     + 101055944 101055970              AB352071     1    27    27
browser |    27  100.0%          1     - 102077366 102077392              AB352071     1    27    27
browser |    27  100.0%          1     - 102079785 102079811              AB352071     1    27    27
browser |    27  100.0%          1     - 105545859 105545885              AB352071     1    27    27
browser |    27  100.0%          1     - 108064963 108064989              AB352071     1    27    27
browser |    27  100.0%          1     - 108067277 108067303              AB352071     1    27    27
browser |    27  100.0%          1     - 114723448 114723474              AB352071     1    27    27
browser |    27  100.0%          1     - 117416489 117416515              AB352071     1    27    27
browser |    27  100.0%          1     - 118667334 118667360              AB352071     1    27    27
browser |    27  100.0%          1     - 120024223 120024249              AB352071     1    27    27
browser |    27  100.0%          1     + 120489568 120489594              AB352071     1    27    27
browser |    27  100.0%          1     + 140094129 140094155              AB352071     1    27    27
browser |    27  100.0%          1     - 160595063 160595089              AB352071     1    27    27
browser |    27  100.0%          1     + 165408536 165408562              AB352071     1    27    27
browser |    25  100.0%          1     - 184331624 184331648              AB352071     1    25    27
browser |    27  100.0%          1     + 188930898 188930924              AB352071     1    27    27
browser |    27  100.0%          1     + 194951246 194951272              AB352071     1    27    27
browser |    27  100.0%         10     -   7314861   7314887              AB352071     1    27    27
browser |    27  100.0%         10     -   7317389   7317415              AB352071     1    27    27
browser |    27  100.0%         10     +  11130331  11130357              AB352071     1    27    27
browser |    27  100.0%         10     -  18689580  18689606              AB352071     1    27    27
browser |    27  100.0%         10     +  28782299  28782325              AB352071     1    27    27
browser |    27  100.0%         10     -  31684042  31684068              AB352071     1    27    27
browser |    27  100.0%         10     +  51676764  51676790              AB352071     1    27    27
browser |    27  100.0%         10     +  73384435  73384461              AB352071     1    27    27
browser |    27  100.0%         10     +  73386987  73387013              AB352071     1    27    27
browser |    27  100.0%         10     +  73690919  73690945              AB352071     1    27    27
browser |    27  100.0%         10     +  73693220  73693246              AB352071     1    27    27
browser |    27  100.0%         10     +  83251473  83251499              AB352071     1    27    27
browser |    27  100.0%         10     +  83255014  83255040              AB352071     1    27    27
browser |    26  100.0%         10     - 110835883 110835908              AB352071     2    27    27
browser |    27  100.0%         10     - 110838480 110838506              AB352071     1    27    27
browser |    25  100.0%         11     -   6741060   6741084              AB352071     1    25    27
browser |    27  100.0%         11     -   6749826   6749852              AB352071     1    27    27
browser |    27  100.0%         11     -   8887930   8887956              AB352071     1    27    27
browser |    27  100.0%         11     +   8963069   8963095              AB352071     1    27    27
browser |    27  100.0%         11     +   9830027   9830053              AB352071     1    27    27
browser |    27  100.0%         11     -  16594910  16594936              AB352071     1    27    27
browser |    27  100.0%         11     -  22636265  22636291              AB352071     1    27    27
browser |    27  100.0%         11     -  27609352  27609378              AB352071     1    27    27
browser |    27  100.0%         11     -  28002495  28002521              AB352071     1    27    27
browser |    27  100.0%         11     +  29116569  29116595              AB352071     1    27    27
browser |    27  100.0%         11     -  30268467  30268493              AB352071     1    27    27
browser |    27  100.0%         11     -  41245051  41245077              AB352071     1    27    27
browser |    27  100.0%         11     +  58412997  58413023              AB352071     1    27    27
browser |    27  100.0%         11     -  70217271  70217297              AB352071     1    27    27
browser |    25  100.0%         12     -   4837804   4837828              AB352071     1    25    27
browser |    25  100.0%         12     -   4840115   4840139              AB352071     1    25    27
browser |    27  100.0%         12     +  11132703  11132729              AB352071     1    27    27
browser |    27  100.0%         12     +  14835299  14835325              AB352071     1    27    27
browser |    27  100.0%         12     +  27282427  27282453              AB352071     1    27    27
browser |    27  100.0%         12     +  27284957  27284983              AB352071     1    27    27
browser |    27  100.0%         12     -  28515144  28515170              AB352071     1    27    27
browser |    27  100.0%         12     -  36666007  36666033              AB352071     1    27    27
browser |    27  100.0%         12     -  36668221  36668247              AB352071     1    27    27
browser |    27  100.0%         12     +  62622969  62622995              AB352071     1    27    27
browser |    27  100.0%         12     -  65732342  65732368              AB352071     1    27    27
browser |    27  100.0%         12     +  65881263  65881289              AB352071     1    27    27
browser |    27  100.0%         12     +  69160301  69160327              AB352071     1    27    27
browser |    27  100.0%         12     +  72662050  72662076              AB352071     1    27    27
browser |    27  100.0%         12     -  79161117  79161143              AB352071     1    27    27
browser |    27  100.0%         12     - 114490540 114490566              AB352071     1    27    27
browser |    27  100.0%         12     - 115365951 115365977              AB352071     1    27    27
browser |    27  100.0%         13     +   3065949   3065975              AB352071     1    27    27
browser |    27  100.0%         13     +   3068284   3068310              AB352071     1    27    27
browser |    27  100.0%         13     -   3664998   3665024              AB352071     1    27    27
browser |    27  100.0%         13     -   3668519   3668545              AB352071     1    27    27
browser |    27  100.0%         13     +   4493309   4493335              AB352071     1    27    27
browser |    27  100.0%         13     +   8319957   8319983              AB352071     1    27    27
browser |    27  100.0%         13     -  21658512  21658538              AB352071     1    27    27
browser |    27  100.0%         13     -  26285199  26285225              AB352071     1    27    27
browser |    27  100.0%         13     -  30751900  30751926              AB352071     1    27    27
browser |    27  100.0%         13     -  35666925  35666951              AB352071     1    27    27
browser |    27  100.0%         13     -  47651571  47651597              AB352071     1    27    27
browser |    27  100.0%         13     +  60476975  60477001              AB352071     1    27    27
browser |    27  100.0%         13     +  65079927  65079953              AB352071     1    27    27
browser |    27  100.0%         13     +  69979549  69979575              AB352071     1    27    27
browser |    27  100.0%         13     -  70347932  70347958              AB352071     1    27    27
browser |    27  100.0%         13     +  84569426  84569452              AB352071     1    27    27
browser |    27  100.0%         13     +  84571791  84571817              AB352071     1    27    27
browser |    27  100.0%         13     +  84882976  84883002              AB352071     1    27    27
browser |    27  100.0%         13     -  92484589  92484615              AB352071     1    27    27
browser |    27  100.0%         13     -  98482913  98482939              AB352071     1    27    27
browser |    27  100.0%         13     + 106025628 106025654              AB352071     1    27    27
browser |    27  100.0%         13     - 118285787 118285813              AB352071     1    27    27
browser |    27  100.0%         13     + 118288425 118288451              AB352071     1    27    27
browser |    27  100.0%         13     + 119073134 119073160              AB352071     1    27    27
browser |    27  100.0%         14     +   3934845   3934871              AB352071     1    27    27
browser |    27  100.0%         14     +   4400248   4400274              AB352071     1    27    27
browser |    27  100.0%         14     -   8957060   8957086              AB352071     1    27    27
browser |    27  100.0%         14     +  15126058  15126084              AB352071     1    27    27
browser |    27  100.0%         14     +  15684005  15684031              AB352071     1    27    27
browser |    27  100.0%         14     +  16332619  16332645              AB352071     1    27    27
browser |    27  100.0%         14     -  18163847  18163873              AB352071     1    27    27
browser |    27  100.0%         14     -  24360266  24360292              AB352071     1    27    27
browser |    27  100.0%         14     +  46859989  46860015              AB352071     1    27    27
browser |    27  100.0%         14     -  49628296  49628322              AB352071     1    27    27
browser |    27  100.0%         14     +  73963785  73963811              AB352071     1    27    27
browser |    27  100.0%         14     +  77061224  77061250              AB352071     1    27    27
browser |    27  100.0%         14     +  80732067  80732093              AB352071     1    27    27
browser |    27  100.0%         14     +  81921709  81921735              AB352071     1    27    27
browser |    27  100.0%         14     +  84078710  84078736              AB352071     1    27    27
browser |    27  100.0%         14     +  84080986  84081012              AB352071     1    27    27
browser |    27  100.0%         14     -  84590235  84590261              AB352071     1    27    27
browser |    27  100.0%         14     +  87962460  87962486              AB352071     1    27    27
browser |    27  100.0%         14     +  90247203  90247229              AB352071     1    27    27
browser |    27  100.0%         14     +  91101118  91101144              AB352071     1    27    27
browser |    27  100.0%         14     - 104165223 104165249              AB352071     1    27    27
browser |    27  100.0%         14     - 106587833 106587859              AB352071     1    27    27
browser |    27  100.0%         14     - 106590269 106590295              AB352071     1    27    27
browser |    27  100.0%         14     - 113915577 113915603              AB352071     1    27    27
browser |    27  100.0%         14     - 113918117 113918143              AB352071     1    27    27
browser |    27  100.0%         14     + 114425753 114425779              AB352071     1    27    27
browser |    27  100.0%         14     + 114428409 114428435              AB352071     1    27    27
browser |    27  100.0%         14     + 120695183 120695209              AB352071     1    27    27
browser |    27  100.0%         15     +   4589965   4589991              AB352071     1    27    27
browser |    27  100.0%         15     -  15100981  15101007              AB352071     1    27    27
browser |    27  100.0%         15     +  15972287  15972313              AB352071     1    27    27
browser |    27  100.0%         15     +  24396611  24396637              AB352071     1    27    27
browser |    27  100.0%         15     -  29131010  29131036              AB352071     1    27    27
browser |    27  100.0%         15     +  29131723  29131749              AB352071     1    27    27
browser |    27  100.0%         15     +  33814702  33814728              AB352071     1    27    27
browser |    27  100.0%         15     -  33917008  33917034              AB352071     1    27    27
browser |    27  100.0%         15     -  36725335  36725361              AB352071     1    27    27
browser |    27  100.0%         15     +  46949467  46949493              AB352071     1    27    27
browser |    27  100.0%         15     -  57763445  57763471              AB352071     1    27    27
browser |    27  100.0%         15     -  57765698  57765724              AB352071     1    27    27
browser |    27  100.0%         15     -  65917096  65917122              AB352071     1    27    27
browser |    27  100.0%         15     -  65919300  65919326              AB352071     1    27    27
browser |    27  100.0%         15     -  65921585  65921611              AB352071     1    27    27
browser |    27  100.0%         15     -  71082399  71082425              AB352071     1    27    27
browser |    27  100.0%         15     -  71084556  71084582              AB352071     1    27    27
browser |    27  100.0%         15     -  77453696  77453722              AB352071     1    27    27
browser |    27  100.0%         15     -  77455834  77455860              AB352071     1    27    27
browser |    27  100.0%         16     -  21502432  21502458              AB352071     1    27    27
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browser |    27  100.0%         16     +  35620242  35620268              AB352071     1    27    27
browser |    27  100.0%         16     +  48999104  48999130              AB352071     1    27    27
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browser |    27  100.0%         16     -  51248825  51248851              AB352071     1    27    27
browser |    27  100.0%         16     -  82996658  82996684              AB352071     1    27    27
browser |    25  100.0%         16     +  84372096  84372120              AB352071     1    25    27
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browser |    27  100.0%         16     +  88684798  88684824              AB352071     1    27    27
browser |    27  100.0%         17     -  16979722  16979748              AB352071     1    27    27
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browser |    27  100.0%         17     -  18217722  18217748              AB352071     1    27    27
browser |    27  100.0%         17     -  44692045  44692071              AB352071     1    27    27
browser |    27  100.0%         17     -  60854224  60854250              AB352071     1    27    27
browser |    27  100.0%         17     -  61318974  61319000              AB352071     1    27    27
browser |    27  100.0%         17     -  61321586  61321612              AB352071     1    27    27
browser |    27  100.0%         17     +  75891163  75891189              AB352071     1    27    27
browser |    27  100.0%         17     -  81222817  81222843              AB352071     1    27    27
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browser |    27  100.0%         17     +  83057727  83057753              AB352071     1    27    27
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browser |    27  100.0%         17     -  91137727  91137753              AB352071     1    27    27
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browser |    27  100.0%         18     -  16644789  16644815              AB352071     1    27    27
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browser |    27  100.0%         18     -  58583653  58583679              AB352071     1    27    27
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browser |    27  100.0%         18     -  67875596  67875622              AB352071     1    27    27
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browser |    27  100.0%         18     -  84213984  84214010              AB352071     1    27    27
browser |    25  100.0%         18     +  85624851  85624875              AB352071     1    25    27
browser |    27  100.0%         18     +  86348651  86348677              AB352071     1    27    27
browser |    27  100.0%         19     +   9617687   9617713              AB352071     1    27    27
browser |    27  100.0%         19     +  15650522  15650548              AB352071     1    27    27
browser |    27  100.0%         19     -  19130567  19130593              AB352071     1    27    27
browser |    27  100.0%         19     -  19133073  19133099              AB352071     1    27    27
browser |    27  100.0%         19     -  19893820  19893846              AB352071     1    27    27
browser |    27  100.0%         19     +  20672840  20672866              AB352071     1    27    27
browser |    27  100.0%         19     -  25795826  25795852              AB352071     1    27    27
browser |    27  100.0%         19     -  26267700  26267726              AB352071     1    27    27
browser |    27  100.0%         19     +  32992396  32992422              AB352071     1    27    27
browser |    27  100.0%         19     +  51808399  51808425              AB352071     1    27    27
browser |    27  100.0%         19     -  52341561  52341587              AB352071     1    27    27
browser |    27  100.0%         19     +  54297630  54297656              AB352071     1    27    27
browser |    27  100.0%         19     -  54881004  54881030              AB352071     1    27    27
browser |    27  100.0%         19     +  59860785  59860811              AB352071     1    27    27
browser |    27  100.0%         19     +  59863254  59863280              AB352071     1    27    27
browser |    27  100.0%          2     -   8383002   8383028              AB352071     1    27    27
browser |    25  100.0%          2     +   9029637   9029661              AB352071     1    25    27
browser |    25  100.0%          2     +   9032202   9032226              AB352071     1    25    27
browser |    27  100.0%          2     -  16996040  16996066              AB352071     1    27    27
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browser |    27  100.0%          X     - 103741859 103741885              AB352071     1    27    27
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browser |    27  100.0%          X     - 104531902 104531928              AB352071     1    27    27
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browser |    27  100.0%          X     - 107374790 107374816              AB352071     1    27    27
browser |    27  100.0%          X     - 111336434 111336460              AB352071     1    27    27
browser |    27  100.0%          X     - 111338760 111338786              AB352071     1    27    27
browser |    27  100.0%          X     - 113639051 113639077              AB352071     1    27    27
browser |    27  100.0%          X     + 117617862 117617888              AB352071     1    27    27
browser |    27  100.0%          X     + 117620499 117620525              AB352071     1    27    27
browser |    27  100.0%          X     + 118495819 118495845              AB352071     1    27    27
browser |    27  100.0%          X     - 120404133 120404159              AB352071     1    27    27
browser |    27  100.0%          X     + 122477735 122477761              AB352071     1    27    27
browser |    27  100.0%          X     - 125189045 125189071              AB352071     1    27    27
browser |    27  100.0%          X     - 126389516 126389542              AB352071     1    27    27
browser |    27  100.0%          X     + 128900483 128900509              AB352071     1    27    27
browser |    27  100.0%          X     - 132125553 132125579              AB352071     1    27    27
browser |    27  100.0%          X     + 137257483 137257509              AB352071     1    27    27
browser |    27  100.0%          X     - 142255112 142255138              AB352071     1    27    27
browser |    27  100.0%          X     + 143740330 143740356              AB352071     1    27    27
browser |    27  100.0%          X     + 148485981 148486007              AB352071     1    27    27
browser |    27  100.0%          X     + 148487957 148487983              AB352071     1    27    27
browser |    27  100.0%          X     - 166327247 166327273              AB352071     1    27    27
browser |    27  100.0%          Y     -  12616399  12616425              AB352071     1    27    27
browser |    27  100.0%          Y     -  17329172  17329198              AB352071     1    27    27

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