AB351887
 

Information on mRNA AB351887

Description: Mus musculus non-coding RNA, oocyte_piRNA2703, 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: AB351887
Position: chr12:56795550-56795575

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 |    26  100.0%         12     -  56795550  56795575              AB351887     1    26    26
browser |    26  100.0%          1     -   5875484   5875509              AB351887     1    26    26
browser |    26  100.0%          1     -   6501514   6501539              AB351887     1    26    26
browser |    26  100.0%          1     +  19698828  19698853              AB351887     1    26    26
browser |    26  100.0%          1     +  23344489  23344514              AB351887     1    26    26
browser |    26  100.0%          1     -  26510369  26510394              AB351887     1    26    26
browser |    26  100.0%          1     +  27225384  27225409              AB351887     1    26    26
browser |    26  100.0%          1     +  34389500  34389525              AB351887     1    26    26
browser |    26  100.0%          1     +  38747095  38747120              AB351887     1    26    26
browser |    26  100.0%          1     +  45777569  45777594              AB351887     1    26    26
browser |    26  100.0%          1     +  48132504  48132529              AB351887     1    26    26
browser |    26  100.0%          1     -  53169702  53169727              AB351887     1    26    26
browser |    26  100.0%          1     +  56817520  56817545              AB351887     1    26    26
browser |    26  100.0%          1     -  58363440  58363465              AB351887     1    26    26
browser |    26  100.0%          1     -  58851750  58851775              AB351887     1    26    26
browser |    26  100.0%          1     +  58973432  58973457              AB351887     1    26    26
browser |    26  100.0%          1     -  60764934  60764959              AB351887     1    26    26
browser |    26  100.0%          1     +  64428420  64428445              AB351887     1    26    26
browser |    26  100.0%          1     -  65000396  65000421              AB351887     1    26    26
browser |    26  100.0%          1     -  66057707  66057732              AB351887     1    26    26
browser |    26  100.0%          1     -  67791513  67791538              AB351887     1    26    26
browser |    26  100.0%          1     -  74693519  74693544              AB351887     1    26    26
browser |    26  100.0%          1     +  79920927  79920952              AB351887     1    26    26
browser |    26  100.0%          1     +  82482775  82482800              AB351887     1    26    26
browser |    26  100.0%          1     -  84974527  84974552              AB351887     1    26    26
browser |    26  100.0%          1     +  89129997  89130022              AB351887     1    26    26
browser |    26  100.0%          1     -  91399867  91399892              AB351887     1    26    26
browser |    26  100.0%          1     - 103133828 103133853              AB351887     1    26    26
browser |    26  100.0%          1     - 107967457 107967482              AB351887     1    26    26
browser |    26  100.0%          1     - 108337516 108337541              AB351887     1    26    26
browser |    26  100.0%          1     - 111182288 111182313              AB351887     1    26    26
browser |    26  100.0%          1     + 125250753 125250778              AB351887     1    26    26
browser |    26  100.0%          1     - 125274784 125274809              AB351887     1    26    26
browser |    26  100.0%          1     + 126356447 126356472              AB351887     1    26    26
browser |    26  100.0%          1     + 126871173 126871198              AB351887     1    26    26
browser |    26  100.0%          1     - 127486927 127486952              AB351887     1    26    26
browser |    26  100.0%          1     + 130466026 130466051              AB351887     1    26    26
browser |    26  100.0%          1     + 139656866 139656891              AB351887     1    26    26
browser |    26  100.0%          1     - 142284952 142284977              AB351887     1    26    26
browser |    26  100.0%          1     - 142513549 142513574              AB351887     1    26    26
browser |    26  100.0%          1     - 144731356 144731381              AB351887     1    26    26
browser |    26  100.0%          1     - 148045263 148045288              AB351887     1    26    26
browser |    26  100.0%          1     + 148154286 148154311              AB351887     1    26    26
browser |    26  100.0%          1     + 148365500 148365525              AB351887     1    26    26
browser |    26  100.0%          1     + 149275158 149275183              AB351887     1    26    26
browser |    26  100.0%          1     + 149463472 149463497              AB351887     1    26    26
browser |    26  100.0%          1     - 154775628 154775653              AB351887     1    26    26
browser |    26  100.0%          1     + 162674281 162674306              AB351887     1    26    26
browser |    26  100.0%          1     - 174870476 174870501              AB351887     1    26    26
browser |    26  100.0%          1     + 177891750 177891775              AB351887     1    26    26
browser |    26  100.0%         10     -  21519141  21519166              AB351887     1    26    26
browser |    26  100.0%         10     -  22560087  22560112              AB351887     1    26    26
browser |    26  100.0%         10     +  31629920  31629945              AB351887     1    26    26
browser |    26  100.0%         10     +  33766092  33766117              AB351887     1    26    26
browser |    26  100.0%         10     +  41722698  41722723              AB351887     1    26    26
browser |    26  100.0%         10     -  45431923  45431948              AB351887     1    26    26
browser |    26  100.0%         10     +  51763069  51763094              AB351887     1    26    26
browser |    26  100.0%         10     +  54468655  54468680              AB351887     1    26    26
browser |    26  100.0%         10     -  55592550  55592575              AB351887     1    26    26
browser |    26  100.0%         10     +  57019926  57019951              AB351887     1    26    26
browser |    26  100.0%         10     +  59221923  59221948              AB351887     1    26    26
browser |    26  100.0%         10     -  66559166  66559191              AB351887     1    26    26
browser |    26  100.0%         10     +  77792770  77792795              AB351887     1    26    26
browser |    26  100.0%         10     +  77860460  77860485              AB351887     1    26    26
browser |    26  100.0%         10     -  94199360  94199385              AB351887     1    26    26
browser |    26  100.0%         10     +  99181147  99181172              AB351887     1    26    26
browser |    26  100.0%         10     + 104677594 104677619              AB351887     1    26    26
browser |    26  100.0%         10     + 105016720 105016745              AB351887     1    26    26
browser |    26  100.0%         10     - 109152001 109152026              AB351887     1    26    26
browser |    26  100.0%         10     - 116443089 116443114              AB351887     1    26    26
browser |    26  100.0%         10     + 117911439 117911464              AB351887     1    26    26
browser |    26  100.0%         10     + 121004236 121004261              AB351887     1    26    26
browser |    26  100.0%         10     - 122202886 122202911              AB351887     1    26    26
browser |    26  100.0%         10     + 124418390 124418415              AB351887     1    26    26
browser |    26  100.0%         11     -   6092415   6092440              AB351887     1    26    26
browser |    26  100.0%         11     +  12518101  12518126              AB351887     1    26    26
browser |    26  100.0%         11     +  20470210  20470235              AB351887     1    26    26
browser |    26  100.0%         11     -  27902003  27902028              AB351887     1    26    26
browser |    26  100.0%         11     +  28053470  28053495              AB351887     1    26    26
browser |    26  100.0%         11     +  43553719  43553744              AB351887     1    26    26
browser |    26  100.0%         11     +  51331938  51331963              AB351887     1    26    26
browser |    26  100.0%         11     +  61317441  61317466              AB351887     1    26    26
browser |    26  100.0%         11     +  63364730  63364755              AB351887     1    26    26
browser |    26  100.0%         11     -  66839579  66839604              AB351887     1    26    26
browser |    26  100.0%         11     -  73627715  73627740              AB351887     1    26    26
browser |    26  100.0%         11     +  74025935  74025960              AB351887     1    26    26
browser |    26  100.0%         11     -  74111443  74111468              AB351887     1    26    26
browser |    26  100.0%         11     -  85177320  85177345              AB351887     1    26    26
browser |    26  100.0%         11     +  90798136  90798161              AB351887     1    26    26
browser |    26  100.0%         11     +  91996063  91996088              AB351887     1    26    26
browser |    26  100.0%         11     -  99604454  99604479              AB351887     1    26    26
browser |    26  100.0%         11     - 106184440 106184465              AB351887     1    26    26
browser |    26  100.0%         11     + 111079509 111079534              AB351887     1    26    26
browser |    26  100.0%         11     - 111107396 111107421              AB351887     1    26    26
browser |    26  100.0%         12     +   3058544   3058569              AB351887     1    26    26
browser |    26  100.0%         12     -   3381731   3381756              AB351887     1    26    26
browser |    26  100.0%         12     +  17178394  17178419              AB351887     1    26    26
browser |    26  100.0%         12     +  24451647  24451672              AB351887     1    26    26
browser |    26  100.0%         12     +  25644154  25644179              AB351887     1    26    26
browser |    26  100.0%         12     +  32955503  32955528              AB351887     1    26    26
browser |    26  100.0%         12     +  41419682  41419707              AB351887     1    26    26
browser |    26  100.0%         12     -  52777809  52777834              AB351887     1    26    26
browser |    26  100.0%         12     +  59493336  59493361              AB351887     1    26    26
browser |    26  100.0%         12     -  61336830  61336855              AB351887     1    26    26
browser |    26  100.0%         12     -  65074869  65074894              AB351887     1    26    26
browser |    26  100.0%         12     -  70708859  70708884              AB351887     1    26    26
browser |    26  100.0%         12     -  73358715  73358740              AB351887     1    26    26
browser |    26  100.0%         12     +  80470243  80470268              AB351887     1    26    26
browser |    26  100.0%         12     -  94004207  94004232              AB351887     1    26    26
browser |    26  100.0%         12     - 103687493 103687518              AB351887     1    26    26
browser |    26  100.0%         12     + 109874527 109874552              AB351887     1    26    26
browser |    26  100.0%         12     + 111358887 111358912              AB351887     1    26    26
browser |    26  100.0%         12     + 119560699 119560724              AB351887     1    26    26
browser |    26  100.0%         13     -   4117152   4117177              AB351887     1    26    26
browser |    26  100.0%         13     +   5333093   5333118              AB351887     1    26    26
browser |    26  100.0%         13     -   8520575   8520600              AB351887     1    26    26
browser |    26  100.0%         13     -   9483615   9483640              AB351887     1    26    26
browser |    26  100.0%         13     +  11522074  11522099              AB351887     1    26    26
browser |    26  100.0%         13     +  15612321  15612346              AB351887     1    26    26
browser |    26  100.0%         13     -  21814906  21814931              AB351887     1    26    26
browser |    26  100.0%         13     +  26557311  26557336              AB351887     1    26    26
browser |    26  100.0%         13     +  30560286  30560311              AB351887     1    26    26
browser |    26  100.0%         13     -  33132490  33132515              AB351887     1    26    26
browser |    26  100.0%         13     +  33627798  33627823              AB351887     1    26    26
browser |    26  100.0%         13     +  34052160  34052185              AB351887     1    26    26
browser |    26  100.0%         13     +  39696554  39696579              AB351887     1    26    26
browser |    26  100.0%         13     +  43437185  43437210              AB351887     1    26    26
browser |    26  100.0%         13     +  43546417  43546442              AB351887     1    26    26
browser |    26  100.0%         13     +  44424003  44424028              AB351887     1    26    26
browser |    26  100.0%         13     +  45170765  45170790              AB351887     1    26    26
browser |    26  100.0%         13     -  51420721  51420746              AB351887     1    26    26
browser |    26  100.0%         13     +  55930625  55930650              AB351887     1    26    26
browser |    26  100.0%         13     -  60170341  60170366              AB351887     1    26    26
browser |    26  100.0%         13     -  63305618  63305643              AB351887     1    26    26
browser |    26  100.0%         13     -  63366752  63366777              AB351887     1    26    26
browser |    26  100.0%         13     +  79717808  79717833              AB351887     1    26    26
browser |    26  100.0%         13     +  83573289  83573314              AB351887     1    26    26
browser |    26  100.0%         13     +  86925177  86925202              AB351887     1    26    26
browser |    26  100.0%         13     -  87318976  87319001              AB351887     1    26    26
browser |    26  100.0%         13     +  94878217  94878242              AB351887     1    26    26
browser |    26  100.0%         13     +  97988860  97988885              AB351887     1    26    26
browser |    26  100.0%         13     -  98463498  98463523              AB351887     1    26    26
browser |    26  100.0%         13     - 100726388 100726413              AB351887     1    26    26
browser |    26  100.0%         13     - 108135203 108135228              AB351887     1    26    26
browser |    26  100.0%         13     + 109994417 109994442              AB351887     1    26    26
browser |    26  100.0%         13     + 111642173 111642198              AB351887     1    26    26
browser |    26  100.0%         13     + 113415666 113415691              AB351887     1    26    26
browser |    26  100.0%         13     + 116107876 116107901              AB351887     1    26    26
browser |    26  100.0%         13     - 116715489 116715514              AB351887     1    26    26
browser |    26  100.0%         13     + 120692336 120692361              AB351887     1    26    26
browser |    26  100.0%         14     +   3609213   3609238              AB351887     1    26    26
browser |    26  100.0%         14     +  15116322  15116347              AB351887     1    26    26
browser |    26  100.0%         14     +  19597408  19597433              AB351887     1    26    26
browser |    26  100.0%         14     -  34106766  34106791              AB351887     1    26    26
browser |    26  100.0%         14     -  41180604  41180629              AB351887     1    26    26
browser |    26  100.0%         14     +  42603702  42603727              AB351887     1    26    26
browser |    26  100.0%         14     -  52996272  52996297              AB351887     1    26    26
browser |    26  100.0%         14     -  68245208  68245233              AB351887     1    26    26
browser |    26  100.0%         14     -  80033831  80033856              AB351887     1    26    26
browser |    26  100.0%         14     +  81331516  81331541              AB351887     1    26    26
browser |    26  100.0%         14     +  86132687  86132712              AB351887     1    26    26
browser |    26  100.0%         14     +  86834103  86834128              AB351887     1    26    26
browser |    26  100.0%         14     +  90538325  90538350              AB351887     1    26    26
browser |    26  100.0%         14     - 104343189 104343214              AB351887     1    26    26
browser |    26  100.0%         14     - 104820978 104821003              AB351887     1    26    26
browser |    26  100.0%         14     + 108411265 108411290              AB351887     1    26    26
browser |    26  100.0%         14     + 110323265 110323290              AB351887     1    26    26
browser |    26  100.0%         14     - 111099278 111099303              AB351887     1    26    26
browser |    26  100.0%         14     - 112571156 112571181              AB351887     1    26    26
browser |    26  100.0%         14     + 114749467 114749492              AB351887     1    26    26
browser |    26  100.0%         14     - 117317286 117317311              AB351887     1    26    26
browser |    26  100.0%         14     - 119716940 119716965              AB351887     1    26    26
browser |    26  100.0%         14     - 120194577 120194602              AB351887     1    26    26
browser |    26  100.0%         14     + 123966767 123966792              AB351887     1    26    26
browser |    26  100.0%         14     + 124928180 124928205              AB351887     1    26    26
browser |    26  100.0%         15     -   4882494   4882519              AB351887     1    26    26
browser |    26  100.0%         15     +   7946548   7946573              AB351887     1    26    26
browser |    26  100.0%         15     -  17157883  17157908              AB351887     1    26    26
browser |    26  100.0%         15     +  22755848  22755873              AB351887     1    26    26
browser |    26  100.0%         15     -  23241386  23241411              AB351887     1    26    26
browser |    26  100.0%         15     -  26906044  26906069              AB351887     1    26    26
browser |    26  100.0%         15     -  36996767  36996792              AB351887     1    26    26
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browser |    26  100.0%         15     +  43198328  43198353              AB351887     1    26    26
browser |    26  100.0%         15     +  44590459  44590484              AB351887     1    26    26
browser |    26  100.0%         15     +  47226170  47226195              AB351887     1    26    26
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browser |    26  100.0%         15     -  54045171  54045196              AB351887     1    26    26
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browser |    26  100.0%         15     +  65544649  65544674              AB351887     1    26    26
browser |    26  100.0%         15     -  72954186  72954211              AB351887     1    26    26
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browser |    26  100.0%         15     -  92368994  92369019              AB351887     1    26    26
browser |    26  100.0%         16     -  12918531  12918556              AB351887     1    26    26
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browser |    26  100.0%         16     -  36117075  36117100              AB351887     1    26    26
browser |    26  100.0%         16     -  36586382  36586407              AB351887     1    26    26
browser |    26  100.0%         16     -  38535639  38535664              AB351887     1    26    26
browser |    26  100.0%         16     -  41016426  41016451              AB351887     1    26    26
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browser |    26  100.0%         16     +  49908769  49908794              AB351887     1    26    26
browser |    26  100.0%         16     +  50734453  50734478              AB351887     1    26    26
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browser |    26  100.0%         16     -  52834786  52834811              AB351887     1    26    26
browser |    26  100.0%         16     -  58943192  58943217              AB351887     1    26    26
browser |    26  100.0%         16     -  60747030  60747055              AB351887     1    26    26
browser |    26  100.0%         16     -  64998272  64998297              AB351887     1    26    26
browser |    26  100.0%         16     -  65584686  65584711              AB351887     1    26    26
browser |    26  100.0%         16     +  66043485  66043510              AB351887     1    26    26
browser |    26  100.0%         16     +  67432948  67432973              AB351887     1    26    26
browser |    26  100.0%         16     -  70431775  70431800              AB351887     1    26    26
browser |    26  100.0%         16     -  74569670  74569695              AB351887     1    26    26
browser |    26  100.0%         16     -  76914844  76914869              AB351887     1    26    26
browser |    26  100.0%         16     -  79166514  79166539              AB351887     1    26    26
browser |    26  100.0%         16     +  80105617  80105642              AB351887     1    26    26
browser |    26  100.0%         16     -  80557688  80557713              AB351887     1    26    26
browser |    26  100.0%         16     +  80874920  80874945              AB351887     1    26    26
browser |    26  100.0%         16     +  83163828  83163853              AB351887     1    26    26
browser |    26  100.0%         16     -  88588455  88588480              AB351887     1    26    26
browser |    26  100.0%         16     -  89854151  89854176              AB351887     1    26    26
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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