AB350406
 

Information on mRNA AB350406

Description: Mus musculus non-coding RNA, oocyte_piRNA1222, 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: AB350406
Position: chr12:56794700-56794727

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%         12     -  56794700  56794727              AB350406     1    27    27
browser |    27  100.0%          1     +   6238600   6238627              AB350406     1    27    27
browser |    27  100.0%          1     +   6242951   6242978              AB350406     1    27    27
browser |    27  100.0%          1     -   8728639   8728666              AB350406     1    27    27
browser |    27  100.0%          1     -   8732480   8732507              AB350406     1    27    27
browser |    27  100.0%          1     -  11102830  11102857              AB350406     1    27    27
browser |    27  100.0%          1     -  11957399  11957425              AB350406     1    27    27
browser |    27  100.0%          1     -  11961610  11961636              AB350406     1    27    27
browser |    27  100.0%          1     -  16918420  16918447              AB350406     1    27    27
browser |    27  100.0%          1     -  18322760  18322787              AB350406     1    27    27
browser |    27  100.0%          1     -  18324975  18325002              AB350406     1    27    27
browser |    27  100.0%          1     +  19692865  19692892              AB350406     1    27    27
browser |    27  100.0%          1     +  19699710  19699737              AB350406     1    27    27
browser |    27  100.0%          1     -  26388325  26388351              AB350406     1    27    27
browser |    27  100.0%          1     -  26393177  26393203              AB350406     1    27    27
browser |    27  100.0%          1     +  27226255  27226282              AB350406     1    27    27
browser |    27  100.0%          1     +  28928440  28928467              AB350406     1    27    27
browser |    27  100.0%          1     +  29694021  29694048              AB350406     1    27    27
browser |    27  100.0%          1     +  29698020  29698047              AB350406     1    27    27
browser |    27  100.0%          1     +  30707250  30707277              AB350406     1    27    27
browser |    27  100.0%          1     +  34386804  34386831              AB350406     1    27    27
browser |    27  100.0%          1     +  34390364  34390391              AB350406     1    27    27
browser |    27  100.0%          1     +  38744202  38744228              AB350406     1    27    27
browser |    27  100.0%          1     +  38748008  38748034              AB350406     1    27    27
browser |    27  100.0%          1     +  48128548  48128574              AB350406     1    27    27
browser |    27  100.0%          1     +  48133363  48133389              AB350406     1    27    27
browser |    27  100.0%          1     +  55817804  55817831              AB350406     1    27    27
browser |    27  100.0%          1     -  62573261  62573287              AB350406     1    27    27
browser |    27  100.0%          1     -  62580085  62580111              AB350406     1    27    27
browser |    27  100.0%          1     -  69737220  69737246              AB350406     1    27    27
browser |    27  100.0%          1     -  69742259  69742285              AB350406     1    27    27
browser |    27  100.0%          1     -  76750038  76750064              AB350406     1    27    27
browser |    27  100.0%          1     -  76754342  76754368              AB350406     1    27    27
browser |    27  100.0%          1     + 103516738 103516764              AB350406     1    27    27
browser |    27  100.0%          1     + 103521707 103521733              AB350406     1    27    27
browser |    27  100.0%          1     - 104217362 104217388              AB350406     1    27    27
browser |    27  100.0%          1     - 104222251 104222277              AB350406     1    27    27
browser |    27  100.0%          1     - 109056465 109056491              AB350406     1    27    27
browser |    27  100.0%          1     - 109061369 109061395              AB350406     1    27    27
browser |    27  100.0%          1     + 110257097 110257123              AB350406     1    27    27
browser |    27  100.0%          1     + 110261905 110261931              AB350406     1    27    27
browser |    27  100.0%          1     + 114113283 114113309              AB350406     1    27    27
browser |    27  100.0%          1     + 114118202 114118228              AB350406     1    27    27
browser |    27  100.0%          1     - 115813047 115813073              AB350406     1    27    27
browser |    27  100.0%          1     - 115818025 115818051              AB350406     1    27    27
browser |    27  100.0%          1     - 116576055 116576081              AB350406     1    27    27
browser |    27  100.0%          1     - 116582817 116582843              AB350406     1    27    27
browser |    27  100.0%          1     - 120498660 120498686              AB350406     1    27    27
browser |    27  100.0%          1     - 120503460 120503486              AB350406     1    27    27
browser |    27  100.0%          1     - 127819781 127819807              AB350406     1    27    27
browser |    27  100.0%          1     - 127824652 127824678              AB350406     1    27    27
browser |    27  100.0%          1     + 139652822 139652848              AB350406     1    27    27
browser |    27  100.0%          1     + 139657778 139657804              AB350406     1    27    27
browser |    27  100.0%          1     + 140744814 140744840              AB350406     1    27    27
browser |    27  100.0%          1     + 140751622 140751648              AB350406     1    27    27
browser |    27  100.0%          1     - 142284085 142284111              AB350406     1    27    27
browser |    27  100.0%          1     - 142288827 142288853              AB350406     1    27    27
browser |    27  100.0%          1     + 148150218 148150244              AB350406     1    27    27
browser |    27  100.0%          1     + 148155260 148155286              AB350406     1    27    27
browser |    27  100.0%          1     + 148361479 148361505              AB350406     1    27    27
browser |    27  100.0%          1     + 148366378 148366404              AB350406     1    27    27
browser |    27  100.0%          1     - 149390089 149390115              AB350406     1    27    27
browser |    27  100.0%          1     - 149396837 149396863              AB350406     1    27    27
browser |    27  100.0%          1     + 152538927 152538953              AB350406     1    27    27
browser |    27  100.0%          1     + 152543816 152543842              AB350406     1    27    27
browser |    27  100.0%          1     - 159797400 159797427              AB350406     1    27    27
browser |    27  100.0%          1     - 159804129 159804156              AB350406     1    27    27
browser |    27  100.0%          1     - 160643527 160643553              AB350406     1    27    27
browser |    27  100.0%          1     - 160648319 160648345              AB350406     1    27    27
browser |    27  100.0%          1     - 163520596 163520622              AB350406     1    27    27
browser |    27  100.0%          1     + 166184186 166184213              AB350406     1    27    27
browser |    27  100.0%          1     + 172097210 172097237              AB350406     1    27    27
browser |    27  100.0%          1     - 174875575 174875602              AB350406     1    27    27
browser |    27  100.0%          1     + 179770030 179770057              AB350406     1    27    27
browser |    25  100.0%          1     + 184332033 184332057              AB350406     1    25    27
browser |    27  100.0%          1     + 191839992 191840018              AB350406     1    27    27
browser |    27  100.0%         10     +   6171661   6171688              AB350406     1    27    27
browser |    27  100.0%         10     +   7191550   7191577              AB350406     1    27    27
browser |    27  100.0%         10     +   7193896   7193923              AB350406     1    27    27
browser |    27  100.0%         10     +  17900646  17900673              AB350406     1    27    27
browser |    27  100.0%         10     +  19677175  19677202              AB350406     1    27    27
browser |    27  100.0%         10     +  21087370  21087396              AB350406     1    27    27
browser |    27  100.0%         10     +  21092370  21092396              AB350406     1    27    27
browser |    27  100.0%         10     -  21518245  21518272              AB350406     1    27    27
browser |    27  100.0%         10     -  21525096  21525123              AB350406     1    27    27
browser |    27  100.0%         10     -  22559179  22559205              AB350406     1    27    27
browser |    27  100.0%         10     -  22566107  22566133              AB350406     1    27    27
browser |    27  100.0%         10     +  24562626  24562652              AB350406     1    27    27
browser |    27  100.0%         10     +  24567427  24567453              AB350406     1    27    27
browser |    27  100.0%         10     -  24982134  24982161              AB350406     1    27    27
browser |    27  100.0%         10     -  28781724  28781751              AB350406     1    27    27
browser |    27  100.0%         10     +  29893675  29893702              AB350406     1    27    27
browser |    27  100.0%         10     +  30964876  30964902              AB350406     1    27    27
browser |    27  100.0%         10     +  30971736  30971762              AB350406     1    27    27
browser |    27  100.0%         10     +  33763097  33763123              AB350406     1    27    27
browser |    27  100.0%         10     +  33767004  33767030              AB350406     1    27    27
browser |    27  100.0%         10     -  34617880  34617907              AB350406     1    27    27
browser |    27  100.0%         10     -  34624629  34624656              AB350406     1    27    27
browser |    27  100.0%         10     -  34651799  34651826              AB350406     1    27    27
browser |    27  100.0%         10     -  45430965  45430991              AB350406     1    27    27
browser |    27  100.0%         10     -  45435990  45436016              AB350406     1    27    27
browser |    27  100.0%         10     +  56597127  56597153              AB350406     1    27    27
browser |    27  100.0%         10     +  56603884  56603910              AB350406     1    27    27
browser |    27  100.0%         10     -  65480440  65480467              AB350406     1    27    27
browser |    27  100.0%         10     -  65786605  65786631              AB350406     1    27    27
browser |    27  100.0%         10     -  65791625  65791651              AB350406     1    27    27
browser |    27  100.0%         10     -  77645199  77645226              AB350406     1    27    27
browser |    27  100.0%         10     +  80816600  80816627              AB350406     1    27    27
browser |    27  100.0%         10     -  81846874  81846901              AB350406     1    27    27
browser |    27  100.0%         10     -  83506845  83506871              AB350406     1    27    27
browser |    27  100.0%         10     -  83513570  83513596              AB350406     1    27    27
browser |    27  100.0%         10     +  83623607  83623633              AB350406     1    27    27
browser |    27  100.0%         10     +  83628378  83628404              AB350406     1    27    27
browser |    27  100.0%         10     +  84580774  84580800              AB350406     1    27    27
browser |    27  100.0%         10     +  84585722  84585748              AB350406     1    27    27
browser |    27  100.0%         10     -  90160550  90160576              AB350406     1    27    27
browser |    27  100.0%         10     -  90165318  90165344              AB350406     1    27    27
browser |    27  100.0%         10     +  92355030  92355057              AB350406     1    27    27
browser |    27  100.0%         10     +  92357426  92357453              AB350406     1    27    27
browser |    27  100.0%         10     -  94198509  94198536              AB350406     1    27    27
browser |    27  100.0%         10     -  94204834  94204861              AB350406     1    27    27
browser |    27  100.0%         10     -  95993143  95993169              AB350406     1    27    27
browser |    27  100.0%         10     -  95997992  95998018              AB350406     1    27    27
browser |    27  100.0%         10     -  97752648  97752675              AB350406     1    27    27
browser |    27  100.0%         10     - 104655371 104655397              AB350406     1    27    27
browser |    27  100.0%         10     - 104660373 104660399              AB350406     1    27    27
browser |    27  100.0%         10     - 104857676 104857703              AB350406     1    27    27
browser |    27  100.0%         10     - 105508522 105508548              AB350406     1    27    27
browser |    27  100.0%         10     - 105513450 105513476              AB350406     1    27    27
browser |    27  100.0%         10     + 107835660 107835687              AB350406     1    27    27
browser |    27  100.0%         10     + 110532396 110532423              AB350406     1    27    27
browser |    27  100.0%         10     + 111889719 111889746              AB350406     1    27    27
browser |    27  100.0%         10     + 113619145 113619172              AB350406     1    27    27
browser |    27  100.0%         10     - 116442224 116442251              AB350406     1    27    27
browser |    27  100.0%         10     + 117906795 117906822              AB350406     1    27    27
browser |    27  100.0%         10     + 117912286 117912313              AB350406     1    27    27
browser |    27  100.0%         10     + 124441931 124441957              AB350406     1    27    27
browser |    27  100.0%         10     + 124446757 124446783              AB350406     1    27    27
browser |    27  100.0%         10     + 129761391 129761418              AB350406     1    27    27
browser |    27  100.0%         11     -   9037049   9037076              AB350406     1    27    27
browser |    27  100.0%         11     -   9658045   9658072              AB350406     1    27    27
browser |    27  100.0%         11     -   9664776   9664803              AB350406     1    27    27
browser |    27  100.0%         11     -  12457368  12457394              AB350406     1    27    27
browser |    27  100.0%         11     -  12462323  12462349              AB350406     1    27    27
browser |    27  100.0%         11     -  12904082  12904108              AB350406     1    27    27
browser |    27  100.0%         11     -  12908919  12908945              AB350406     1    27    27
browser |    27  100.0%         11     -  14391650  14391677              AB350406     1    27    27
browser |    27  100.0%         11     +  14521461  14521488              AB350406     1    27    27
browser |    27  100.0%         11     -  14849725  14849752              AB350406     1    27    27
browser |    27  100.0%         11     +  15177999  15178026              AB350406     1    27    27
browser |    27  100.0%         11     -  19516196  19516223              AB350406     1    27    27
browser |    27  100.0%         11     +  20471105  20471132              AB350406     1    27    27
browser |    27  100.0%         11     -  22285284  22285310              AB350406     1    27    27
browser |    27  100.0%         11     -  22290211  22290237              AB350406     1    27    27
browser |    27  100.0%         11     +  26505744  26505770              AB350406     1    27    27
browser |    27  100.0%         11     +  26510699  26510725              AB350406     1    27    27
browser |    27  100.0%         11     +  27088015  27088042              AB350406     1    27    27
browser |    27  100.0%         11     +  29074808  29074834              AB350406     1    27    27
browser |    27  100.0%         11     +  29079692  29079718              AB350406     1    27    27
browser |    27  100.0%         11     -  51555932  51555958              AB350406     1    27    27
browser |    27  100.0%         11     -  51560768  51560794              AB350406     1    27    27
browser |    27  100.0%         11     -  55131812  55131838              AB350406     1    27    27
browser |    27  100.0%         11     -  55138548  55138574              AB350406     1    27    27
browser |    27  100.0%         11     +  61311477  61311503              AB350406     1    27    27
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browser |    27  100.0%         11     +  64683215  64683241              AB350406     1    27    27
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browser |    27  100.0%         11     +  74431304  74431330              AB350406     1    27    27
browser |    27  100.0%         11     +  74436137  74436163              AB350406     1    27    27
browser |    27  100.0%         11     +  81436603  81436629              AB350406     1    27    27
browser |    27  100.0%         11     +  81443432  81443458              AB350406     1    27    27
browser |    27  100.0%         11     -  90202984  90203011              AB350406     1    27    27
browser |    27  100.0%         11     -  90720393  90720419              AB350406     1    27    27
browser |    27  100.0%         11     -  90725349  90725375              AB350406     1    27    27
browser |    27  100.0%         11     +  90792819  90792846              AB350406     1    27    27
browser |    27  100.0%         11     -  90857820  90857847              AB350406     1    27    27
browser |    27  100.0%         11     +  98504355  98504382              AB350406     1    27    27
browser |    27  100.0%         11     +  98511116  98511143              AB350406     1    27    27
browser |    27  100.0%         11     -  99603605  99603632              AB350406     1    27    27
browser |    27  100.0%         11     - 101289890 101289917              AB350406     1    27    27
browser |    27  100.0%         11     - 108290093 108290119              AB350406     1    27    27
browser |    27  100.0%         11     - 108294928 108294954              AB350406     1    27    27
browser |    27  100.0%         11     + 108885031 108885058              AB350406     1    27    27
browser |    27  100.0%         11     - 109621067 109621093              AB350406     1    27    27
browser |    27  100.0%         11     - 115645784 115645810              AB350406     1    27    27
browser |    27  100.0%         11     - 115652534 115652560              AB350406     1    27    27
browser |    27  100.0%         11     + 116280533 116280559              AB350406     1    27    27
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browser |    27  100.0%         11     + 120961050 120961077              AB350406     1    27    27
browser |    27  100.0%         11     + 120965646 120965673              AB350406     1    27    27
browser |    27  100.0%         12     -   3387659   3387686              AB350406     1    27    27
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browser |    27  100.0%         12     -  54336393  54336419              AB350406     1    27    27
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browser |    27  100.0%         12     -  65854819  65854846              AB350406     1    27    27
browser |    27  100.0%         12     -  68668546  68668573              AB350406     1    27    27
browser |    27  100.0%         12     -  68675356  68675383              AB350406     1    27    27
browser |    27  100.0%         12     +  68792295  68792321              AB350406     1    27    27
browser |    27  100.0%         12     +  68797140  68797166              AB350406     1    27    27
browser |    27  100.0%         12     -  70795305  70795332              AB350406     1    27    27
browser |    27  100.0%         12     -  73357826  73357853              AB350406     1    27    27
browser |    27  100.0%         12     +  75906721  75906748              AB350406     1    27    27
browser |    27  100.0%         12     +  80471100  80471127              AB350406     1    27    27
browser |    27  100.0%         12     +  81630166  81630193              AB350406     1    27    27
browser |    27  100.0%         12     -  82507852  82507878              AB350406     1    27    27
browser |    27  100.0%         12     -  82512858  82512884              AB350406     1    27    27
browser |    27  100.0%         12     -  94003264  94003290              AB350406     1    27    27
browser |    27  100.0%         12     -  94010169  94010195              AB350406     1    27    27
browser |    25  100.0%         12     -  96200986  96201011              AB350406     1    25    27
browser |    27  100.0%         12     +  96907115  96907142              AB350406     1    27    27
browser |    25  100.0%         12     - 101336341 101336366              AB350406     1    25    27
browser |    27  100.0%         12     - 108045610 108045636              AB350406     1    27    27
browser |    27  100.0%         12     - 108050382 108050408              AB350406     1    27    27
browser |    27  100.0%         12     + 111354923 111354949              AB350406     1    27    27
browser |    27  100.0%         12     + 111359767 111359793              AB350406     1    27    27
browser |    27  100.0%         12     - 113419395 113419422              AB350406     1    27    27
browser |    27  100.0%         12     + 113603910 113603937              AB350406     1    27    27
browser |    25  100.0%         12     - 114483786 114483811              AB350406     1    25    27
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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