AB352623
 

Information on mRNA AB352623

Description: Mus musculus non-coding RNA, oocyte_piRNA3439, 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: AB352623
Position: chr12:57097143-57097164

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 |    22  100.0%         12     +  57097143  57097164              AB352623     3    24    24
browser |    22  100.0%          1     -   8898497   8898518              AB352623     3    24    24
browser |    22  100.0%          1     +  17150056  17150077              AB352623     3    24    24
browser |    22  100.0%          1     +  21568421  21568442              AB352623     3    24    24
browser |    22  100.0%          1     +  23604342  23604363              AB352623     3    24    24
browser |    22  100.0%          1     +  25008426  25008447              AB352623     3    24    24
browser |    22  100.0%          1     +  25182268  25182289              AB352623     3    24    24
browser |    22  100.0%          1     -  27241616  27241637              AB352623     3    24    24
browser |    22  100.0%          1     -  27787823  27787844              AB352623     3    24    24
browser |    22  100.0%          1     -  29989882  29989903              AB352623     3    24    24
browser |    22  100.0%          1     +  33458551  33458572              AB352623     3    24    24
browser |    22  100.0%          1     +  35795367  35795388              AB352623     3    24    24
browser |    22  100.0%          1     +  43963655  43963676              AB352623     3    24    24
browser |    24  100.0%          1     -  44985898  44985921              AB352623     1    24    24
browser |    22  100.0%          1     +  45051510  45051531              AB352623     3    24    24
browser |    24  100.0%          1     +  47927954  47927977              AB352623     1    24    24
browser |    22  100.0%          1     -  49217392  49217413              AB352623     3    24    24
browser |    22  100.0%          1     +  50194433  50194454              AB352623     3    24    24
browser |    22  100.0%          1     -  50319180  50319201              AB352623     3    24    24
browser |    22  100.0%          1     +  50695916  50695937              AB352623     3    24    24
browser |    22  100.0%          1     +  57695945  57695966              AB352623     3    24    24
browser |    22  100.0%          1     -  67917468  67917489              AB352623     3    24    24
browser |    22  100.0%          1     +  76765195  76765216              AB352623     3    24    24
browser |    22  100.0%          1     +  77866350  77866371              AB352623     3    24    24
browser |    22  100.0%          1     -  78754454  78754475              AB352623     3    24    24
browser |    22  100.0%          1     -  80821342  80821363              AB352623     3    24    24
browser |    22  100.0%          1     -  86775861  86775882              AB352623     3    24    24
browser |    22  100.0%          1     +  95727503  95727524              AB352623     3    24    24
browser |    22  100.0%          1     +  96596131  96596152              AB352623     3    24    24
browser |    22  100.0%          1     -  98340626  98340647              AB352623     3    24    24
browser |    22  100.0%          1     -  98990821  98990842              AB352623     3    24    24
browser |    22  100.0%          1     -  99153208  99153229              AB352623     3    24    24
browser |    22  100.0%          1     + 100633674 100633695              AB352623     3    24    24
browser |    22  100.0%          1     - 101850267 101850288              AB352623     3    24    24
browser |    22  100.0%          1     - 103489285 103489306              AB352623     3    24    24
browser |    24  100.0%          1     - 105319188 105319211              AB352623     1    24    24
browser |    22  100.0%          1     + 107602593 107602614              AB352623     3    24    24
browser |    22  100.0%          1     - 109899149 109899170              AB352623     3    24    24
browser |    22  100.0%          1     + 110768547 110768568              AB352623     3    24    24
browser |    22  100.0%          1     + 112299974 112299995              AB352623     3    24    24
browser |    22  100.0%          1     + 112600368 112600389              AB352623     3    24    24
browser |    22  100.0%          1     - 114312213 114312234              AB352623     3    24    24
browser |    24  100.0%          1     + 114365968 114365991              AB352623     1    24    24
browser |    22  100.0%          1     + 117381650 117381671              AB352623     3    24    24
browser |    22  100.0%          1     + 138356899 138356920              AB352623     3    24    24
browser |    22  100.0%          1     + 140495881 140495902              AB352623     3    24    24
browser |    24  100.0%          1     - 140795828 140795851              AB352623     1    24    24
browser |    22  100.0%          1     + 141733667 141733688              AB352623     3    24    24
browser |    24  100.0%          1     - 148043640 148043663              AB352623     1    24    24
browser |    22  100.0%          1     - 165084061 165084082              AB352623     3    24    24
browser |    22  100.0%          1     + 168919364 168919385              AB352623     3    24    24
browser |    22  100.0%          1     - 176074370 176074391              AB352623     3    24    24
browser |    22  100.0%         10     -   4799041   4799062              AB352623     3    24    24
browser |    22  100.0%         10     +   5173990   5174011              AB352623     3    24    24
browser |    22  100.0%         10     +   5634744   5634765              AB352623     3    24    24
browser |    22  100.0%         10     +   6051324   6051345              AB352623     3    24    24
browser |    22  100.0%         10     +   6205270   6205291              AB352623     3    24    24
browser |    22  100.0%         10     +  11865648  11865669              AB352623     3    24    24
browser |    22  100.0%         10     +  30037148  30037169              AB352623     3    24    24
browser |    22  100.0%         10     -  31024163  31024184              AB352623     3    24    24
browser |    22  100.0%         10     +  40380806  40380827              AB352623     3    24    24
browser |    22  100.0%         10     -  40415253  40415274              AB352623     3    24    24
browser |    22  100.0%         10     +  45130576  45130597              AB352623     3    24    24
browser |    24  100.0%         10     +  47502621  47502644              AB352623     1    24    24
browser |    22  100.0%         10     -  47693834  47693855              AB352623     3    24    24
browser |    22  100.0%         10     +  48306570  48306591              AB352623     3    24    24
browser |    22  100.0%         10     +  48906665  48906686              AB352623     3    24    24
browser |    22  100.0%         10     -  49691381  49691402              AB352623     3    24    24
browser |    22  100.0%         10     -  50175600  50175621              AB352623     3    24    24
browser |    22  100.0%         10     -  52505895  52505916              AB352623     3    24    24
browser |    22  100.0%         10     -  52837486  52837507              AB352623     3    24    24
browser |    22  100.0%         10     -  53657571  53657592              AB352623     3    24    24
browser |    22  100.0%         10     +  54842510  54842531              AB352623     3    24    24
browser |    22  100.0%         10     -  56522676  56522697              AB352623     3    24    24
browser |    22  100.0%         10     +  64254765  64254786              AB352623     3    24    24
browser |    22  100.0%         10     +  64862021  64862042              AB352623     3    24    24
browser |    22  100.0%         10     +  66163243  66163264              AB352623     3    24    24
browser |    22  100.0%         10     -  71451712  71451733              AB352623     3    24    24
browser |    22  100.0%         10     -  73306721  73306742              AB352623     3    24    24
browser |    22  100.0%         10     -  79310298  79310319              AB352623     3    24    24
browser |    22  100.0%         10     -  86859340  86859361              AB352623     3    24    24
browser |    22  100.0%         10     - 100745263 100745284              AB352623     3    24    24
browser |    22  100.0%         10     - 117890767 117890788              AB352623     3    24    24
browser |    22  100.0%         10     + 124109654 124109675              AB352623     3    24    24
browser |    22  100.0%         10     + 124556596 124556617              AB352623     3    24    24
browser |    22  100.0%         10     + 129176544 129176565              AB352623     3    24    24
browser |    22  100.0%         10     + 130328421 130328442              AB352623     3    24    24
browser |    22  100.0%         11     -   9991178   9991199              AB352623     3    24    24
browser |    22  100.0%         11     -  10214652  10214673              AB352623     3    24    24
browser |    22  100.0%         11     +  12537102  12537123              AB352623     3    24    24
browser |    22  100.0%         11     -  13707340  13707361              AB352623     3    24    24
browser |    22  100.0%         11     +  14679456  14679477              AB352623     3    24    24
browser |    22  100.0%         11     -  14923649  14923670              AB352623     3    24    24
browser |    22  100.0%         11     +  15031677  15031698              AB352623     3    24    24
browser |    22  100.0%         11     -  21422116  21422137              AB352623     3    24    24
browser |    22  100.0%         11     +  25355905  25355926              AB352623     3    24    24
browser |    22  100.0%         11     -  26453745  26453766              AB352623     3    24    24
browser |    22  100.0%         11     -  27461535  27461556              AB352623     3    24    24
browser |    22  100.0%         11     +  39231516  39231537              AB352623     3    24    24
browser |    22  100.0%         11     +  40067115  40067136              AB352623     3    24    24
browser |    22  100.0%         11     -  46850034  46850055              AB352623     3    24    24
browser |    22  100.0%         11     +  47621500  47621521              AB352623     3    24    24
browser |    22  100.0%         11     +  58596977  58596998              AB352623     3    24    24
browser |    22  100.0%         11     +  71104694  71104715              AB352623     3    24    24
browser |    22  100.0%         11     - 108426220 108426241              AB352623     3    24    24
browser |    22  100.0%         12     -   8212313   8212334              AB352623     3    24    24
browser |    22  100.0%         12     +   8215678   8215699              AB352623     3    24    24
browser |    22  100.0%         12     -  13619232  13619253              AB352623     3    24    24
browser |    22  100.0%         12     +  17554026  17554047              AB352623     3    24    24
browser |    22  100.0%         12     +  29545241  29545262              AB352623     3    24    24
browser |    22  100.0%         12     +  39181621  39181642              AB352623     3    24    24
browser |    22  100.0%         12     -  40053843  40053864              AB352623     3    24    24
browser |    22  100.0%         12     -  41333725  41333746              AB352623     3    24    24
browser |    22  100.0%         12     +  42478115  42478136              AB352623     3    24    24
browser |    22  100.0%         12     +  42975746  42975767              AB352623     3    24    24
browser |    22  100.0%         12     +  43552757  43552778              AB352623     3    24    24
browser |    24  100.0%         12     -  46233426  46233449              AB352623     1    24    24
browser |    22  100.0%         12     +  46284500  46284521              AB352623     3    24    24
browser |    22  100.0%         12     +  46790890  46790911              AB352623     3    24    24
browser |    22  100.0%         12     -  48123282  48123303              AB352623     3    24    24
browser |    22  100.0%         12     -  49533819  49533840              AB352623     3    24    24
browser |    22  100.0%         12     -  59723083  59723104              AB352623     3    24    24
browser |    24  100.0%         12     +  60437188  60437211              AB352623     1    24    24
browser |    22  100.0%         12     -  63113464  63113485              AB352623     3    24    24
browser |    22  100.0%         12     +  68107024  68107045              AB352623     3    24    24
browser |    22  100.0%         12     -  92378501  92378522              AB352623     3    24    24
browser |    22  100.0%         12     +  95383815  95383836              AB352623     3    24    24
browser |    22  100.0%         12     +  95829230  95829251              AB352623     3    24    24
browser |    22  100.0%         12     -  97458915  97458936              AB352623     3    24    24
browser |    22  100.0%         12     + 109136189 109136210              AB352623     3    24    24
browser |    22  100.0%         13     -   3092629   3092650              AB352623     3    24    24
browser |    22  100.0%         13     -   4374219   4374240              AB352623     3    24    24
browser |    22  100.0%         13     -   5550677   5550698              AB352623     3    24    24
browser |    24  100.0%         13     -   7059844   7059867              AB352623     1    24    24
browser |    22  100.0%         13     -   8340446   8340467              AB352623     3    24    24
browser |    22  100.0%         13     +  14461499  14461520              AB352623     3    24    24
browser |    22  100.0%         13     -  18139158  18139179              AB352623     3    24    24
browser |    22  100.0%         13     -  18732058  18732079              AB352623     3    24    24
browser |    22  100.0%         13     +  22411407  22411428              AB352623     3    24    24
browser |    22  100.0%         13     +  26070866  26070887              AB352623     3    24    24
browser |    22  100.0%         13     +  29859962  29859983              AB352623     3    24    24
browser |    22  100.0%         13     +  33729039  33729060              AB352623     3    24    24
browser |    22  100.0%         13     -  33732079  33732100              AB352623     3    24    24
browser |    22  100.0%         13     -  36557198  36557219              AB352623     3    24    24
browser |    22  100.0%         13     +  39515841  39515862              AB352623     3    24    24
browser |    22  100.0%         13     -  50435711  50435732              AB352623     3    24    24
browser |    22  100.0%         13     +  50734931  50734952              AB352623     3    24    24
browser |    22  100.0%         13     -  61819164  61819185              AB352623     1    22    24
browser |    22  100.0%         13     +  76074682  76074703              AB352623     3    24    24
browser |    22  100.0%         13     +  78612138  78612159              AB352623     3    24    24
browser |    22  100.0%         13     -  85125538  85125559              AB352623     3    24    24
browser |    22  100.0%         13     + 102738394 102738415              AB352623     3    24    24
browser |    22  100.0%         13     - 107486054 107486075              AB352623     3    24    24
browser |    22  100.0%         13     + 110106487 110106508              AB352623     3    24    24
browser |    22  100.0%         14     -  11541763  11541784              AB352623     3    24    24
browser |    22  100.0%         14     -  20999500  20999521              AB352623     3    24    24
browser |    24  100.0%         14     +  38666917  38666940              AB352623     1    24    24
browser |    22  100.0%         14     +  40100183  40100204              AB352623     3    24    24
browser |    22  100.0%         14     +  45657394  45657415              AB352623     3    24    24
browser |    22  100.0%         14     -  50552607  50552628              AB352623     3    24    24
browser |    22  100.0%         14     +  50811487  50811508              AB352623     3    24    24
browser |    22  100.0%         14     -  50920870  50920891              AB352623     3    24    24
browser |    22  100.0%         14     -  51859720  51859741              AB352623     3    24    24
browser |    22  100.0%         14     +  56486189  56486210              AB352623     3    24    24
browser |    22  100.0%         14     +  84870858  84870879              AB352623     3    24    24
browser |    22  100.0%         14     +  84906042  84906063              AB352623     3    24    24
browser |    22  100.0%         14     +  86506307  86506328              AB352623     3    24    24
browser |    22  100.0%         14     +  89283158  89283179              AB352623     3    24    24
browser |    22  100.0%         14     -  90415896  90415917              AB352623     3    24    24
browser |    22  100.0%         14     -  95267218  95267239              AB352623     3    24    24
browser |    22  100.0%         14     +  95354198  95354219              AB352623     3    24    24
browser |    22  100.0%         14     - 108709497 108709518              AB352623     3    24    24
browser |    22  100.0%         14     - 110495276 110495297              AB352623     3    24    24
browser |    22  100.0%         14     + 119788811 119788832              AB352623     3    24    24
browser |    22  100.0%         14     - 120390169 120390190              AB352623     3    24    24
browser |    22  100.0%         14     - 121279296 121279317              AB352623     3    24    24
browser |    22  100.0%         14     + 124690541 124690562              AB352623     3    24    24
browser |    22  100.0%         15     +   3883366   3883387              AB352623     3    24    24
browser |    22  100.0%         15     +   6017928   6017949              AB352623     3    24    24
browser |    23  100.0%         15     +  10356258  10356280              AB352623     2    24    24
browser |    24  100.0%         15     -  10361508  10361531              AB352623     1    24    24
browser |    22  100.0%         15     +  13344539  13344560              AB352623     3    24    24
browser |    22  100.0%         15     -  14943453  14943474              AB352623     3    24    24
browser |    22  100.0%         15     -  16395152  16395173              AB352623     3    24    24
browser |    22  100.0%         15     -  17547980  17548001              AB352623     3    24    24
browser |    22  100.0%         15     +  27456173  27456194              AB352623     3    24    24
browser |    22  100.0%         15     -  28477890  28477911              AB352623     3    24    24
browser |    22  100.0%         15     -  28630823  28630844              AB352623     3    24    24
browser |    22  100.0%         15     -  33128546  33128567              AB352623     3    24    24
browser |    22  100.0%         15     -  33849033  33849054              AB352623     3    24    24
browser |    22  100.0%         15     -  42591357  42591378              AB352623     3    24    24
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browser |    22  100.0%         15     -  47768370  47768391              AB352623     3    24    24
browser |    22  100.0%         15     +  52119444  52119465              AB352623     3    24    24
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browser |    22  100.0%         15     +  54686677  54686698              AB352623     3    24    24
browser |    22  100.0%         15     -  55994192  55994213              AB352623     3    24    24
browser |    22  100.0%         15     -  55997393  55997414              AB352623     3    24    24
browser |    24  100.0%         15     -  56261233  56261256              AB352623     1    24    24
browser |    22  100.0%         15     -  64778158  64778179              AB352623     3    24    24
browser |    24  100.0%         15     +  75241813  75241836              AB352623     1    24    24
browser |    22  100.0%         15     +  84254844  84254865              AB352623     3    24    24
browser |    22  100.0%         15     - 101512166 101512187              AB352623     3    24    24
browser |    22  100.0%         15     - 101967096 101967117              AB352623     3    24    24
browser |    22  100.0%         16     +   4176024   4176045              AB352623     3    24    24
browser |    22  100.0%         16     +  15125150  15125171              AB352623     3    24    24
browser |    22  100.0%         16     -  16305947  16305968              AB352623     3    24    24
browser |    22  100.0%         16     +  18955747  18955768              AB352623     3    24    24
browser |    22  100.0%         16     -  19006892  19006913              AB352623     3    24    24
browser |    22  100.0%         16     +  36090713  36090734              AB352623     3    24    24
browser |    22  100.0%         16     +  47750547  47750568              AB352623     3    24    24
browser |    22  100.0%         16     -  47833847  47833868              AB352623     3    24    24
browser |    22  100.0%         16     -  49550046  49550067              AB352623     3    24    24
browser |    22  100.0%         16     -  54637862  54637883              AB352623     3    24    24
browser |    22  100.0%         16     -  58637426  58637447              AB352623     3    24    24
browser |    22  100.0%         16     -  59756103  59756124              AB352623     3    24    24
browser |    22  100.0%         16     +  59762083  59762104              AB352623     3    24    24
browser |    22  100.0%         16     +  60124329  60124350              AB352623     3    24    24
browser |    22  100.0%         16     -  60850767  60850788              AB352623     3    24    24
browser |    22  100.0%         16     +  61373270  61373291              AB352623     3    24    24
browser |    22  100.0%         16     +  62419601  62419622              AB352623     3    24    24
browser |    24  100.0%         16     +  65060511  65060534              AB352623     1    24    24
browser |    22  100.0%         16     +  66370368  66370389              AB352623     3    24    24
browser |    22  100.0%         16     -  66378600  66378621              AB352623     3    24    24
browser |    22  100.0%         16     +  67711398  67711419              AB352623     3    24    24
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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