AB352683
 

Information on mRNA AB352683

Description: Mus musculus non-coding RNA, oocyte_piRNA3499, 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: AB352683
Position: chr12:56796496-56796520

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    25  100.0%         12     +  56796496  56796520              AB352683     1    25    25
browser |    25  100.0%          1     +   5879181   5879205              AB352683     1    25    25
browser |    25  100.0%          1     -   8228855   8228879              AB352683     1    25    25
browser |    25  100.0%          1     -  13623279  13623303              AB352683     1    25    25
browser |    25  100.0%          1     +  22070074  22070098              AB352683     1    25    25
browser |    25  100.0%          1     -  26455541  26455565              AB352683     1    25    25
browser |    25  100.0%          1     +  29985916  29985940              AB352683     1    25    25
browser |    25  100.0%          1     +  48399971  48399995              AB352683     1    25    25
browser |    25  100.0%          1     -  56813825  56813849              AB352683     1    25    25
browser |    25  100.0%          1     +  58855444  58855468              AB352683     1    25    25
browser |    25  100.0%          1     +  60768630  60768654              AB352683     1    25    25
browser |    25  100.0%          1     -  70278707  70278731              AB352683     1    25    25
browser |    25  100.0%          1     +  72169317  72169341              AB352683     1    25    25
browser |    25  100.0%          1     +  74697212  74697236              AB352683     1    25    25
browser |    25  100.0%          1     -  78999002  78999026              AB352683     1    25    25
browser |    25  100.0%          1     +  81546505  81546529              AB352683     1    25    25
browser |    25  100.0%          1     + 101910495 101910519              AB352683     1    25    25
browser |    25  100.0%          1     + 111185981 111186005              AB352683     1    25    25
browser |    25  100.0%          1     + 112196690 112196714              AB352683     1    25    25
browser |    25  100.0%          1     - 112946273 112946297              AB352683     1    25    25
browser |    25  100.0%          1     + 125275730 125275754              AB352683     1    25    25
browser |    25  100.0%          1     - 140747016 140747040              AB352683     1    25    25
browser |    25  100.0%          1     - 140965614 140965638              AB352683     1    25    25
browser |    25  100.0%          1     - 144262373 144262397              AB352683     1    25    25
browser |    25  100.0%          1     + 144735052 144735076              AB352683     1    25    25
browser |    25  100.0%          1     + 148047642 148047666              AB352683     1    25    25
browser |    25  100.0%          1     - 172095621 172095645              AB352683     1    25    25
browser |    25  100.0%          1     - 179724033 179724057              AB352683     1    25    25
browser |    25  100.0%          1     - 181322927 181322951              AB352683     1    25    25
browser |    25  100.0%          1     - 183298745 183298769              AB352683     1    25    25
browser |    25  100.0%         10     +  22403728  22403752              AB352683     1    25    25
browser |    25  100.0%         10     +  22563783  22563807              AB352683     1    25    25
browser |    25  100.0%         10     -  31361079  31361103              AB352683     1    25    25
browser |    25  100.0%         10     +  34622441  34622465              AB352683     1    25    25
browser |    25  100.0%         10     -  41719005  41719029              AB352683     1    25    25
browser |    25  100.0%         10     +  43647713  43647737              AB352683     1    25    25
browser |    25  100.0%         10     -  47548992  47549016              AB352683     1    25    25
browser |    25  100.0%         10     -  51761563  51761587              AB352683     1    25    25
browser |    25  100.0%         10     +  65478244  65478268              AB352683     1    25    25
browser |    25  100.0%         10     +  66562859  66562883              AB352683     1    25    25
browser |    25  100.0%         10     +  78656408  78656432              AB352683     1    25    25
browser |    25  100.0%         10     +  81510993  81511017              AB352683     1    25    25
browser |    25  100.0%         10     +  81670121  81670145              AB352683     1    25    25
browser |    25  100.0%         10     -  81806195  81806219              AB352683     1    25    25
browser |    25  100.0%         10     +  83306349  83306373              AB352683     1    25    25
browser |    25  100.0%         10     -  85553529  85553553              AB352683     1    25    25
browser |    25  100.0%         10     - 104393682 104393706              AB352683     1    25    25
browser |    25  100.0%         10     - 104673899 104673923              AB352683     1    25    25
browser |    25  100.0%         10     - 105015418 105015442              AB352683     1    25    25
browser |    25  100.0%         10     + 109155698 109155722              AB352683     1    25    25
browser |    25  100.0%         10     + 113563224 113563248              AB352683     1    25    25
browser |    25  100.0%         10     + 116446785 116446809              AB352683     1    25    25
browser |    25  100.0%         10     - 123697719 123697743              AB352683     1    25    25
browser |    25  100.0%         10     + 124519465 124519489              AB352683     1    25    25
browser |    25  100.0%         10     + 130399519 130399543              AB352683     1    25    25
browser |    25  100.0%         11     -  10712795  10712819              AB352683     1    25    25
browser |    25  100.0%         11     -  12514405  12514429              AB352683     1    25    25
browser |    25  100.0%         11     -  12748077  12748101              AB352683     1    25    25
browser |    25  100.0%         11     -  15180175  15180199              AB352683     1    25    25
browser |    25  100.0%         11     -  38374807  38374831              AB352683     1    25    25
browser |    25  100.0%         11     -  61313746  61313770              AB352683     1    25    25
browser |    25  100.0%         11     +  66842689  66842713              AB352683     1    25    25
browser |    25  100.0%         11     -  74022243  74022267              AB352683     1    25    25
browser |    25  100.0%         11     -  84954011  84954035              AB352683     1    25    25
browser |    25  100.0%         11     +  99605566  99605590              AB352683     1    25    25
browser |    25  100.0%         11     - 100556228 100556252              AB352683     1    25    25
browser |    25  100.0%         11     + 111111092 111111116              AB352683     1    25    25
browser |    25  100.0%         11     + 115650346 115650370              AB352683     1    25    25
browser |    25  100.0%         11     - 120214465 120214489              AB352683     1    25    25
browser |    25  100.0%         12     -   6569020   6569044              AB352683     1    25    25
browser |    25  100.0%         12     +  18329708  18329732              AB352683     1    25    25
browser |    25  100.0%         12     -  19826989  19827013              AB352683     1    25    25
browser |    25  100.0%         12     +  19850095  19850119              AB352683     1    25    25
browser |    25  100.0%         12     -  22094455  22094479              AB352683     1    25    25
browser |    25  100.0%         12     -  23253324  23253348              AB352683     1    25    25
browser |    25  100.0%         12     -  24744412  24744436              AB352683     1    25    25
browser |    25  100.0%         12     -  32080479  32080503              AB352683     1    25    25
browser |    25  100.0%         12     +  44816546  44816570              AB352683     1    25    25
browser |    25  100.0%         12     +  60758302  60758326              AB352683     1    25    25
browser |    25  100.0%         12     +  61337961  61337985              AB352683     1    25    25
browser |    25  100.0%         12     +  65078564  65078588              AB352683     1    25    25
browser |    25  100.0%         12     +  70969404  70969428              AB352683     1    25    25
browser |    25  100.0%         12     -  76793848  76793872              AB352683     1    25    25
browser |    25  100.0%         12     -  80466548  80466572              AB352683     1    25    25
browser |    25  100.0%         12     +  94007903  94007927              AB352683     1    25    25
browser |    25  100.0%         12     +  96198826  96198850              AB352683     1    25    25
browser |    25  100.0%         12     + 105271102 105271126              AB352683     1    25    25
browser |    25  100.0%         12     - 115524330 115524354              AB352683     1    25    25
browser |    25  100.0%         12     - 118320585 118320609              AB352683     1    25    25
browser |    25  100.0%         12     - 119557004 119557028              AB352683     1    25    25
browser |    25  100.0%         13     -   3666829   3666853              AB352683     1    25    25
browser |    25  100.0%         13     -   4390929   4390953              AB352683     1    25    25
browser |    25  100.0%         13     +   7327082   7327106              AB352683     1    25    25
browser |    25  100.0%         13     +   8003797   8003821              AB352683     1    25    25
browser |    25  100.0%         13     +   9487311   9487335              AB352683     1    25    25
browser |    25  100.0%         13     +  10943827  10943851              AB352683     1    25    25
browser |    25  100.0%         13     -  11518441  11518465              AB352683     1    25    25
browser |    25  100.0%         13     -  15608626  15608650              AB352683     1    25    25
browser |    25  100.0%         13     +  21818599  21818623              AB352683     1    25    25
browser |    25  100.0%         13     -  22301644  22301668              AB352683     1    25    25
browser |    25  100.0%         13     -  26553614  26553638              AB352683     1    25    25
browser |    25  100.0%         13     +  31421953  31421977              AB352683     1    25    25
browser |    25  100.0%         13     -  33624102  33624126              AB352683     1    25    25
browser |    25  100.0%         13     +  34355407  34355431              AB352683     1    25    25
browser |    25  100.0%         13     -  37223196  37223220              AB352683     1    25    25
browser |    25  100.0%         13     -  44420308  44420332              AB352683     1    25    25
browser |    25  100.0%         13     -  45167070  45167094              AB352683     1    25    25
browser |    25  100.0%         13     +  46534276  46534300              AB352683     1    25    25
browser |    25  100.0%         13     -  66162580  66162604              AB352683     1    25    25
browser |    25  100.0%         13     -  68145216  68145240              AB352683     1    25    25
browser |    25  100.0%         13     +  77380780  77380804              AB352683     1    25    25
browser |    25  100.0%         13     +  77750927  77750951              AB352683     1    25    25
browser |    25  100.0%         13     +  82355732  82355756              AB352683     1    25    25
browser |    25  100.0%         13     -  85749479  85749503              AB352683     1    25    25
browser |    25  100.0%         13     +  99271938  99271962              AB352683     1    25    25
browser |    25  100.0%         13     - 113411971 113411995              AB352683     1    25    25
browser |    25  100.0%         13     + 113700366 113700390              AB352683     1    25    25
browser |    25  100.0%         13     + 114677618 114677642              AB352683     1    25    25
browser |    25  100.0%         13     - 116028286 116028310              AB352683     1    25    25
browser |    25  100.0%         13     - 116104181 116104205              AB352683     1    25    25
browser |    25  100.0%         13     + 116719186 116719210              AB352683     1    25    25
browser |    25  100.0%         14     -   4325357   4325381              AB352683     1    25    25
browser |    25  100.0%         14     -  12286369  12286393              AB352683     1    25    25
browser |    25  100.0%         14     +  12738502  12738526              AB352683     1    25    25
browser |    25  100.0%         14     -  14878206  14878230              AB352683     1    25    25
browser |    25  100.0%         14     -  19593722  19593746              AB352683     1    25    25
browser |    25  100.0%         14     -  20332500  20332524              AB352683     1    25    25
browser |    25  100.0%         14     +  24431650  24431674              AB352683     1    25    25
browser |    25  100.0%         14     +  32119848  32119872              AB352683     1    25    25
browser |    25  100.0%         14     -  35616308  35616332              AB352683     1    25    25
browser |    25  100.0%         14     -  35923164  35923188              AB352683     1    25    25
browser |    25  100.0%         14     -  38179511  38179535              AB352683     1    25    25
browser |    25  100.0%         14     -  39455920  39455944              AB352683     1    25    25
browser |    25  100.0%         14     -  50227363  50227387              AB352683     1    25    25
browser |    25  100.0%         14     +  62882098  62882122              AB352683     1    25    25
browser |    25  100.0%         14     -  75665216  75665240              AB352683     1    25    25
browser |    25  100.0%         14     +  80034777  80034801              AB352683     1    25    25
browser |    25  100.0%         14     +  85760483  85760507              AB352683     1    25    25
browser |    25  100.0%         14     -  86371437  86371461              AB352683     1    25    25
browser |    25  100.0%         14     -  86830412  86830436              AB352683     1    25    25
browser |    25  100.0%         14     +  90925235  90925259              AB352683     1    25    25
browser |    25  100.0%         14     +  95803551  95803575              AB352683     1    25    25
browser |    25  100.0%         14     -  96523805  96523829              AB352683     1    25    25
browser |    25  100.0%         14     + 110597934 110597958              AB352683     1    25    25
browser |    25  100.0%         14     + 111102973 111102997              AB352683     1    25    25
browser |    25  100.0%         14     - 111619830 111619854              AB352683     1    25    25
browser |    25  100.0%         14     + 112869795 112869819              AB352683     1    25    25
browser |    25  100.0%         14     - 114745774 114745798              AB352683     1    25    25
browser |    25  100.0%         14     + 117318425 117318449              AB352683     1    25    25
browser |    25  100.0%         14     + 119718449 119718473              AB352683     1    25    25
browser |    25  100.0%         14     - 124924485 124924509              AB352683     1    25    25
browser |    25  100.0%         15     +  12060706  12060730              AB352683     1    25    25
browser |    25  100.0%         15     +  21922420  21922444              AB352683     1    25    25
browser |    25  100.0%         15     +  22364733  22364757              AB352683     1    25    25
browser |    25  100.0%         15     -  24323803  24323827              AB352683     1    25    25
browser |    25  100.0%         15     +  26907486  26907510              AB352683     1    25    25
browser |    25  100.0%         15     -  38481530  38481554              AB352683     1    25    25
browser |    25  100.0%         15     -  44588953  44588977              AB352683     1    25    25
browser |    25  100.0%         15     -  46571983  46572008              AB352683     1    25    25
browser |    25  100.0%         15     -  49188532  49188556              AB352683     1    25    25
browser |    25  100.0%         15     +  54048867  54048891              AB352683     1    25    25
browser |    25  100.0%         15     -  56041772  56041796              AB352683     1    25    25
browser |    25  100.0%         15     +  71106916  71106940              AB352683     1    25    25
browser |    25  100.0%         15     -  71472351  71472375              AB352683     1    25    25
browser |    25  100.0%         15     +  73749624  73749648              AB352683     1    25    25
browser |    25  100.0%         15     +  75082116  75082140              AB352683     1    25    25
browser |    25  100.0%         15     -  81380086  81380110              AB352683     1    25    25
browser |    25  100.0%         15     +  82479595  82479619              AB352683     1    25    25
browser |    25  100.0%         15     +  96791450  96791474              AB352683     1    25    25
browser |    25  100.0%         15     - 103812931 103812955              AB352683     1    25    25
browser |    25  100.0%         16     +   8886173   8886197              AB352683     1    25    25
browser |    25  100.0%         16     -  12160023  12160047              AB352683     1    25    25
browser |    25  100.0%         16     +  19859941  19859965              AB352683     1    25    25
browser |    25  100.0%         16     -  34405216  34405240              AB352683     1    25    25
browser |    25  100.0%         16     +  36118021  36118045              AB352683     1    25    25
browser |    25  100.0%         16     +  41020120  41020144              AB352683     1    25    25
browser |    25  100.0%         16     -  41313713  41313737              AB352683     1    25    25
browser |    25  100.0%         16     -  46942890  46942914              AB352683     1    25    25
browser |    25  100.0%         16     -  49907824  49907848              AB352683     1    25    25
browser |    25  100.0%         16     -  50909972  50909996              AB352683     1    25    25
browser |    25  100.0%         16     +  58946887  58946911              AB352683     1    25    25
browser |    25  100.0%         16     -  64788816  64788840              AB352683     1    25    25
browser |    25  100.0%         16     -  66041400  66041424              AB352683     1    25    25
browser |    25  100.0%         16     +  70434063  70434087              AB352683     1    25    25
browser |    25  100.0%         16     +  75436169  75436193              AB352683     1    25    25
browser |    25  100.0%         16     +  75971091  75971115              AB352683     1    25    25
browser |    25  100.0%         16     +  79170212  79170236              AB352683     1    25    25
browser |    25  100.0%         16     +  79341183  79341207              AB352683     1    25    25
browser |    25  100.0%         16     +  80561380  80561404              AB352683     1    25    25
browser |    25  100.0%         16     -  82382866  82382890              AB352683     1    25    25
browser |    25  100.0%         16     -  82433030  82433054              AB352683     1    25    25
browser |    25  100.0%         16     -  83160133  83160157              AB352683     1    25    25
browser |    25  100.0%         16     +  97576359  97576383              AB352683     1    25    25
browser |    25  100.0%         17     -   8437332   8437356              AB352683     1    25    25
browser |    25  100.0%         17     +  13376646  13376670              AB352683     1    25    25
browser |    25  100.0%         17     +  15827727  15827751              AB352683     1    25    25
browser |    25  100.0%         17     -  22708974  22708998              AB352683     1    25    25
browser |    25  100.0%         17     +  23340225  23340249              AB352683     1    25    25
browser |    25  100.0%         17     +  23718882  23718906              AB352683     1    25    25
browser |    25  100.0%         17     +  38851336  38851360              AB352683     1    25    25
browser |    25  100.0%         17     +  41294618  41294642              AB352683     1    25    25
browser |    25  100.0%         17     +  47393611  47393635              AB352683     1    25    25
browser |    25  100.0%         17     -  52173911  52173935              AB352683     1    25    25
browser |    25  100.0%         17     -  55985713  55985737              AB352683     1    25    25
browser |    25  100.0%         17     -  58041752  58041776              AB352683     1    25    25
browser |    25  100.0%         17     -  63435461  63435485              AB352683     1    25    25
browser |    25  100.0%         17     +  68139647  68139671              AB352683     1    25    25
browser |    25  100.0%         17     -  68606277  68606301              AB352683     1    25    25
browser |    25  100.0%         17     -  72924685  72924709              AB352683     1    25    25
browser |    25  100.0%         17     -  75215119  75215143              AB352683     1    25    25
browser |    25  100.0%         17     -  78084291  78084315              AB352683     1    25    25
browser |    25  100.0%         17     -  83565948  83565972              AB352683     1    25    25
browser |    25  100.0%         17     -  90412348  90412372              AB352683     1    25    25
browser |    25  100.0%         17     +  94100943  94100967              AB352683     1    25    25
browser |    25  100.0%         17     +  94608387  94608411              AB352683     1    25    25
browser |    25  100.0%         18     +   4699329   4699353              AB352683     1    25    25
browser |    25  100.0%         18     +   6260600   6260624              AB352683     1    25    25
browser |    25  100.0%         18     +   8773946   8773970              AB352683     1    25    25
browser |    25  100.0%         18     +  15732862  15732886              AB352683     1    25    25
browser |    25  100.0%         18     -  21397283  21397307              AB352683     1    25    25
browser |    25  100.0%         18     +  29152432  29152456              AB352683     1    25    25
browser |    25  100.0%         18     +  36611664  36611688              AB352683     1    25    25
browser |    25  100.0%         18     +  44396015  44396039              AB352683     1    25    25
browser |    25  100.0%         18     +  49826987  49827011              AB352683     1    25    25
browser |    25  100.0%         18     -  52523482  52523506              AB352683     1    25    25
browser |    25  100.0%         18     +  55447496  55447520              AB352683     1    25    25
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View details of parts of alignment within browser window
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View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518