AB352321
 

Information on mRNA AB352321

Description: Mus musculus non-coding RNA, oocyte_piRNA3137, 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: AB352321
Position: chr12:56795086-56795112

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     -  56795086  56795112              AB352321     1    27    27
browser |    27  100.0%          1     -   5635397   5635423              AB352321     1    27    27
browser |    27  100.0%          1     +   5818959   5818985              AB352321     1    27    27
browser |    27  100.0%          1     -   5875019   5875045              AB352321     1    27    27
browser |    27  100.0%          1     -   6501049   6501075              AB352321     1    27    27
browser |    27  100.0%          1     +   8070565   8070591              AB352321     1    27    27
browser |    27  100.0%          1     +   8233000   8233026              AB352321     1    27    27
browser |    27  100.0%          1     -  10800545  10800571              AB352321     1    27    27
browser |    27  100.0%          1     -  11957798  11957824              AB352321     1    27    27
browser |    27  100.0%          1     +  13627429  13627455              AB352321     1    27    27
browser |    27  100.0%          1     +  16815078  16815104              AB352321     1    27    27
browser |    27  100.0%          1     -  17595252  17595278              AB352321     1    27    27
browser |    27  100.0%          1     +  18033666  18033692              AB352321     1    27    27
browser |    27  100.0%          1     -  18323258  18323284              AB352321     1    27    27
browser |    27  100.0%          1     +  18590951  18590977              AB352321     1    27    27
browser |    27  100.0%          1     +  21654658  21654684              AB352321     1    27    27
browser |    27  100.0%          1     -  22065934  22065960              AB352321     1    27    27
browser |    27  100.0%          1     +  23344953  23344979              AB352321     1    27    27
browser |    27  100.0%          1     +  26459693  26459719              AB352321     1    27    27
browser |    27  100.0%          1     -  26509905  26509931              AB352321     1    27    27
browser |    27  100.0%          1     +  27177671  27177697              AB352321     1    27    27
browser |    27  100.0%          1     +  27225841  27225867              AB352321     1    27    27
browser |    27  100.0%          1     -  28495775  28495801              AB352321     1    27    27
browser |    27  100.0%          1     +  28930311  28930337              AB352321     1    27    27
browser |    27  100.0%          1     -  29982264  29982290              AB352321     1    27    27
browser |    27  100.0%          1     +  31046225  31046251              AB352321     1    27    27
browser |    27  100.0%          1     +  31512367  31512393              AB352321     1    27    27
browser |    27  100.0%          1     +  34389964  34389990              AB352321     1    27    27
browser |    27  100.0%          1     -  47995473  47995499              AB352321     1    27    27
browser |    27  100.0%          1     -  48393952  48393978              AB352321     1    27    27
browser |    27  100.0%          1     -  48710934  48710960              AB352321     1    27    27
browser |    27  100.0%          1     -  48841479  48841505              AB352321     1    27    27
browser |    27  100.0%          1     -  58851291  58851317              AB352321     1    27    27
browser |    27  100.0%          1     -  81542345  81542371              AB352321     1    27    27
browser |    27  100.0%          1     +  81962407  81962433              AB352321     1    27    27
browser |    27  100.0%          1     +  82483239  82483265              AB352321     1    27    27
browser |    27  100.0%          1     -  86245934  86245960              AB352321     1    27    27
browser |    27  100.0%          1     -  91399402  91399428              AB352321     1    27    27
browser |    27  100.0%          1     -  93035669  93035695              AB352321     1    27    27
browser |    27  100.0%          1     +  93888547  93888573              AB352321     1    27    27
browser |    27  100.0%          1     -  96895156  96895182              AB352321     1    27    27
browser |    27  100.0%          1     +  97108467  97108493              AB352321     1    27    27
browser |    27  100.0%          1     - 100457173 100457199              AB352321     1    27    27
browser |    27  100.0%          1     - 101906337 101906363              AB352321     1    27    27
browser |    27  100.0%          1     + 102079615 102079641              AB352321     1    27    27
browser |    27  100.0%          1     + 102966015 102966041              AB352321     1    27    27
browser |    27  100.0%          1     - 103133370 103133396              AB352321     1    27    27
browser |    27  100.0%          1     - 107966992 107967018              AB352321     1    27    27
browser |    27  100.0%          1     + 109062786 109062812              AB352321     1    27    27
browser |    27  100.0%          1     - 110865799 110865825              AB352321     1    27    27
browser |    27  100.0%          1     - 111181824 111181850              AB352321     1    27    27
browser |    27  100.0%          1     + 112862711 112862737              AB352321     1    27    27
browser |    27  100.0%          1     - 117630126 117630152              AB352321     1    27    27
browser |    27  100.0%          1     - 117675412 117675438              AB352321     1    27    27
browser |    27  100.0%          1     + 117920069 117920095              AB352321     1    27    27
browser |    27  100.0%          1     - 121705584 121705610              AB352321     1    27    27
browser |    27  100.0%          1     + 125251210 125251236              AB352321     1    27    27
browser |    27  100.0%          1     - 125274320 125274346              AB352321     1    27    27
browser |    27  100.0%          1     + 126356911 126356937              AB352321     1    27    27
browser |    27  100.0%          1     - 127486469 127486495              AB352321     1    27    27
browser |    27  100.0%          1     + 129020214 129020240              AB352321     1    27    27
browser |    27  100.0%          1     + 130466490 130466516              AB352321     1    27    27
browser |    27  100.0%          1     + 140751173 140751199              AB352321     1    27    27
browser |    27  100.0%          1     + 149275621 149275647              AB352321     1    27    27
browser |    27  100.0%          1     + 149463935 149463961              AB352321     1    27    27
browser |    27  100.0%          1     - 159797800 159797826              AB352321     1    27    27
browser |    27  100.0%          1     - 163296529 163296555              AB352321     1    27    27
browser |    27  100.0%          1     + 166183806 166183832              AB352321     1    27    27
browser |    27  100.0%          1     - 166591172 166591198              AB352321     1    27    27
browser |    27  100.0%          1     + 169375989 169376015              AB352321     1    27    27
browser |    27  100.0%          1     + 169949980 169950006              AB352321     1    27    27
browser |    27  100.0%          1     + 171659607 171659633              AB352321     1    27    27
browser |    27  100.0%          1     + 172096819 172096845              AB352321     1    27    27
browser |    27  100.0%          1     - 174870012 174870038              AB352321     1    27    27
browser |    27  100.0%          1     - 176371094 176371120              AB352321     1    27    27
browser |    27  100.0%          1     + 178008297 178008323              AB352321     1    27    27
browser |    27  100.0%          1     + 179728184 179728210              AB352321     1    27    27
browser |    27  100.0%          1     + 180443484 180443510              AB352321     1    27    27
browser |    27  100.0%          1     - 181091550 181091576              AB352321     1    27    27
browser |    27  100.0%          1     + 181326577 181326603              AB352321     1    27    27
browser |    27  100.0%          1     + 183302896 183302922              AB352321     1    27    27
browser |    27  100.0%          1     + 185038085 185038111              AB352321     1    27    27
browser |    27  100.0%          1     + 191236119 191236145              AB352321     1    27    27
browser |    27  100.0%         10     -   3551389   3551415              AB352321     1    27    27
browser |    27  100.0%         10     -   6517237   6517263              AB352321     1    27    27
browser |    27  100.0%         10     +   7365984   7366010              AB352321     1    27    27
browser |    27  100.0%         10     -  15056212  15056238              AB352321     1    27    27
browser |    27  100.0%         10     +  16380235  16380261              AB352321     1    27    27
browser |    27  100.0%         10     -  19415104  19415130              AB352321     1    27    27
browser |    27  100.0%         10     -  21518677  21518703              AB352321     1    27    27
browser |    27  100.0%         10     -  24977908  24977934              AB352321     1    27    27
browser |    27  100.0%         10     +  25848713  25848739              AB352321     1    27    27
browser |    27  100.0%         10     +  30361078  30361104              AB352321     1    27    27
browser |    27  100.0%         10     +  30696608  30696634              AB352321     1    27    27
browser |    27  100.0%         10     +  31365240  31365266              AB352321     1    27    27
browser |    27  100.0%         10     +  33766555  33766581              AB352321     1    27    27
browser |    27  100.0%         10     -  35599386  35599412              AB352321     1    27    27
browser |    27  100.0%         10     -  39637373  39637399              AB352321     1    27    27
browser |    27  100.0%         10     +  41723161  41723187              AB352321     1    27    27
browser |    27  100.0%         10     -  43646130  43646156              AB352321     1    27    27
browser |    27  100.0%         10     -  47908888  47908914              AB352321     1    27    27
browser |    27  100.0%         10     +  50371082  50371108              AB352321     1    27    27
browser |    27  100.0%         10     +  51763532  51763558              AB352321     1    27    27
browser |    27  100.0%         10     +  54469119  54469145              AB352321     1    27    27
browser |    27  100.0%         10     +  56603470  56603496              AB352321     1    27    27
browser |    27  100.0%         10     +  59222380  59222406              AB352321     1    27    27
browser |    27  100.0%         10     +  62448515  62448541              AB352321     1    27    27
browser |    27  100.0%         10     +  62946387  62946413              AB352321     1    27    27
browser |    27  100.0%         10     -  65096942  65096968              AB352321     1    27    27
browser |    27  100.0%         10     -  65475157  65475183              AB352321     1    27    27
browser |    27  100.0%         10     -  66558707  66558733              AB352321     1    27    27
browser |    27  100.0%         10     +  70633883  70633909              AB352321     1    27    27
browser |    27  100.0%         10     -  73691089  73691115              AB352321     1    27    27
browser |    27  100.0%         10     -  75216908  75216934              AB352321     1    27    27
browser |    27  100.0%         10     -  78652750  78652776              AB352321     1    27    27
browser |    27  100.0%         10     +  80816201  80816227              AB352321     1    27    27
browser |    27  100.0%         10     +  81810350  81810376              AB352321     1    27    27
browser |    27  100.0%         10     +  82777267  82777293              AB352321     1    27    27
browser |    27  100.0%         10     -  83507244  83507270              AB352321     1    27    27
browser |    27  100.0%         10     +  85556069  85556095              AB352321     1    27    27
browser |    27  100.0%         10     -  85604755  85604781              AB352321     1    27    27
browser |    27  100.0%         10     +  88803570  88803596              AB352321     1    27    27
browser |    27  100.0%         10     -  91650784  91650810              AB352321     1    27    27
browser |    27  100.0%         10     +  92356927  92356953              AB352321     1    27    27
browser |    27  100.0%         10     -  92586845  92586871              AB352321     1    27    27
browser |    27  100.0%         10     -  94198895  94198921              AB352321     1    27    27
browser |    27  100.0%         10     -  96028857  96028883              AB352321     1    27    27
browser |    25  100.0%         10     +  99181612  99181636              AB352321     3    27    27
browser |    27  100.0%         10     -  99382234  99382260              AB352321     1    27    27
browser |    27  100.0%         10     + 104397832 104397858              AB352321     1    27    27
browser |    27  100.0%         10     - 104411421 104411447              AB352321     1    27    27
browser |    27  100.0%         10     + 105017184 105017210              AB352321     1    27    27
browser |    27  100.0%         10     + 107841986 107842012              AB352321     1    27    27
browser |    27  100.0%         10     - 109151536 109151562              AB352321     1    27    27
browser |    27  100.0%         10     + 110838310 110838336              AB352321     1    27    27
browser |    27  100.0%         10     - 113559073 113559099              AB352321     1    27    27
browser |    27  100.0%         10     + 117911902 117911928              AB352321     1    27    27
browser |    27  100.0%         10     + 121004693 121004719              AB352321     1    27    27
browser |    27  100.0%         10     - 122140000 122140026              AB352321     1    27    27
browser |    27  100.0%         10     - 122202428 122202454              AB352321     1    27    27
browser |    27  100.0%         10     + 124418854 124418880              AB352321     1    27    27
browser |    27  100.0%         10     - 124516812 124516838              AB352321     1    27    27
browser |    27  100.0%         10     - 129225156 129225182              AB352321     1    27    27
browser |    27  100.0%         10     + 129765050 129765076              AB352321     1    27    27
browser |    27  100.0%         10     - 130396468 130396494              AB352321     1    27    27
browser |    27  100.0%         11     +   5312480   5312506              AB352321     1    27    27
browser |    27  100.0%         11     -   6091956   6091982              AB352321     1    27    27
browser |    27  100.0%         11     +   6485307   6485333              AB352321     1    27    27
browser |    27  100.0%         11     +   7856741   7856767              AB352321     1    27    27
browser |    27  100.0%         11     -   7984313   7984339              AB352321     1    27    27
browser |    27  100.0%         11     +  10716947  10716973              AB352321     1    27    27
browser |    27  100.0%         11     +  12518558  12518584              AB352321     1    27    27
browser |    27  100.0%         11     +  12752233  12752259              AB352321     1    27    27
browser |    27  100.0%         11     +  13825229  13825255              AB352321     1    27    27
browser |    27  100.0%         11     +  14216954  14216980              AB352321     1    27    27
browser |    27  100.0%         11     -  15233007  15233033              AB352321     1    27    27
browser |    27  100.0%         11     +  15812213  15812239              AB352321     1    27    27
browser |    27  100.0%         11     +  15837331  15837357              AB352321     1    27    27
browser |    27  100.0%         11     -  20459665  20459691              AB352321     1    27    27
browser |    27  100.0%         11     +  20470673  20470699              AB352321     1    27    27
browser |    27  100.0%         11     -  23169042  23169068              AB352321     1    27    27
browser |    27  100.0%         11     -  27365565  27365591              AB352321     1    27    27
browser |    27  100.0%         11     -  27901544  27901570              AB352321     1    27    27
browser |    27  100.0%         11     +  28053933  28053959              AB352321     1    27    27
browser |    27  100.0%         11     +  31165030  31165056              AB352321     1    27    27
browser |    27  100.0%         11     -  31398031  31398057              AB352321     1    27    27
browser |    27  100.0%         11     +  31726511  31726537              AB352321     1    27    27
browser |    27  100.0%         11     -  39955016  39955042              AB352321     1    27    27
browser |    27  100.0%         11     -  65343078  65343104              AB352321     1    27    27
browser |    27  100.0%         11     -  66839115  66839141              AB352321     1    27    27
browser |    27  100.0%         11     +  74026393  74026419              AB352321     1    27    27
browser |    27  100.0%         11     -  74110979  74111005              AB352321     1    27    27
browser |    27  100.0%         11     +  74781858  74781884              AB352321     1    27    27
browser |    27  100.0%         11     -  79124084  79124110              AB352321     1    27    27
browser |    27  100.0%         11     -  82225289  82225315              AB352321     1    27    27
browser |    27  100.0%         11     +  84958145  84958171              AB352321     1    27    27
browser |    27  100.0%         11     -  85176856  85176882              AB352321     1    27    27
browser |    27  100.0%         11     +  86740513  86740539              AB352321     1    27    27
browser |    27  100.0%         11     -  88802254  88802280              AB352321     1    27    27
browser |    27  100.0%         11     -  90201672  90201698              AB352321     1    27    27
browser |    27  100.0%         11     +  90798599  90798625              AB352321     1    27    27
browser |    27  100.0%         11     -  90851460  90851486              AB352321     1    27    27
browser |    27  100.0%         11     +  98510731  98510757              AB352321     1    27    27
browser |    27  100.0%         11     -  99603990  99604016              AB352321     1    27    27
browser |    27  100.0%         11     + 100559878 100559904              AB352321     1    27    27
browser |    27  100.0%         11     - 105919547 105919573              AB352321     1    27    27
browser |    27  100.0%         11     - 106183982 106184008              AB352321     1    27    27
browser |    27  100.0%         11     + 111079973 111079999              AB352321     1    27    27
browser |    27  100.0%         11     - 111106930 111106956              AB352321     1    27    27
browser |    27  100.0%         11     + 113809657 113809683              AB352321     1    27    27
browser |    27  100.0%         11     + 116654666 116654692              AB352321     1    27    27
browser |    27  100.0%         11     + 116683029 116683055              AB352321     1    27    27
browser |    27  100.0%         11     + 117395309 117395335              AB352321     1    27    27
browser |    27  100.0%         11     + 120218618 120218644              AB352321     1    27    27
browser |    27  100.0%         11     + 120965186 120965212              AB352321     1    27    27
browser |    27  100.0%         12     +   3059008   3059034              AB352321     1    27    27
browser |    27  100.0%         12     -   3381267   3381293              AB352321     1    27    27
browser |    27  100.0%         12     +   6573179   6573205              AB352321     1    27    27
browser |    27  100.0%         12     -  11154120  11154146              AB352321     1    27    27
browser |    27  100.0%         12     +  17178857  17178883              AB352321     1    27    27
browser |    27  100.0%         12     +  17297920  17297946              AB352321     1    27    27
browser |    27  100.0%         12     +  17909273  17909299              AB352321     1    27    27
browser |    27  100.0%         12     +  17980701  17980727              AB352321     1    27    27
browser |    27  100.0%         12     -  19308706  19308732              AB352321     1    27    27
browser |    27  100.0%         12     +  24452104  24452130              AB352321     1    27    27
browser |    27  100.0%         12     +  25644617  25644643              AB352321     1    27    27
browser |    27  100.0%         12     -  27282597  27282623              AB352321     1    27    27
browser |    27  100.0%         12     -  31408616  31408642              AB352321     1    27    27
browser |    27  100.0%         12     +  32650083  32650109              AB352321     1    27    27
browser |    27  100.0%         12     +  32955961  32955987              AB352321     1    27    27
browser |    27  100.0%         12     +  36668051  36668077              AB352321     1    27    27
browser |    27  100.0%         12     +  40233786  40233812              AB352321     1    27    27
browser |    27  100.0%         12     +  40458729  40458755              AB352321     1    27    27
browser |    27  100.0%         12     +  41420139  41420165              AB352321     1    27    27
browser |    27  100.0%         12     +  42921984  42922010              AB352321     1    27    27
browser |    27  100.0%         12     -  44198979  44199005              AB352321     1    27    27
browser |    27  100.0%         12     -  44812948  44812974              AB352321     1    27    27
browser |    27  100.0%         12     -  52777350  52777376              AB352321     1    27    27
browser |    27  100.0%         12     +  54676783  54676809              AB352321     1    27    27
browser |    27  100.0%         12     -  61336366  61336392              AB352321     1    27    27
browser |    27  100.0%         12     -  65074405  65074431              AB352321     1    27    27
browser |    27  100.0%         12     -  65848468  65848494              AB352321     1    27    27
browser |    27  100.0%         12     -  66454267  66454293              AB352321     1    27    27
browser |    27  100.0%         12     -  68669021  68669047              AB352321     1    27    27
browser |    27  100.0%         12     -  70965243  70965269              AB352321     1    27    27
browser |    27  100.0%         12     -  79609073  79609099              AB352321     1    27    27
browser |    27  100.0%         12     +  81634136  81634162              AB352321     1    27    27
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View details of parts of alignment within browser window
.
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