AB347221
 

Information on mRNA AB347221

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA12422, 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: n/a
Development stage: growing stage
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB347221
Position: chrX:15589821-15589840

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 |    20  100.0%          X     -  15589821  15589840              AB347221     3    22    22
browser |    20  100.0%          1     +   4887333   4887352              AB347221     3    22    22
browser |    20  100.0%          1     -   6396690   6396709              AB347221     3    22    22
browser |    20  100.0%          1     +   7351329   7351348              AB347221     3    22    22
browser |    20  100.0%          1     -   7676587   7676606              AB347221     3    22    22
browser |    20  100.0%          1     -   7909101   7909120              AB347221     3    22    22
browser |    20  100.0%          1     +   8783257   8783276              AB347221     3    22    22
browser |    20  100.0%          1     +   8868543   8868562              AB347221     3    22    22
browser |    20  100.0%          1     -  11777846  11777865              AB347221     3    22    22
browser |    20  100.0%          1     -  12552452  12552471              AB347221     3    22    22
browser |    20  100.0%          1     -  12997761  12997780              AB347221     3    22    22
browser |    20  100.0%          1     +  14153748  14153767              AB347221     3    22    22
browser |    20  100.0%          1     -  15282513  15282532              AB347221     3    22    22
browser |    20  100.0%          1     -  15776414  15776433              AB347221     3    22    22
browser |    20  100.0%          1     +  16087876  16087895              AB347221     3    22    22
browser |    20  100.0%          1     -  16452530  16452549              AB347221     3    22    22
browser |    20  100.0%          1     -  18227515  18227534              AB347221     3    22    22
browser |    20  100.0%          1     +  19380396  19380415              AB347221     3    22    22
browser |    20  100.0%          1     -  19395540  19395559              AB347221     3    22    22
browser |    20  100.0%          1     +  20197071  20197090              AB347221     3    22    22
browser |    20  100.0%          1     -  20464175  20464194              AB347221     3    22    22
browser |    20  100.0%          1     +  20773291  20773310              AB347221     3    22    22
browser |    20  100.0%          1     -  22225457  22225476              AB347221     3    22    22
browser |    20  100.0%          1     +  27108358  27108377              AB347221     3    22    22
browser |    20  100.0%          1     -  30305875  30305894              AB347221     3    22    22
browser |    20  100.0%          1     -  30715077  30715096              AB347221     3    22    22
browser |    20  100.0%          1     +  30933386  30933405              AB347221     3    22    22
browser |    20  100.0%          1     -  31811315  31811334              AB347221     3    22    22
browser |    20  100.0%          1     +  32524908  32524927              AB347221     3    22    22
browser |    20  100.0%          1     +  36789800  36789819              AB347221     3    22    22
browser |    20  100.0%          1     +  37643757  37643776              AB347221     3    22    22
browser |    20  100.0%          1     +  40277681  40277700              AB347221     3    22    22
browser |    20  100.0%          1     +  46524559  46524578              AB347221     3    22    22
browser |    20  100.0%          1     +  80959329  80959348              AB347221     3    22    22
browser |    20  100.0%          1     -  84314903  84314922              AB347221     3    22    22
browser |    20  100.0%          1     +  85137181  85137200              AB347221     3    22    22
browser |    20  100.0%          1     +  85414614  85414633              AB347221     3    22    22
browser |    20  100.0%          1     -  86002417  86002436              AB347221     3    22    22
browser |    20  100.0%          1     +  87545586  87545605              AB347221     3    22    22
browser |    20  100.0%          1     +  88542425  88542444              AB347221     3    22    22
browser |    20  100.0%          1     -  91161547  91161566              AB347221     3    22    22
browser |    20  100.0%          1     -  91397143  91397162              AB347221     3    22    22
browser |    20  100.0%          1     +  92280638  92280657              AB347221     3    22    22
browser |    20  100.0%          1     +  97029372  97029391              AB347221     3    22    22
browser |    20  100.0%          1     -  97107382  97107401              AB347221     3    22    22
browser |    20  100.0%          1     +  98570614  98570633              AB347221     3    22    22
browser |    20  100.0%          1     +  98995746  98995765              AB347221     3    22    22
browser |    20  100.0%          1     +  99028116  99028135              AB347221     3    22    22
browser |    20  100.0%          1     - 101917105 101917124              AB347221     3    22    22
browser |    20  100.0%          1     + 102000830 102000849              AB347221     3    22    22
browser |    22  100.0%          1     + 102063416 102063438              AB347221     1    22    22
browser |    20  100.0%          1     - 102123352 102123371              AB347221     3    22    22
browser |    20  100.0%          1     + 103083356 103083375              AB347221     3    22    22
browser |    20  100.0%          1     - 104329226 104329245              AB347221     3    22    22
browser |    20  100.0%          1     + 105317217 105317236              AB347221     3    22    22
browser |    20  100.0%          1     - 106992734 106992753              AB347221     3    22    22
browser |    20  100.0%          1     - 108940599 108940618              AB347221     3    22    22
browser |    20  100.0%          1     - 109471061 109471080              AB347221     3    22    22
browser |    20  100.0%          1     + 111419222 111419241              AB347221     3    22    22
browser |    20  100.0%          1     + 111658493 111658512              AB347221     3    22    22
browser |    20  100.0%          1     - 125584233 125584252              AB347221     3    22    22
browser |    20  100.0%          1     - 125710849 125710868              AB347221     3    22    22
browser |    20  100.0%          1     - 127210920 127210939              AB347221     3    22    22
browser |    20  100.0%          1     - 129768353 129768372              AB347221     3    22    22
browser |    20  100.0%          1     - 130158988 130159007              AB347221     3    22    22
browser |    20  100.0%          1     + 158634001 158634020              AB347221     3    22    22
browser |    20  100.0%          1     - 158946261 158946280              AB347221     3    22    22
browser |    20  100.0%          1     - 159824728 159824747              AB347221     3    22    22
browser |    20  100.0%          1     + 162778378 162778397              AB347221     3    22    22
browser |    20  100.0%          1     + 167385518 167385537              AB347221     3    22    22
browser |    20  100.0%          1     - 174016163 174016182              AB347221     3    22    22
browser |    20  100.0%          1     - 176174043 176174062              AB347221     3    22    22
browser |    20  100.0%          1     - 178300218 178300237              AB347221     3    22    22
browser |    20  100.0%          1     + 182855320 182855339              AB347221     3    22    22
browser |    20  100.0%          1     + 185250839 185250858              AB347221     3    22    22
browser |    20  100.0%          1     + 188972654 188972673              AB347221     3    22    22
browser |    20  100.0%          1     + 190879631 190879650              AB347221     3    22    22
browser |    20  100.0%          1     + 191386457 191386476              AB347221     3    22    22
browser |    20  100.0%          1     - 191603432 191603451              AB347221     3    22    22
browser |    20  100.0%         10     -   8027948   8027967              AB347221     3    22    22
browser |    20  100.0%         10     -   9440648   9440667              AB347221     3    22    22
browser |    20  100.0%         10     +  10285724  10285743              AB347221     3    22    22
browser |    20  100.0%         10     +  10354771  10354790              AB347221     3    22    22
browser |    20  100.0%         10     +  14538973  14538992              AB347221     3    22    22
browser |    20  100.0%         10     +  15331899  15331918              AB347221     3    22    22
browser |    20  100.0%         10     -  15673244  15673263              AB347221     3    22    22
browser |    20  100.0%         10     +  17376143  17376162              AB347221     3    22    22
browser |    20  100.0%         10     +  18104989  18105008              AB347221     3    22    22
browser |    20  100.0%         10     +  18107452  18107471              AB347221     3    22    22
browser |    20  100.0%         10     +  19165762  19165781              AB347221     3    22    22
browser |    20  100.0%         10     -  22897092  22897111              AB347221     3    22    22
browser |    20  100.0%         10     -  23707476  23707495              AB347221     3    22    22
browser |    20  100.0%         10     -  24047114  24047133              AB347221     3    22    22
browser |    20  100.0%         10     -  28218752  28218771              AB347221     3    22    22
browser |    20  100.0%         10     +  29673824  29673843              AB347221     3    22    22
browser |    20  100.0%         10     +  31591510  31591529              AB347221     3    22    22
browser |    20  100.0%         10     +  32213374  32213393              AB347221     3    22    22
browser |    20  100.0%         10     -  33585201  33585220              AB347221     3    22    22
browser |    20  100.0%         10     -  34102763  34102782              AB347221     3    22    22
browser |    20  100.0%         10     +  36471717  36471736              AB347221     3    22    22
browser |    20  100.0%         10     +  37171221  37171240              AB347221     3    22    22
browser |    20  100.0%         10     +  37676534  37676553              AB347221     3    22    22
browser |    20  100.0%         10     +  41198700  41198719              AB347221     3    22    22
browser |    20  100.0%         10     -  44467692  44467711              AB347221     3    22    22
browser |    20  100.0%         10     +  45444142  45444161              AB347221     3    22    22
browser |    20  100.0%         10     -  45858138  45858157              AB347221     3    22    22
browser |    20  100.0%         10     -  46861435  46861454              AB347221     3    22    22
browser |    20  100.0%         10     -  52513488  52513507              AB347221     3    22    22
browser |    20  100.0%         10     -  62473462  62473481              AB347221     3    22    22
browser |    20  100.0%         10     -  64376445  64376464              AB347221     3    22    22
browser |    20  100.0%         10     -  65442337  65442356              AB347221     3    22    22
browser |    20  100.0%         10     +  82293767  82293786              AB347221     3    22    22
browser |    20  100.0%         10     +  82353905  82353924              AB347221     3    22    22
browser |    20  100.0%         10     -  83634878  83634897              AB347221     3    22    22
browser |    20  100.0%         10     -  84308764  84308783              AB347221     3    22    22
browser |    20  100.0%         10     +  87611704  87611723              AB347221     3    22    22
browser |    20  100.0%         10     +  87886368  87886387              AB347221     3    22    22
browser |    20  100.0%         10     -  87909213  87909232              AB347221     3    22    22
browser |    20  100.0%         10     +  88704025  88704044              AB347221     3    22    22
browser |    20  100.0%         10     -  90124531  90124550              AB347221     3    22    22
browser |    20  100.0%         10     -  94122002  94122021              AB347221     3    22    22
browser |    20  100.0%         10     -  97160032  97160051              AB347221     3    22    22
browser |    20  100.0%         10     -  98789428  98789447              AB347221     3    22    22
browser |    20  100.0%         10     - 100906891 100906910              AB347221     3    22    22
browser |    20  100.0%         10     - 101151401 101151420              AB347221     3    22    22
browser |    20  100.0%         10     + 103317056 103317075              AB347221     3    22    22
browser |    20  100.0%         10     - 103359794 103359813              AB347221     3    22    22
browser |    20  100.0%         10     + 104670902 104670921              AB347221     3    22    22
browser |    20  100.0%         10     - 104811649 104811668              AB347221     3    22    22
browser |    20  100.0%         10     + 108832675 108832694              AB347221     3    22    22
browser |    20  100.0%         10     + 118100400 118100419              AB347221     3    22    22
browser |    20  100.0%         10     - 121242930 121242949              AB347221     3    22    22
browser |    20  100.0%         10     + 121402728 121402747              AB347221     3    22    22
browser |    20  100.0%         10     + 124749875 124749894              AB347221     3    22    22
browser |    20  100.0%         10     + 125424322 125424341              AB347221     3    22    22
browser |    20  100.0%         10     - 126296370 126296389              AB347221     3    22    22
browser |    20  100.0%         10     + 126622179 126622198              AB347221     3    22    22
browser |    20  100.0%         10     + 128647306 128647325              AB347221     3    22    22
browser |    20  100.0%         10     - 128691179 128691198              AB347221     3    22    22
browser |    20  100.0%         10     - 130300123 130300142              AB347221     3    22    22
browser |    20  100.0%         10     - 130301612 130301631              AB347221     3    22    22
browser |    20  100.0%         11     -   3953651   3953670              AB347221     3    22    22
browser |    21  100.0%         11     -   6238493   6238513              AB347221     2    22    22
browser |    20  100.0%         11     +   7534864   7534883              AB347221     3    22    22
browser |    20  100.0%         11     -  10341083  10341102              AB347221     3    22    22
browser |    20  100.0%         11     +  11348998  11349017              AB347221     3    22    22
browser |    20  100.0%         11     +  13008403  13008422              AB347221     3    22    22
browser |    20  100.0%         11     -  13860533  13860552              AB347221     3    22    22
browser |    20  100.0%         11     -  18407918  18407937              AB347221     3    22    22
browser |    20  100.0%         11     +  21344430  21344449              AB347221     3    22    22
browser |    20  100.0%         11     -  21542109  21542128              AB347221     3    22    22
browser |    20  100.0%         11     -  22486040  22486059              AB347221     3    22    22
browser |    20  100.0%         11     -  22519414  22519433              AB347221     3    22    22
browser |    20  100.0%         11     -  22651371  22651390              AB347221     3    22    22
browser |    20  100.0%         11     +  23036063  23036082              AB347221     3    22    22
browser |    20  100.0%         11     +  24478308  24478327              AB347221     3    22    22
browser |    20  100.0%         11     +  25192046  25192065              AB347221     3    22    22
browser |    20  100.0%         11     +  27139867  27139886              AB347221     3    22    22
browser |    20  100.0%         11     -  27592338  27592357              AB347221     3    22    22
browser |    20  100.0%         11     -  28914962  28914981              AB347221     3    22    22
browser |    20  100.0%         11     -  31294894  31294913              AB347221     3    22    22
browser |    20  100.0%         11     +  31372398  31372417              AB347221     3    22    22
browser |    20  100.0%         11     +  34858545  34858564              AB347221     3    22    22
browser |    20  100.0%         11     -  40161796  40161815              AB347221     3    22    22
browser |    20  100.0%         11     -  40621423  40621442              AB347221     3    22    22
browser |    20  100.0%         11     -  43129317  43129336              AB347221     3    22    22
browser |    20  100.0%         11     +  45541858  45541877              AB347221     3    22    22
browser |    20  100.0%         11     -  48795093  48795112              AB347221     3    22    22
browser |    20  100.0%         11     +  50240807  50240826              AB347221     3    22    22
browser |    20  100.0%         11     +  60705853  60705872              AB347221     3    22    22
browser |    20  100.0%         11     +  61336431  61336450              AB347221     3    22    22
browser |    20  100.0%         11     +  71157453  71157472              AB347221     3    22    22
browser |    20  100.0%         11     +  77146687  77146706              AB347221     3    22    22
browser |    20  100.0%         11     -  81397734  81397753              AB347221     3    22    22
browser |    20  100.0%         11     -  83576667  83576686              AB347221     3    22    22
browser |    20  100.0%         11     -  83618507  83618526              AB347221     3    22    22
browser |    20  100.0%         11     -  87349606  87349625              AB347221     3    22    22
browser |    20  100.0%         11     -  88066628  88066647              AB347221     3    22    22
browser |    20  100.0%         11     +  90938866  90938885              AB347221     3    22    22
browser |    20  100.0%         11     +  91058659  91058678              AB347221     3    22    22
browser |    20  100.0%         11     -  92716020  92716039              AB347221     3    22    22
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browser |    20  100.0%         11     -  95212430  95212449              AB347221     3    22    22
browser |    20  100.0%         11     +  96134999  96135018              AB347221     3    22    22
browser |    20  100.0%         11     +  99065225  99065244              AB347221     3    22    22
browser |    20  100.0%         11     + 103559448 103559467              AB347221     3    22    22
browser |    20  100.0%         11     - 104151590 104151609              AB347221     3    22    22
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browser |    20  100.0%         11     + 114463707 114463726              AB347221     3    22    22
browser |    20  100.0%         11     + 115027221 115027240              AB347221     3    22    22
browser |    20  100.0%         11     - 115623508 115623527              AB347221     3    22    22
browser |    20  100.0%         11     + 119551502 119551521              AB347221     3    22    22
browser |    20  100.0%         11     + 121097100 121097119              AB347221     3    22    22
browser |    20  100.0%         12     -   3276511   3276530              AB347221     3    22    22
browser |    20  100.0%         12     -   8679149   8679168              AB347221     3    22    22
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browser |    20  100.0%         12     -  17262389  17262408              AB347221     3    22    22
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browser |    20  100.0%         12     +  19852284  19852303              AB347221     3    22    22
browser |    20  100.0%         12     +  20100709  20100728              AB347221     3    22    22
browser |    20  100.0%         12     +  20637683  20637702              AB347221     3    22    22
browser |    20  100.0%         12     +  22440599  22440618              AB347221     3    22    22
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browser |    20  100.0%         12     -  27829838  27829857              AB347221     3    22    22
browser |    20  100.0%         12     +  28808231  28808250              AB347221     3    22    22
browser |    20  100.0%         12     -  29155485  29155504              AB347221     3    22    22
browser |    20  100.0%         12     -  29449991  29450010              AB347221     3    22    22
browser |    20  100.0%         12     -  30106426  30106445              AB347221     3    22    22
browser |    20  100.0%         12     +  31213408  31213427              AB347221     3    22    22
browser |    20  100.0%         12     +  32268402  32268421              AB347221     3    22    22
browser |    20  100.0%         12     -  36730250  36730269              AB347221     3    22    22
browser |    20  100.0%         12     -  37680333  37680352              AB347221     3    22    22
browser |    20  100.0%         12     -  40237514  40237533              AB347221     3    22    22
browser |    20  100.0%         12     -  44603467  44603486              AB347221     3    22    22
browser |    20  100.0%         12     +  81873595  81873614              AB347221     3    22    22
browser |    20  100.0%         12     -  82407176  82407195              AB347221     3    22    22
browser |    20  100.0%         12     -  82946363  82946382              AB347221     3    22    22
browser |    20  100.0%         12     -  83335887  83335906              AB347221     3    22    22
browser |    20  100.0%         12     -  83337452  83337471              AB347221     3    22    22
browser |    20  100.0%         12     +  89766684  89766703              AB347221     3    22    22
browser |    20  100.0%         12     +  91563245  91563264              AB347221     3    22    22
browser |    20  100.0%         12     +  96077606  96077625              AB347221     3    22    22
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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