AB350230
 

Information on mRNA AB350230

Description: Mus musculus non-coding RNA, oocyte_piRNA1046, 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: AB350230
Position: chr12:56795204-56795231

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 |    28  100.0%         12     +  56795204  56795231              AB350230     1    28    28
browser |    28  100.0%          1     +   5875138   5875165              AB350230     1    28    28
browser |    28  100.0%          1     -   6242431   6242458              AB350230     1    28    28
browser |    28  100.0%          1     +   6501167   6501194              AB350230     1    28    28
browser |    28  100.0%          1     -   8070445   8070472              AB350230     1    28    28
browser |    28  100.0%          1     -   8232880   8232907              AB350230     1    28    28
browser |    28  100.0%          1     +  10800664  10800691              AB350230     1    28    28
browser |    28  100.0%          1     +  11957916  11957943              AB350230     1    28    28
browser |    28  100.0%          1     -  16814958  16814985              AB350230     1    28    28
browser |    28  100.0%          1     -  18590832  18590859              AB350230     1    28    28
browser |    28  100.0%          1     -  19699172  19699199              AB350230     1    28    28
browser |    28  100.0%          1     -  23344834  23344861              AB350230     1    28    28
browser |    28  100.0%          1     +  26388829  26388856              AB350230     1    28    28
browser |    28  100.0%          1     -  26459573  26459600              AB350230     1    28    28
browser |    28  100.0%          1     +  26510023  26510050              AB350230     1    28    28
browser |    28  100.0%          1     +  29982383  29982410              AB350230     1    28    28
browser |    28  100.0%          1     -  34389845  34389872              AB350230     1    28    28
browser |    28  100.0%          1     -  34957671  34957698              AB350230     1    28    28
browser |    28  100.0%          1     -  35834058  35834085              AB350230     1    28    28
browser |    28  100.0%          1     -  37817099  37817126              AB350230     1    28    28
browser |    28  100.0%          1     -  38747433  38747460              AB350230     1    28    28
browser |    28  100.0%          1     -  40741017  40741044              AB350230     1    28    28
browser |    28  100.0%          1     -  48132843  48132870              AB350230     1    28    28
browser |    28  100.0%          1     +  48394071  48394098              AB350230     1    28    28
browser |    28  100.0%          1     +  48841597  48841624              AB350230     1    28    28
browser |    28  100.0%          1     -  52632697  52632724              AB350230     1    28    28
browser |    28  100.0%          1     +  53169361  53169388              AB350230     1    28    28
browser |    28  100.0%          1     +  58363100  58363127              AB350230     1    28    28
browser |    28  100.0%          1     +  58851410  58851437              AB350230     1    28    28
browser |    28  100.0%          1     +  60764588  60764615              AB350230     1    28    28
browser |    28  100.0%          1     +  62573856  62573883              AB350230     1    28    28
browser |    28  100.0%          1     +  64217923  64217950              AB350230     1    28    28
browser |    28  100.0%          1     +  66057360  66057387              AB350230     1    28    28
browser |    28  100.0%          1     +  81542463  81542490              AB350230     1    28    28
browser |    28  100.0%          1     -  82483119  82483146              AB350230     1    28    28
browser |    28  100.0%          1     +  84974181  84974208              AB350230     1    28    28
browser |    28  100.0%          1     -  87394379  87394406              AB350230     1    28    28
browser |    28  100.0%          1     -  89130341  89130368              AB350230     1    28    28
browser |    28  100.0%          1     +  91399520  91399547              AB350230     1    28    28
browser |    28  100.0%          1     +  93035788  93035815              AB350230     1    28    28
browser |    28  100.0%          1     -  93888428  93888455              AB350230     1    28    28
browser |    28  100.0%          1     -  97108347  97108374              AB350230     1    28    28
browser |    28  100.0%          1     + 101906456 101906483              AB350230     1    28    28
browser |    28  100.0%          1     - 102965896 102965923              AB350230     1    28    28
browser |    28  100.0%          1     + 103133488 103133515              AB350230     1    28    28
browser |    28  100.0%          1     - 103521154 103521181              AB350230     1    28    28
browser |    28  100.0%          1     + 104217878 104217905              AB350230     1    28    28
browser |    28  100.0%          1     + 107967110 107967137              AB350230     1    28    28
browser |    28  100.0%          1     + 108337175 108337202              AB350230     1    28    28
browser |    28  100.0%          1     + 109056984 109057011              AB350230     1    28    28
browser |    28  100.0%          1     - 109547628 109547655              AB350230     1    28    28
browser |    28  100.0%          1     - 110261400 110261427              AB350230     1    28    28
browser |    28  100.0%          1     + 110865917 110865944              AB350230     1    28    28
browser |    28  100.0%          1     + 111181942 111181969              AB350230     1    28    28
browser |    28  100.0%          1     - 112862591 112862618              AB350230     1    28    28
browser |    28  100.0%          1     - 112950307 112950334              AB350230     1    28    28
browser |    28  100.0%          1     - 114117616 114117643              AB350230     1    28    28
browser |    28  100.0%          1     + 115813683 115813710              AB350230     1    28    28
browser |    28  100.0%          1     + 116576586 116576613              AB350230     1    28    28
browser |    28  100.0%          1     + 117630244 117630271              AB350230     1    28    28
browser |    28  100.0%          1     + 120499164 120499191              AB350230     1    28    28
browser |    28  100.0%          1     - 125251091 125251118              AB350230     1    28    28
browser |    28  100.0%          1     - 126356792 126356819              AB350230     1    28    28
browser |    28  100.0%          1     - 126871512 126871539              AB350230     1    28    28
browser |    28  100.0%          1     - 130466371 130466398              AB350230     1    28    28
browser |    28  100.0%          1     + 159797918 159797945              AB350230     1    28    28
browser |    28  100.0%          1     + 160644031 160644058              AB350230     1    28    28
browser |    28  100.0%          1     - 162674620 162674647              AB350230     1    28    28
browser |    28  100.0%          1     + 163296648 163296675              AB350230     1    28    28
browser |    28  100.0%          1     - 166183686 166183713              AB350230     1    28    28
browser |    28  100.0%          1     + 166591291 166591318              AB350230     1    28    28
browser |    28  100.0%          1     - 169375869 169375896              AB350230     1    28    28
browser |    28  100.0%          1     - 169949860 169949887              AB350230     1    28    28
browser |    28  100.0%          1     - 172096699 172096726              AB350230     1    28    28
browser |    28  100.0%          1     + 174870130 174870157              AB350230     1    28    28
browser |    28  100.0%          1     + 176371212 176371239              AB350230     1    28    28
browser |    28  100.0%          1     - 178008178 178008205              AB350230     1    28    28
browser |    28  100.0%          1     - 180443364 180443391              AB350230     1    28    28
browser |    28  100.0%          1     + 181091668 181091695              AB350230     1    28    28
browser |    28  100.0%          1     - 181326457 181326484              AB350230     1    28    28
browser |    28  100.0%          1     - 191844281 191844308              AB350230     1    28    28
browser |    28  100.0%         10     +   3551507   3551534              AB350230     1    28    28
browser |    28  100.0%         10     +  19415222  19415249              AB350230     1    28    28
browser |    28  100.0%         10     -  21091852  21091879              AB350230     1    28    28
browser |    28  100.0%         10     +  21518795  21518822              AB350230     1    28    28
browser |    28  100.0%         10     +  22559741  22559768              AB350230     1    28    28
browser |    28  100.0%         10     -  24566876  24566903              AB350230     1    28    28
browser |    28  100.0%         10     +  24978026  24978053              AB350230     1    28    28
browser |    28  100.0%         10     -  25848593  25848620              AB350230     1    28    28
browser |    28  100.0%         10     -  30696489  30696516              AB350230     1    28    28
browser |    28  100.0%         10     -  30971171  30971198              AB350230     1    28    28
browser |    28  100.0%         10     -  31365120  31365147              AB350230     1    28    28
browser |    28  100.0%         10     -  31630264  31630291              AB350230     1    28    28
browser |    28  100.0%         10     -  33766436  33766463              AB350230     1    28    28
browser |    28  100.0%         10     +  34618399  34618426              AB350230     1    28    28
browser |    28  100.0%         10     -  41723042  41723069              AB350230     1    28    28
browser |    28  100.0%         10     +  43646248  43646275              AB350230     1    28    28
browser |    28  100.0%         10     +  45431577  45431604              AB350230     1    28    28
browser |    28  100.0%         10     -  50370963  50370990              AB350230     1    28    28
browser |    28  100.0%         10     -  51763413  51763440              AB350230     1    28    28
browser |    28  100.0%         10     -  54469000  54469027              AB350230     1    28    28
browser |    28  100.0%         10     +  55592209  55592236              AB350230     1    28    28
browser |    28  100.0%         10     -  56603351  56603378              AB350230     1    28    28
browser |    28  100.0%         10     -  57020270  57020297              AB350230     1    28    28
browser |    28  100.0%         10     -  59222261  59222288              AB350230     1    28    28
browser |    28  100.0%         10     -  62448395  62448422              AB350230     1    28    28
browser |    28  100.0%         10     +  65475276  65475303              AB350230     1    28    28
browser |    28  100.0%         10     +  65787174  65787201              AB350230     1    28    28
browser |    28  100.0%         10     +  66558826  66558853              AB350230     1    28    28
browser |    28  100.0%         10     +  75217026  75217053              AB350230     1    28    28
browser |    28  100.0%         10     +  78652869  78652896              AB350230     1    28    28
browser |    28  100.0%         10     -  80816082  80816109              AB350230     1    28    28
browser |    28  100.0%         10     -  81810230  81810257              AB350230     1    28    28
browser |    28  100.0%         10     +  83507362  83507389              AB350230     1    28    28
browser |    28  100.0%         10     -  83627857  83627884              AB350230     1    28    28
browser |    28  100.0%         10     -  84585148  84585175              AB350230     1    28    28
browser |    28  100.0%         10     -  85555949  85555976              AB350230     1    28    28
browser |    28  100.0%         10     -  88803451  88803478              AB350230     1    28    28
browser |    28  100.0%         10     +  90161052  90161079              AB350230     1    28    28
browser |    28  100.0%         10     +  94199013  94199040              AB350230     1    28    28
browser |    28  100.0%         10     +  95993684  95993711              AB350230     1    28    28
browser |    28  100.0%         10     +  96028976  96029003              AB350230     1    28    28
browser |    28  100.0%         10     +  98934635  98934662              AB350230     1    28    28
browser |    28  100.0%         10     -  99181491  99181518              AB350230     1    28    28
browser |    28  100.0%         10     - 104397712 104397739              AB350230     1    28    28
browser |    28  100.0%         10     + 104655928 104655955              AB350230     1    28    28
browser |    28  100.0%         10     - 104677940 104677967              AB350230     1    28    28
browser |    28  100.0%         10     + 105509093 105509120              AB350230     1    28    28
browser |    28  100.0%         10     - 107841867 107841894              AB350230     1    28    28
browser |    28  100.0%         10     + 109151654 109151681              AB350230     1    28    28
browser |    28  100.0%         10     - 111893663 111893690              AB350230     1    28    28
browser |    28  100.0%         10     + 113559191 113559218              AB350230     1    28    28
browser |    28  100.0%         10     + 116442743 116442770              AB350230     1    28    28
browser |    28  100.0%         10     - 117911783 117911810              AB350230     1    28    28
browser |    28  100.0%         10     - 121004574 121004601              AB350230     1    28    28
browser |    28  100.0%         10     + 122202546 122202573              AB350230     1    28    28
browser |    28  100.0%         10     - 124418735 124418762              AB350230     1    28    28
browser |    28  100.0%         10     - 124446235 124446262              AB350230     1    28    28
browser |    28  100.0%         10     + 124516930 124516957              AB350230     1    28    28
browser |    28  100.0%         10     + 129225274 129225301              AB350230     1    28    28
browser |    28  100.0%         10     - 129764931 129764958              AB350230     1    28    28
browser |    28  100.0%         10     + 130396587 130396614              AB350230     1    28    28
browser |    28  100.0%         11     -   5312360   5312387              AB350230     1    28    28
browser |    28  100.0%         11     -   6485188   6485215              AB350230     1    28    28
browser |    28  100.0%         11     +   9658563   9658590              AB350230     1    28    28
browser |    28  100.0%         11     -  10716827  10716854              AB350230     1    28    28
browser |    28  100.0%         11     +  12457872  12457899              AB350230     1    28    28
browser |    28  100.0%         11     -  12518439  12518466              AB350230     1    28    28
browser |    28  100.0%         11     +  12904599  12904626              AB350230     1    28    28
browser |    28  100.0%         11     -  15184214  15184241              AB350230     1    28    28
browser |    28  100.0%         11     -  15837211  15837238              AB350230     1    28    28
browser |    28  100.0%         11     -  16182063  16182090              AB350230     1    28    28
browser |    28  100.0%         11     +  19516759  19516786              AB350230     1    28    28
browser |    28  100.0%         11     +  22285836  22285863              AB350230     1    28    28
browser |    28  100.0%         11     -  22532399  22532426              AB350230     1    28    28
browser |    28  100.0%         11     +  23169160  23169187              AB350230     1    28    28
browser |    28  100.0%         11     -  26510148  26510175              AB350230     1    28    28
browser |    28  100.0%         11     +  27901662  27901689              AB350230     1    28    28
browser |    28  100.0%         11     -  28053814  28053841              AB350230     1    28    28
browser |    28  100.0%         11     -  29079187  29079214              AB350230     1    28    28
browser |    28  100.0%         11     -  38377563  38377590              AB350230     1    28    28
browser |    28  100.0%         11     +  39955135  39955162              AB350230     1    28    28
browser |    28  100.0%         11     -  43554057  43554084              AB350230     1    28    28
browser |    28  100.0%         11     +  51556436  51556463              AB350230     1    28    28
browser |    28  100.0%         11     +  55132346  55132373              AB350230     1    28    28
browser |    28  100.0%         11     -  61317785  61317812              AB350230     1    28    28
browser |    28  100.0%         11     -  63365068  63365095              AB350230     1    28    28
browser |    28  100.0%         11     -  64687597  64687624              AB350230     1    28    28
browser |    28  100.0%         11     +  65343197  65343224              AB350230     1    28    28
browser |    28  100.0%         11     +  66839233  66839260              AB350230     1    28    28
browser |    28  100.0%         11     +  73627375  73627402              AB350230     1    28    28
browser |    28  100.0%         11     +  74111097  74111124              AB350230     1    28    28
browser |    28  100.0%         11     +  79124203  79124230              AB350230     1    28    28
browser |    28  100.0%         11     -  81442883  81442910              AB350230     1    28    28
browser |    28  100.0%         11     +  82225407  82225434              AB350230     1    28    28
browser |    28  100.0%         11     +  85176974  85177001              AB350230     1    28    28
browser |    28  100.0%         11     +  88802372  88802399              AB350230     1    28    28
browser |    28  100.0%         11     +  90721031  90721058              AB350230     1    28    28
browser |    28  100.0%         11     -  90798480  90798507              AB350230     1    28    28
browser |    28  100.0%         11     +  90851578  90851605              AB350230     1    28    28
browser |    28  100.0%         11     -  91996408  91996435              AB350230     1    28    28
browser |    28  100.0%         11     -  98510612  98510639              AB350230     1    28    28
browser |    28  100.0%         11     +  99604108  99604135              AB350230     1    28    28
browser |    28  100.0%         11     - 100559758 100559785              AB350230     1    28    28
browser |    28  100.0%         11     + 105919665 105919692              AB350230     1    28    28
browser |    28  100.0%         11     + 106184100 106184127              AB350230     1    28    28
browser |    28  100.0%         11     + 108290663 108290690              AB350230     1    28    28
browser |    28  100.0%         11     - 108545408 108545435              AB350230     1    28    28
browser |    28  100.0%         11     - 109914617 109914644              AB350230     1    28    28
browser |    28  100.0%         11     - 111079854 111079881              AB350230     1    28    28
browser |    28  100.0%         11     + 111107049 111107076              AB350230     1    28    28
browser |    28  100.0%         11     - 113809538 113809565              AB350230     1    28    28
browser |    28  100.0%         11     + 115646303 115646330              AB350230     1    28    28
browser |    28  100.0%         11     - 116284894 116284921              AB350230     1    28    28
browser |    28  100.0%         11     - 116682910 116682937              AB350230     1    28    28
browser |    28  100.0%         11     - 117395190 117395217              AB350230     1    28    28
browser |    28  100.0%         11     - 120218498 120218525              AB350230     1    28    28
browser |    25  100.0%         11     - 120965070 120965094              AB350230     1    25    28
browser |    28  100.0%         12     -   3058889   3058916              AB350230     1    28    28
browser |    28  100.0%         12     +   3084299   3084326              AB350230     1    28    28
browser |    28  100.0%         12     +   3381385   3381412              AB350230     1    28    28
browser |    28  100.0%         12     -   6573060   6573087              AB350230     1    28    28
browser |    28  100.0%         12     -   8457824   8457851              AB350230     1    28    28
browser |    28  100.0%         12     +  11154238  11154265              AB350230     1    28    28
browser |    28  100.0%         12     -  17178738  17178765              AB350230     1    28    28
browser |    28  100.0%         12     -  24451985  24452012              AB350230     1    28    28
browser |    28  100.0%         12     -  25644498  25644525              AB350230     1    28    28
browser |    28  100.0%         12     +  31408734  31408761              AB350230     1    28    28
browser |    28  100.0%         12     -  32081763  32081790              AB350230     1    28    28
browser |    28  100.0%         12     -  32955841  32955868              AB350230     1    28    28
browser |    28  100.0%         12     -  40458610  40458637              AB350230     1    28    28
browser |    28  100.0%         12     -  41420020  41420047              AB350230     1    28    28
browser |    28  100.0%         12     +  44813067  44813094              AB350230     1    28    28
browser |    28  100.0%         12     -  44831758  44831785              AB350230     1    28    28
browser |    28  100.0%         12     -  48585481  48585508              AB350230     1    28    28
browser |    28  100.0%         12     -  49048085  49048112              AB350230     1    28    28
browser |    28  100.0%         12     +  52777468  52777495              AB350230     1    28    28
browser |    28  100.0%         12     -  59493681  59493708              AB350230     1    28    28
browser |    28  100.0%         12     +  61336484  61336511              AB350230     1    28    28
browser |    28  100.0%         12     -  62585381  62585408              AB350230     1    28    28
browser |    28  100.0%         12     +  65074523  65074550              AB350230     1    28    28
browser |    28  100.0%         12     -  65686567  65686594              AB350230     1    28    28
browser |    28  100.0%         12     +  65848586  65848613              AB350230     1    28    28
browser |    28  100.0%         12     +  66454386  66454413              AB350230     1    28    28
browser |    28  100.0%         12     +  68669139  68669166              AB350230     1    28    28
browser |    28  100.0%         12     +  70708518  70708545              AB350230     1    28    28
browser |    28  100.0%         12     +  73358375  73358402              AB350230     1    28    28
browser |    28  100.0%         12     -  80470581  80470608              AB350230     1    28    28
browser |    28  100.0%         12     -  81634017  81634044              AB350230     1    28    28
browser |    28  100.0%         12     +  82508440  82508467              AB350230     1    28    28
browser |    28  100.0%         12     +  85448383  85448410              AB350230     1    28    28
browser |    28  100.0%         12     -  93482841  93482868              AB350230     1    28    28
browser |    28  100.0%         12     +  94003861  94003888              AB350230     1    28    28
browser |    28  100.0%         12     +  96197540  96197567              AB350230     1    28    28
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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