AB352140
 

Information on mRNA AB352140

Description: Mus musculus non-coding RNA, oocyte_piRNA2956, 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: AB352140
Position: chr12:56795328-56795356

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 |    29  100.0%         12     -  56795328  56795356              AB352140     1    29    29
browser |    29  100.0%          1     -   4628022   4628050              AB352140     1    29    29
browser |    29  100.0%          1     -   5875262   5875290              AB352140     1    29    29
browser |    29  100.0%          1     +   6242306   6242334              AB352140     1    29    29
browser |    29  100.0%          1     -   6501291   6501319              AB352140     1    29    29
browser |    29  100.0%          1     +   8070320   8070348              AB352140     1    29    29
browser |    29  100.0%          1     +   8232755   8232783              AB352140     1    29    29
browser |    29  100.0%          1     -   8729255   8729283              AB352140     1    29    29
browser |    29  100.0%          1     -  10800788  10800816              AB352140     1    29    29
browser |    29  100.0%          1     -  11100469  11100497              AB352140     1    29    29
browser |    29  100.0%          1     -  11958040  11958068              AB352140     1    29    29
browser |    29  100.0%          1     +  13627184  13627212              AB352140     1    29    29
browser |    29  100.0%          1     +  16814833  16814861              AB352140     1    29    29
browser |    29  100.0%          1     +  18590707  18590735              AB352140     1    29    29
browser |    29  100.0%          1     +  19699047  19699075              AB352140     1    29    29
browser |    29  100.0%          1     +  21654412  21654440              AB352140     1    29    29
browser |    29  100.0%          1     -  22066177  22066205              AB352140     1    29    29
browser |    29  100.0%          1     -  26388953  26388981              AB352140     1    29    29
browser |    29  100.0%          1     +  26459448  26459476              AB352140     1    29    29
browser |    29  100.0%          1     -  26510147  26510175              AB352140     1    29    29
browser |    29  100.0%          1     +  27225597  27225625              AB352140     1    29    29
browser |    29  100.0%          1     -  29982507  29982535              AB352140     1    29    29
browser |    29  100.0%          1     +  34389720  34389748              AB352140     1    29    29
browser |    29  100.0%          1     +  34957546  34957574              AB352140     1    29    29
browser |    29  100.0%          1     +  35833933  35833961              AB352140     1    29    29
browser |    29  100.0%          1     -  37318589  37318617              AB352140     1    29    29
browser |    29  100.0%          1     +  37816974  37817002              AB352140     1    29    29
browser |    29  100.0%          1     +  38747308  38747336              AB352140     1    29    29
browser |    29  100.0%          1     +  40740892  40740920              AB352140     1    29    29
browser |    29  100.0%          1     -  47263290  47263318              AB352140     1    29    29
browser |    29  100.0%          1     -  48394195  48394223              AB352140     1    29    29
browser |    29  100.0%          1     -  53169485  53169513              AB352140     1    29    29
browser |    29  100.0%          1     -  58851534  58851562              AB352140     1    29    29
browser |    29  100.0%          1     -  81542587  81542615              AB352140     1    29    29
browser |    29  100.0%          1     +  82482994  82483022              AB352140     1    29    29
browser |    29  100.0%          1     -  84974305  84974333              AB352140     1    29    29
browser |    29  100.0%          1     -  87062074  87062102              AB352140     1    29    29
browser |    29  100.0%          1     +  87394254  87394282              AB352140     1    29    29
browser |    29  100.0%          1     +  89130216  89130244              AB352140     1    29    29
browser |    29  100.0%          1     -  91399644  91399672              AB352140     1    29    29
browser |    29  100.0%          1     -  93035912  93035940              AB352140     1    29    29
browser |    29  100.0%          1     +  93888303  93888331              AB352140     1    29    29
browser |    29  100.0%          1     +  97108222  97108250              AB352140     1    29    29
browser |    29  100.0%          1     - 101906580 101906608              AB352140     1    29    29
browser |    29  100.0%          1     + 102965771 102965799              AB352140     1    29    29
browser |    29  100.0%          1     - 103133612 103133640              AB352140     1    29    29
browser |    29  100.0%          1     + 103521029 103521057              AB352140     1    29    29
browser |    29  100.0%          1     - 104218002 104218030              AB352140     1    29    29
browser |    29  100.0%          1     - 107967234 107967262              AB352140     1    29    29
browser |    29  100.0%          1     - 108337299 108337327              AB352140     1    29    29
browser |    29  100.0%          1     - 109057108 109057136              AB352140     1    29    29
browser |    29  100.0%          1     + 109547503 109547531              AB352140     1    29    29
browser |    29  100.0%          1     + 110261275 110261303              AB352140     1    29    29
browser |    29  100.0%          1     - 110866041 110866069              AB352140     1    29    29
browser |    29  100.0%          1     - 111182066 111182094              AB352140     1    29    29
browser |    29  100.0%          1     + 111637473 111637501              AB352140     1    29    29
browser |    29  100.0%          1     - 112492737 112492765              AB352140     1    29    29
browser |    29  100.0%          1     + 112862466 112862494              AB352140     1    29    29
browser |    29  100.0%          1     + 112950182 112950210              AB352140     1    29    29
browser |    29  100.0%          1     + 114117491 114117519              AB352140     1    29    29
browser |    29  100.0%          1     - 115813807 115813835              AB352140     1    29    29
browser |    29  100.0%          1     - 116576710 116576738              AB352140     1    29    29
browser |    29  100.0%          1     + 125250966 125250994              AB352140     1    29    29
browser |    29  100.0%          1     + 126356667 126356695              AB352140     1    29    29
browser |    29  100.0%          1     + 126871387 126871415              AB352140     1    29    29
browser |    29  100.0%          1     - 159798042 159798070              AB352140     1    29    29
browser |    29  100.0%          1     - 160644155 160644183              AB352140     1    29    29
browser |    29  100.0%          1     + 162674495 162674523              AB352140     1    29    29
browser |    29  100.0%          1     - 163296772 163296800              AB352140     1    29    29
browser |    29  100.0%          1     - 166591415 166591443              AB352140     1    29    29
browser |    29  100.0%          1     + 169375744 169375772              AB352140     1    29    29
browser |    29  100.0%          1     + 169949735 169949763              AB352140     1    29    29
browser |    29  100.0%          1     - 174870254 174870282              AB352140     1    29    29
browser |    29  100.0%          1     - 176371336 176371364              AB352140     1    29    29
browser |    29  100.0%          1     + 177891964 177891992              AB352140     1    29    29
browser |    29  100.0%          1     + 178008053 178008081              AB352140     1    29    29
browser |    29  100.0%          1     + 180443239 180443267              AB352140     1    29    29
browser |    29  100.0%          1     - 181091792 181091820              AB352140     1    29    29
browser |    29  100.0%          1     + 181326332 181326360              AB352140     1    29    29
browser |    26  100.0%          1     + 191844156 191844181              AB352140     1    26    29
browser |    29  100.0%          1     + 195009027 195009055              AB352140     1    29    29
browser |    29  100.0%         10     -   3267045   3267073              AB352140     1    29    29
browser |    29  100.0%         10     -   3551631   3551659              AB352140     1    29    29
browser |    29  100.0%         10     -   6517480   6517508              AB352140     1    29    29
browser |    29  100.0%         10     +   7365739   7365767              AB352140     1    29    29
browser |    29  100.0%         10     +   8481419   8481447              AB352140     1    29    29
browser |    29  100.0%         10     +   9726802   9726830              AB352140     1    29    29
browser |    29  100.0%         10     +  11576397  11576425              AB352140     1    29    29
browser |    29  100.0%         10     -  15056455  15056483              AB352140     1    29    29
browser |    29  100.0%         10     -  19415346  19415374              AB352140     1    29    29
browser |    29  100.0%         10     +  19676535  19676563              AB352140     1    29    29
browser |    29  100.0%         10     -  19887082  19887110              AB352140     1    29    29
browser |    29  100.0%         10     +  21091727  21091755              AB352140     1    29    29
browser |    29  100.0%         10     -  21518919  21518947              AB352140     1    29    29
browser |    29  100.0%         10     -  22559865  22559893              AB352140     1    29    29
browser |    29  100.0%         10     -  23747926  23747954              AB352140     1    29    29
browser |    29  100.0%         10     +  24566751  24566779              AB352140     1    29    29
browser |    29  100.0%         10     -  24978150  24978178              AB352140     1    29    29
browser |    29  100.0%         10     +  25848468  25848496              AB352140     1    29    29
browser |    29  100.0%         10     +  30360833  30360861              AB352140     1    29    29
browser |    29  100.0%         10     +  30696364  30696392              AB352140     1    29    29
browser |    29  100.0%         10     +  30971046  30971074              AB352140     1    29    29
browser |    29  100.0%         10     +  31364995  31365023              AB352140     1    29    29
browser |    29  100.0%         10     +  31630139  31630167              AB352140     1    29    29
browser |    29  100.0%         10     +  32814434  32814462              AB352140     1    29    29
browser |    29  100.0%         10     +  33766311  33766339              AB352140     1    29    29
browser |    29  100.0%         10     -  34618523  34618551              AB352140     1    29    29
browser |    29  100.0%         10     +  41722917  41722945              AB352140     1    29    29
browser |    29  100.0%         10     -  43646373  43646401              AB352140     1    29    29
browser |    29  100.0%         10     -  45431701  45431729              AB352140     1    29    29
browser |    29  100.0%         10     -  55592333  55592361              AB352140     1    29    29
browser |    29  100.0%         10     -  65475400  65475428              AB352140     1    29    29
browser |    29  100.0%         10     -  65787298  65787326              AB352140     1    29    29
browser |    29  100.0%         10     +  80815957  80815985              AB352140     1    29    29
browser |    29  100.0%         10     +  81810105  81810133              AB352140     1    29    29
browser |    29  100.0%         10     -  83507486  83507514              AB352140     1    29    29
browser |    29  100.0%         10     +  83627732  83627760              AB352140     1    29    29
browser |    29  100.0%         10     +  84585023  84585051              AB352140     1    29    29
browser |    29  100.0%         10     +  85555824  85555852              AB352140     1    29    29
browser |    29  100.0%         10     -  85604998  85605026              AB352140     1    29    29
browser |    29  100.0%         10     +  88493205  88493233              AB352140     1    29    29
browser |    29  100.0%         10     +  88803326  88803354              AB352140     1    29    29
browser |    29  100.0%         10     -  90161176  90161204              AB352140     1    29    29
browser |    29  100.0%         10     -  94199137  94199165              AB352140     1    29    29
browser |    29  100.0%         10     -  95993808  95993836              AB352140     1    29    29
browser |    29  100.0%         10     -  96029100  96029128              AB352140     1    29    29
browser |    29  100.0%         10     -  97157128  97157156              AB352140     1    29    29
browser |    29  100.0%         10     -  98934759  98934787              AB352140     1    29    29
browser |    29  100.0%         10     +  99181366  99181394              AB352140     1    29    29
browser |    29  100.0%         10     -  99382477  99382505              AB352140     1    29    29
browser |    29  100.0%         10     + 100418896 100418924              AB352140     1    29    29
browser |    29  100.0%         10     + 104397587 104397615              AB352140     1    29    29
browser |    29  100.0%         10     - 104656052 104656080              AB352140     1    29    29
browser |    29  100.0%         10     + 104677815 104677843              AB352140     1    29    29
browser |    29  100.0%         10     + 105016940 105016968              AB352140     1    29    29
browser |    29  100.0%         10     - 105509217 105509245              AB352140     1    29    29
browser |    29  100.0%         10     + 107841742 107841770              AB352140     1    29    29
browser |    29  100.0%         10     - 109151778 109151806              AB352140     1    29    29
browser |    29  100.0%         10     + 110535956 110535984              AB352140     1    29    29
browser |    29  100.0%         10     + 111893538 111893566              AB352140     1    29    29
browser |    29  100.0%         10     - 116442867 116442895              AB352140     1    29    29
browser |    29  100.0%         10     - 122140244 122140272              AB352140     1    29    29
browser |    29  100.0%         10     - 122202670 122202698              AB352140     1    29    29
browser |    29  100.0%         10     - 122669470 122669498              AB352140     1    29    29
browser |    29  100.0%         10     + 129764806 129764834              AB352140     1    29    29
browser |    29  100.0%         11     +   5312235   5312263              AB352140     1    29    29
browser |    29  100.0%         11     -   6092198   6092226              AB352140     1    29    29
browser |    29  100.0%         11     +   6485063   6485091              AB352140     1    29    29
browser |    29  100.0%         11     -   7526395   7526423              AB352140     1    29    29
browser |    29  100.0%         11     -   9658687   9658715              AB352140     1    29    29
browser |    29  100.0%         11     +  10716702  10716730              AB352140     1    29    29
browser |    29  100.0%         11     -  12457996  12458024              AB352140     1    29    29
browser |    29  100.0%         11     +  12518314  12518342              AB352140     1    29    29
browser |    29  100.0%         11     -  12904723  12904751              AB352140     1    29    29
browser |    29  100.0%         11     +  15184089  15184117              AB352140     1    29    29
browser |    29  100.0%         11     -  15233250  15233278              AB352140     1    29    29
browser |    29  100.0%         11     +  15837086  15837114              AB352140     1    29    29
browser |    29  100.0%         11     +  16181938  16181966              AB352140     1    29    29
browser |    29  100.0%         11     -  18757164  18757192              AB352140     1    29    29
browser |    29  100.0%         11     -  19516883  19516911              AB352140     1    29    29
browser |    29  100.0%         11     -  19739433  19739461              AB352140     1    29    29
browser |    29  100.0%         11     +  20470429  20470457              AB352140     1    29    29
browser |    29  100.0%         11     -  22285960  22285988              AB352140     1    29    29
browser |    29  100.0%         11     +  22532274  22532302              AB352140     1    29    29
browser |    29  100.0%         11     -  23169284  23169312              AB352140     1    29    29
browser |    29  100.0%         11     -  23193476  23193504              AB352140     1    29    29
browser |    29  100.0%         11     +  26510023  26510051              AB352140     1    29    29
browser |    29  100.0%         11     -  27901786  27901814              AB352140     1    29    29
browser |    29  100.0%         11     +  28053689  28053717              AB352140     1    29    29
browser |    29  100.0%         11     +  29079062  29079090              AB352140     1    29    29
browser |    29  100.0%         11     +  38377438  38377466              AB352140     1    29    29
browser |    29  100.0%         11     -  39955259  39955287              AB352140     1    29    29
browser |    29  100.0%         11     +  43553932  43553960              AB352140     1    29    29
browser |    29  100.0%         11     +  51332152  51332180              AB352140     1    29    29
browser |    29  100.0%         11     -  51556560  51556588              AB352140     1    29    29
browser |    29  100.0%         11     -  54468108  54468136              AB352140     1    29    29
browser |    29  100.0%         11     +  61317660  61317688              AB352140     1    29    29
browser |    29  100.0%         11     +  81442758  81442786              AB352140     1    29    29
browser |    29  100.0%         11     -  82225531  82225559              AB352140     1    29    29
browser |    29  100.0%         11     +  84957900  84957928              AB352140     1    29    29
browser |    29  100.0%         11     -  85177098  85177126              AB352140     1    29    29
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browser |    29  100.0%         11     -  88802496  88802524              AB352140     1    29    29
browser |    29  100.0%         11     -  90721155  90721183              AB352140     1    29    29
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browser |    29  100.0%         11     -  90851702  90851730              AB352140     1    29    29
browser |    29  100.0%         11     +  91996283  91996311              AB352140     1    29    29
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browser |    29  100.0%         11     - 105919789 105919817              AB352140     1    29    29
browser |    29  100.0%         11     - 106184224 106184252              AB352140     1    29    29
browser |    29  100.0%         11     - 108290787 108290815              AB352140     1    29    29
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browser |    29  100.0%         11     - 111107173 111107201              AB352140     1    29    29
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browser |    29  100.0%         11     + 120218373 120218401              AB352140     1    29    29
browser |    29  100.0%         12     +   3058764   3058792              AB352140     1    29    29
browser |    29  100.0%         12     +   3112531   3112559              AB352140     1    29    29
browser |    29  100.0%         12     -   3381509   3381537              AB352140     1    29    29
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browser |    29  100.0%         12     +  17297675  17297703              AB352140     1    29    29
browser |    29  100.0%         12     -  19308948  19308976              AB352140     1    29    29
browser |    29  100.0%         12     +  24451860  24451888              AB352140     1    29    29
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browser |    29  100.0%         12     -  31408858  31408886              AB352140     1    29    29
browser |    29  100.0%         12     +  32081638  32081666              AB352140     1    29    29
browser |    29  100.0%         12     +  32649838  32649866              AB352140     1    29    29
browser |    29  100.0%         12     +  32955716  32955744              AB352140     1    29    29
browser |    29  100.0%         12     +  40458485  40458513              AB352140     1    29    29
browser |    29  100.0%         12     +  41419895  41419923              AB352140     1    29    29
browser |    29  100.0%         12     -  44199222  44199250              AB352140     1    29    29
browser |    29  100.0%         12     +  44831633  44831661              AB352140     1    29    29
browser |    29  100.0%         12     +  48585356  48585384              AB352140     1    29    29
browser |    29  100.0%         12     +  49047960  49047988              AB352140     1    29    29
browser |    29  100.0%         12     -  49267833  49267861              AB352140     1    29    29
browser |    29  100.0%         12     -  52777592  52777620              AB352140     1    29    29
browser |    29  100.0%         12     +  54407573  54407601              AB352140     1    29    29
browser |    29  100.0%         12     -  61336608  61336636              AB352140     1    29    29
browser |    29  100.0%         12     -  65074647  65074675              AB352140     1    29    29
browser |    29  100.0%         12     -  65848710  65848738              AB352140     1    29    29
browser |    29  100.0%         12     -  66454510  66454538              AB352140     1    29    29
browser |    29  100.0%         12     -  68669263  68669291              AB352140     1    29    29
browser |    29  100.0%         12     -  70708642  70708670              AB352140     1    29    29
browser |    29  100.0%         12     -  73358499  73358527              AB352140     1    29    29
browser |    29  100.0%         12     -  79609315  79609343              AB352140     1    29    29
browser |    29  100.0%         12     +  80470456  80470484              AB352140     1    29    29
browser |    29  100.0%         12     +  81633892  81633920              AB352140     1    29    29
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browser |    29  100.0%          Y     +  87791502  87791530              AB352140     1    29    29
browser |    29  100.0%          Y     +  88476193  88476221              AB352140     1    29    29
browser |    28  100.0%          Y     +  89142706  89142733              AB352140     2    29    29

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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