AB350051
 

Information on mRNA AB350051

Description: Mus musculus non-coding RNA, oocyte_piRNA867, 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: AB350051
Position: chr12:56795751-56795779

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     -  56795751  56795779              AB350051     1    29    29
browser |    29  100.0%          1     -   5875686   5875714              AB350051     1    29    29
browser |    29  100.0%          1     -   6501715   6501743              AB350051     1    29    29
browser |    29  100.0%          1     +   8069902   8069930              AB350051     1    29    29
browser |    27  100.0%          1     +   8232347   8232373              AB350051     1    27    29
browser |    29  100.0%          1     -  11100892  11100920              AB350051     1    29    29
browser |    29  100.0%          1     -  11958463  11958491              AB350051     1    29    29
browser |    27  100.0%          1     +  16814416  16814442              AB350051     1    27    29
browser |    27  100.0%          1     +  18033004  18033030              AB350051     1    27    29
browser |    29  100.0%          1     +  18590290  18590318              AB350051     1    29    29
browser |    29  100.0%          1     +  19698624  19698652              AB350051     1    29    29
browser |    27  100.0%          1     +  23344284  23344310              AB350051     1    27    29
browser |    29  100.0%          1     -  26389372  26389400              AB350051     1    29    29
browser |    29  100.0%          1     +  34957129  34957157              AB350051     1    29    29
browser |    29  100.0%          1     +  37816552  37816580              AB350051     1    29    29
browser |    29  100.0%          1     +  38746891  38746919              AB350051     1    29    29
browser |    29  100.0%          1     +  40740460  40740488              AB350051     1    29    29
browser |    29  100.0%          1     +  45777365  45777393              AB350051     1    29    29
browser |    27  100.0%          1     -  48842146  48842172              AB350051     1    27    29
browser |    29  100.0%          1     +  55821274  55821302              AB350051     1    29    29
browser |    29  100.0%          1     +  56817316  56817344              AB350051     1    29    29
browser |    29  100.0%          1     -  58363641  58363669              AB350051     1    29    29
browser |    27  100.0%          1     -  60765137  60765163              AB350051     1    27    29
browser |    29  100.0%          1     -  62574399  62574427              AB350051     1    29    29
browser |    29  100.0%          1     -  64218464  64218492              AB350051     1    29    29
browser |    29  100.0%          1     +  64428216  64428244              AB350051     1    29    29
browser |    29  100.0%          1     -  65000597  65000625              AB350051     1    29    29
browser |    27  100.0%          1     -  66057910  66057936              AB350051     1    27    29
browser |    29  100.0%          1     -  67791714  67791742              AB350051     1    29    29
browser |    29  100.0%          1     -  74693720  74693748              AB350051     1    29    29
browser |    29  100.0%          1     -  76751121  76751149              AB350051     1    29    29
browser |    27  100.0%          1     -  81543012  81543038              AB350051     1    27    29
browser |    29  100.0%          1     +  82482571  82482599              AB350051     1    29    29
browser |    29  100.0%          1     -  84974728  84974756              AB350051     1    29    29
browser |    29  100.0%          1     +  87393836  87393864              AB350051     1    29    29
browser |    29  100.0%          1     -  91400068  91400096              AB350051     1    29    29
browser |    29  100.0%          1     +  97105945  97105973              AB350051     1    29    29
browser |    29  100.0%          1     - 101906997 101907025              AB350051     1    29    29
browser |    29  100.0%          1     + 102965347 102965375              AB350051     1    29    29
browser |    29  100.0%          1     - 103134029 103134057              AB350051     1    29    29
browser |    29  100.0%          1     - 104218422 104218450              AB350051     1    29    29
browser |    29  100.0%          1     - 108337717 108337745              AB350051     1    29    29
browser |    29  100.0%          1     - 109057533 109057561              AB350051     1    29    29
browser |    29  100.0%          1     + 109547086 109547114              AB350051     1    29    29
browser |    29  100.0%          1     + 110260857 110260885              AB350051     1    29    29
browser |    29  100.0%          1     - 110866464 110866492              AB350051     1    29    29
browser |    29  100.0%          1     + 112949764 112949792              AB350051     1    29    29
browser |    29  100.0%          1     - 120499707 120499735              AB350051     1    29    29
browser |    29  100.0%          1     + 126870968 126870996              AB350051     1    29    29
browser |    29  100.0%          1     - 127487128 127487156              AB350051     1    29    29
browser |    29  100.0%          1     - 127820890 127820918              AB350051     1    29    29
browser |    29  100.0%          1     + 130465822 130465850              AB350051     1    29    29
browser |    29  100.0%          1     - 137202784 137202812              AB350051     1    29    29
browser |    29  100.0%          1     + 139656662 139656690              AB350051     1    29    29
browser |    29  100.0%          1     + 140969103 140969131              AB350051     1    29    29
browser |    29  100.0%          1     - 142285152 142285180              AB350051     1    29    29
browser |    29  100.0%          1     - 142513750 142513778              AB350051     1    29    29
browser |    29  100.0%          1     - 144731557 144731585              AB350051     1    29    29
browser |    29  100.0%          1     - 148045464 148045492              AB350051     1    29    29
browser |    29  100.0%          1     + 148154082 148154110              AB350051     1    29    29
browser |    29  100.0%          1     + 148365296 148365324              AB350051     1    29    29
browser |    27  100.0%          1     + 149274954 149274980              AB350051     1    27    29
browser |    29  100.0%          1     + 149463268 149463296              AB350051     1    29    29
browser |    29  100.0%          1     + 152542712 152542740              AB350051     1    29    29
browser |    27  100.0%          1     - 159798462 159798488              AB350051     1    27    29
browser |    29  100.0%          1     - 160644574 160644602              AB350051     1    29    29
browser |    29  100.0%          1     + 162674077 162674105              AB350051     1    29    29
browser |    29  100.0%          1     - 163297190 163297218              AB350051     1    29    29
browser |    29  100.0%          1     + 166183149 166183177              AB350051     1    29    29
browser |    29  100.0%          1     + 169375321 169375349              AB350051     1    29    29
browser |    29  100.0%          1     + 169949312 169949340              AB350051     1    29    29
browser |    29  100.0%          1     - 176371759 176371787              AB350051     1    29    29
browser |    27  100.0%          1     + 178007629 178007655              AB350051     1    27    29
browser |    27  100.0%          1     - 181092217 181092243              AB350051     1    27    29
browser |    29  100.0%          1     + 191843737 191843765              AB350051     1    29    29
browser |    27  100.0%          1     + 195008610 195008636              AB350051     1    27    29
browser |    27  100.0%         10     -   3552057   3552083              AB350051     1    27    29
browser |    29  100.0%         10     -  19415769  19415797              AB350051     1    29    29
browser |    29  100.0%         10     +  19676103  19676131              AB350051     1    29    29
browser |    29  100.0%         10     +  21091304  21091332              AB350051     1    29    29
browser |    27  100.0%         10     -  21519344  21519370              AB350051     1    27    29
browser |    29  100.0%         10     -  22560288  22560316              AB350051     1    29    29
browser |    27  100.0%         10     -  23748345  23748371              AB350051     1    27    29
browser |    29  100.0%         10     +  24566332  24566360              AB350051     1    29    29
browser |    29  100.0%         10     -  24978567  24978595              AB350051     1    29    29
browser |    29  100.0%         10     +  30695942  30695970              AB350051     1    29    29
browser |    29  100.0%         10     +  30970627  30970655              AB350051     1    29    29
browser |    27  100.0%         10     +  31364572  31364598              AB350051     1    27    29
browser |    29  100.0%         10     +  31629716  31629744              AB350051     1    29    29
browser |    29  100.0%         10     +  33765888  33765916              AB350051     1    29    29
browser |    29  100.0%         10     -  34618946  34618974              AB350051     1    29    29
browser |    29  100.0%         10     +  41722494  41722522              AB350051     1    29    29
browser |    29  100.0%         10     -  45432124  45432152              AB350051     1    29    29
browser |    29  100.0%         10     -  55592751  55592779              AB350051     1    29    29
browser |    29  100.0%         10     +  57019722  57019750              AB350051     1    29    29
browser |    29  100.0%         10     +  59221719  59221747              AB350051     1    29    29
browser |    29  100.0%         10     +  62447853  62447881              AB350051     1    29    29
browser |    27  100.0%         10     -  65787725  65787751              AB350051     1    27    29
browser |    27  100.0%         10     -  66559369  66559395              AB350051     1    27    29
browser |    27  100.0%         10     +  77792568  77792594              AB350051     3    29    29
browser |    29  100.0%         10     +  77860256  77860284              AB350051     1    29    29
browser |    29  100.0%         10     -  78653416  78653444              AB350051     1    29    29
browser |    29  100.0%         10     +  80815533  80815561              AB350051     1    29    29
browser |    27  100.0%         10     +  81809682  81809708              AB350051     1    27    29
browser |    29  100.0%         10     -  83507909  83507937              AB350051     1    29    29
browser |    29  100.0%         10     +  83627313  83627341              AB350051     1    29    29
browser |    29  100.0%         10     +  84584604  84584632              AB350051     1    29    29
browser |    27  100.0%         10     +  85555407  85555433              AB350051     1    27    29
browser |    27  100.0%         10     -  85605417  85605443              AB350051     1    27    29
browser |    27  100.0%         10     +  88802909  88802935              AB350051     1    27    29
browser |    29  100.0%         10     -  90161595  90161623              AB350051     1    29    29
browser |    29  100.0%         10     -  94199561  94199589              AB350051     1    29    29
browser |    27  100.0%         10     -  95994235  95994261              AB350051     1    27    29
browser |    27  100.0%         10     -  96029519  96029545              AB350051     1    27    29
browser |    29  100.0%         10     -  98935182  98935210              AB350051     1    29    29
browser |    27  100.0%         10     +  99180943  99180969              AB350051     1    27    29
browser |    27  100.0%         10     + 100418479 100418505              AB350051     1    27    29
browser |    29  100.0%         10     - 104656477 104656505              AB350051     1    29    29
browser |    29  100.0%         10     + 104677390 104677418              AB350051     1    29    29
browser |    27  100.0%         10     + 105016516 105016542              AB350051     1    27    29
browser |    29  100.0%         10     - 105509636 105509664              AB350051     1    29    29
browser |    27  100.0%         10     + 107841319 107841345              AB350051     1    27    29
browser |    29  100.0%         10     - 109152202 109152230              AB350051     1    29    29
browser |    29  100.0%         10     + 110535524 110535552              AB350051     1    29    29
browser |    29  100.0%         10     + 111893115 111893143              AB350051     1    29    29
browser |    29  100.0%         10     - 116443290 116443318              AB350051     1    29    29
browser |    29  100.0%         10     + 121004032 121004060              AB350051     1    29    29
browser |    27  100.0%         10     - 122140663 122140689              AB350051     1    27    29
browser |    27  100.0%         10     - 122203090 122203116              AB350051     1    27    29
browser |    29  100.0%         10     + 124418186 124418214              AB350051     1    29    29
browser |    29  100.0%         10     + 124445691 124445719              AB350051     1    29    29
browser |    29  100.0%         10     - 129225815 129225843              AB350051     1    29    29
browser |    27  100.0%         10     + 129764383 129764409              AB350051     1    27    29
browser |    29  100.0%         11     -   6092616   6092644              AB350051     1    29    29
browser |    27  100.0%         11     +   6484639   6484665              AB350051     1    27    29
browser |    27  100.0%         11     +  10716285  10716311              AB350051     1    27    29
browser |    29  100.0%         11     -  12458415  12458443              AB350051     1    29    29
browser |    27  100.0%         11     +  12517896  12517922              AB350051     1    27    29
browser |    29  100.0%         11     -  12905142  12905170              AB350051     1    29    29
browser |    29  100.0%         11     +  15183666  15183694              AB350051     1    29    29
browser |    29  100.0%         11     +  15836668  15836696              AB350051     1    29    29
browser |    27  100.0%         11     +  16181521  16181547              AB350051     1    27    29
browser |    29  100.0%         11     -  19517300  19517328              AB350051     1    29    29
browser |    27  100.0%         11     +  20470006  20470032              AB350051     1    27    29
browser |    29  100.0%         11     -  22286379  22286407              AB350051     1    29    29
browser |    27  100.0%         11     +  22531857  22531883              AB350051     1    27    29
browser |    29  100.0%         11     -  23169708  23169736              AB350051     1    29    29
browser |    29  100.0%         11     +  28053266  28053294              AB350051     1    29    29
browser |    29  100.0%         11     +  29078637  29078665              AB350051     1    29    29
browser |    27  100.0%         11     -  39955684  39955710              AB350051     1    27    29
browser |    29  100.0%         11     +  43553514  43553542              AB350051     1    29    29
browser |    29  100.0%         11     -  51556979  51557007              AB350051     1    29    29
browser |    27  100.0%         11     -  54468527  54468553              AB350051     1    27    29
browser |    27  100.0%         11     -  55132890  55132916              AB350051     1    27    29
browser |    26  100.0%         11     +  63364529  63364554              AB350051     4    29    29
browser |    26  100.0%         11     +  64687058  64687083              AB350051     4    29    29
browser |    29  100.0%         11     -  65343738  65343766              AB350051     1    29    29
browser |    27  100.0%         11     -  70932328  70932354              AB350051     1    27    29
browser |    29  100.0%         11     -  73627916  73627944              AB350051     1    29    29
browser |    29  100.0%         11     -  74111644  74111672              AB350051     1    29    29
browser |    29  100.0%         11     +  74435032  74435060              AB350051     1    29    29
browser |    29  100.0%         11     +  74781196  74781224              AB350051     1    29    29
browser |    27  100.0%         11     -  79124746  79124772              AB350051     1    27    29
browser |    29  100.0%         11     -  79633420  79633448              AB350051     1    29    29
browser |    29  100.0%         11     -  85177521  85177549              AB350051     1    29    29
browser |    29  100.0%         11     +  86739846  86739874              AB350051     1    29    29
browser |    29  100.0%         11     -  88802913  88802941              AB350051     1    29    29
browser |    27  100.0%         11     -  90721574  90721600              AB350051     1    27    29
browser |    29  100.0%         11     +  90797932  90797960              AB350051     1    29    29
browser |    27  100.0%         11     +  98510063  98510089              AB350051     1    27    29
browser |    27  100.0%         11     + 100559216 100559242              AB350051     1    27    29
browser |    27  100.0%         11     - 105920207 105920233              AB350051     3    29    29
browser |    27  100.0%         11     - 106184643 106184669              AB350051     1    27    29
browser |    29  100.0%         11     - 108291206 108291234              AB350051     1    29    29
browser |    29  100.0%         11     + 109914068 109914096              AB350051     1    29    29
browser |    27  100.0%         11     - 111107599 111107625              AB350051     1    27    29
browser |    29  100.0%         11     + 113808995 113809023              AB350051     1    29    29
browser |    29  100.0%         11     - 115646851 115646879              AB350051     1    29    29
browser |    29  100.0%         11     + 116284349 116284377              AB350051     1    29    29
browser |    27  100.0%         11     + 116682362 116682388              AB350051     1    27    29
browser |    27  100.0%         11     + 117394648 117394674              AB350051     1    27    29
browser |    27  100.0%         11     + 120964519 120964545              AB350051     1    27    29
browser |    29  100.0%         12     +   3058340   3058368              AB350051     1    29    29
browser |    29  100.0%         12     -   3084856   3084884              AB350051     1    29    29
browser |    29  100.0%         12     -   3381933   3381961              AB350051     1    29    29
browser |    29  100.0%         12     +   6572512   6572540              AB350051     1    29    29
browser |    29  100.0%         12     +   8457276   8457304              AB350051     1    29    29
browser |    27  100.0%         12     -  11154783  11154809              AB350051     1    27    29
browser |    29  100.0%         12     +  24451443  24451471              AB350051     1    29    29
browser |    29  100.0%         12     -  31409276  31409304              AB350051     1    29    29
browser |    29  100.0%         12     +  32649421  32649449              AB350051     1    29    29
browser |    27  100.0%         12     +  32955298  32955324              AB350051     1    27    29
browser |    29  100.0%         12     +  40458061  40458089              AB350051     1    29    29
browser |    29  100.0%         12     +  41419478  41419506              AB350051     1    29    29
browser |    29  100.0%         12     +  44831209  44831237              AB350051     1    29    29
browser |    27  100.0%         12     +  49047542  49047568              AB350051     1    27    29
browser |    29  100.0%         12     +  59493132  59493160              AB350051     1    29    29
browser |    29  100.0%         12     -  61337031  61337059              AB350051     1    29    29
browser |    29  100.0%         12     +  62584839  62584867              AB350051     1    29    29
browser |    29  100.0%         12     -  65075071  65075099              AB350051     1    29    29
browser |    29  100.0%         12     +  65686019  65686047              AB350051     1    29    29
browser |    27  100.0%         12     -  65849129  65849155              AB350051     1    27    29
browser |    27  100.0%         12     -  66454929  66454955              AB350051     1    27    29
browser |    29  100.0%         12     -  68669680  68669708              AB350051     1    29    29
browser |    29  100.0%         12     +  68796000  68796028              AB350051     1    29    29
browser |    29  100.0%         12     -  70709060  70709088              AB350051     1    29    29
browser |    29  100.0%         12     -  73358916  73358944              AB350051     1    29    29
browser |    29  100.0%         12     -  79609739  79609767              AB350051     1    29    29
browser |    29  100.0%         12     +  80470039  80470067              AB350051     1    29    29
browser |    29  100.0%         12     +  81633469  81633497              AB350051     1    29    29
browser |    27  100.0%         12     -  82508989  82509015              AB350051     1    27    29
browser |    27  100.0%         12     -  85448926  85448952              AB350051     1    27    29
browser |    27  100.0%         12     +  88482251  88482277              AB350051     1    27    29
browser |    29  100.0%         12     +  93482298  93482326              AB350051     1    29    29
browser |    27  100.0%         12     -  94004410  94004436              AB350051     1    27    29
browser |    29  100.0%         12     -  96198081  96198109              AB350051     1    29    29
browser |    29  100.0%         12     - 108046684 108046712              AB350051     1    29    29
browser |    27  100.0%         12     + 109874323 109874349              AB350051     1    27    29
browser |    29  100.0%         12     + 111358683 111358711              AB350051     1    29    29
browser |    29  100.0%         12     + 119560495 119560523              AB350051     1    29    29
browser |    29  100.0%         13     -   4117353   4117381              AB350051     1    29    29
browser |    29  100.0%         13     +   4394417   4394445              AB350051     1    29    29
browser |    29  100.0%         13     +   5332889   5332917              AB350051     1    29    29
browser |    29  100.0%         13     -   8000302   8000330              AB350051     1    29    29
browser |    29  100.0%         13     -   8520776   8520804              AB350051     1    29    29
browser |    29  100.0%         13     +  11521899  11521927              AB350051     1    29    29
browser |    29  100.0%         13     +  15612117  15612145              AB350051     1    29    29
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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