AB350025
 

Information on mRNA AB350025

Description: Mus musculus non-coding RNA, oocyte_piRNA841, 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: AB350025
Position: chr12:56795212-56795238

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    27  100.0%         12     -  56795212  56795238              AB350025     1    27    27
browser |    27  100.0%          1     +   6242424   6242450              AB350025     1    27    27
browser |    27  100.0%          1     -   6501175   6501201              AB350025     1    27    27
browser |    27  100.0%          1     -  11957924  11957950              AB350025     1    27    27
browser |    27  100.0%          1     +  16814951  16814977              AB350025     1    27    27
browser |    27  100.0%          1     +  18590825  18590851              AB350025     1    27    27
browser |    27  100.0%          1     +  19699165  19699191              AB350025     1    27    27
browser |    27  100.0%          1     +  23344827  23344853              AB350025     1    27    27
browser |    27  100.0%          1     -  26388837  26388863              AB350025     1    27    27
browser |    27  100.0%          1     -  26510031  26510057              AB350025     1    27    27
browser |    27  100.0%          1     +  34389838  34389864              AB350025     1    27    27
browser |    27  100.0%          1     +  35834051  35834077              AB350025     1    27    27
browser |    27  100.0%          1     +  38747426  38747452              AB350025     1    27    27
browser |    27  100.0%          1     +  40741010  40741036              AB350025     1    27    27
browser |    27  100.0%          1     +  48132836  48132862              AB350025     1    27    27
browser |    27  100.0%          1     -  53169369  53169395              AB350025     1    27    27
browser |    27  100.0%          1     +  55821810  55821836              AB350025     1    27    27
browser |    27  100.0%          1     +  56817851  56817877              AB350025     1    27    27
browser |    27  100.0%          1     -  58363108  58363134              AB350025     1    27    27
browser |    27  100.0%          1     +  58973769  58973795              AB350025     1    27    27
browser |    27  100.0%          1     -  60764596  60764622              AB350025     1    27    27
browser |    27  100.0%          1     -  62573864  62573890              AB350025     1    27    27
browser |    27  100.0%          1     +  64428752  64428778              AB350025     1    27    27
browser |    27  100.0%          1     -  66057368  66057394              AB350025     1    27    27
browser |    27  100.0%          1     -  67791175  67791201              AB350025     1    27    27
browser |    27  100.0%          1     -  69737812  69737838              AB350025     1    27    27
browser |    27  100.0%          1     +  70280173  70280199              AB350025     1    27    27
browser |    27  100.0%          1     -  74693180  74693206              AB350025     1    27    27
browser |    27  100.0%          1     -  76750579  76750605              AB350025     1    27    27
browser |    27  100.0%          1     +  79921264  79921290              AB350025     1    27    27
browser |    27  100.0%          1     -  81542471  81542497              AB350025     1    27    27
browser |    27  100.0%          1     -  84974189  84974215              AB350025     1    27    27
browser |    27  100.0%          1     +  87394372  87394398              AB350025     1    27    27
browser |    27  100.0%          1     +  89130334  89130360              AB350025     1    27    27
browser |    27  100.0%          1     -  91399528  91399554              AB350025     1    27    27
browser |    27  100.0%          1     +  93888421  93888447              AB350025     1    27    27
browser |    27  100.0%          1     - 103133496 103133522              AB350025     1    27    27
browser |    27  100.0%          1     + 103521147 103521173              AB350025     1    27    27
browser |    27  100.0%          1     - 104217886 104217912              AB350025     1    27    27
browser |    27  100.0%          1     - 107967118 107967144              AB350025     1    27    27
browser |    27  100.0%          1     - 108337183 108337209              AB350025     1    27    27
browser |    27  100.0%          1     - 109056992 109057018              AB350025     1    27    27
browser |    27  100.0%          1     + 109547621 109547647              AB350025     1    27    27
browser |    27  100.0%          1     + 110261393 110261419              AB350025     1    27    27
browser |    27  100.0%          1     - 110865925 110865951              AB350025     1    27    27
browser |    27  100.0%          1     - 111181950 111181976              AB350025     1    27    27
browser |    27  100.0%          1     + 112950300 112950326              AB350025     1    27    27
browser |    27  100.0%          1     + 114117609 114117635              AB350025     1    27    27
browser |    27  100.0%          1     - 115813691 115813717              AB350025     1    27    27
browser |    27  100.0%          1     - 116576594 116576620              AB350025     1    27    27
browser |    27  100.0%          1     - 117630252 117630278              AB350025     1    27    27
browser |    27  100.0%          1     - 120499172 120499198              AB350025     1    27    27
browser |    27  100.0%          1     + 125251084 125251110              AB350025     1    27    27
browser |    27  100.0%          1     - 125274446 125274472              AB350025     1    27    27
browser |    27  100.0%          1     + 126356785 126356811              AB350025     1    27    27
browser |    27  100.0%          1     + 126871505 126871531              AB350025     1    27    27
browser |    27  100.0%          1     - 127486595 127486621              AB350025     1    27    27
browser |    27  100.0%          1     + 130466364 130466390              AB350025     1    27    27
browser |    27  100.0%          1     + 139657203 139657229              AB350025     1    27    27
browser |    27  100.0%          1     + 140751047 140751073              AB350025     1    27    27
browser |    27  100.0%          1     + 140969644 140969670              AB350025     1    27    27
browser |    27  100.0%          1     + 146003172 146003198              AB350025     1    27    27
browser |    27  100.0%          1     - 159797926 159797952              AB350025     1    27    27
browser |    27  100.0%          1     - 160644039 160644065              AB350025     1    27    27
browser |    27  100.0%          1     + 162674613 162674639              AB350025     1    27    27
browser |    27  100.0%          1     - 174870138 174870164              AB350025     1    27    27
browser |    27  100.0%          1     - 176371220 176371246              AB350025     1    27    27
browser |    27  100.0%          1     + 178008171 178008197              AB350025     1    27    27
browser |    27  100.0%          1     - 181091676 181091702              AB350025     1    27    27
browser |    27  100.0%          1     + 191844274 191844300              AB350025     1    27    27
browser |    27  100.0%         10     -   3551515   3551541              AB350025     1    27    27
browser |    27  100.0%         10     -  19415230  19415256              AB350025     1    27    27
browser |    27  100.0%         10     +  21091845  21091871              AB350025     1    27    27
browser |    27  100.0%         10     -  21518803  21518829              AB350025     1    27    27
browser |    27  100.0%         10     -  22559749  22559775              AB350025     1    27    27
browser |    27  100.0%         10     +  24566869  24566895              AB350025     1    27    27
browser |    27  100.0%         10     -  24978034  24978060              AB350025     1    27    27
browser |    27  100.0%         10     +  25848586  25848612              AB350025     1    27    27
browser |    27  100.0%         10     +  30696482  30696508              AB350025     1    27    27
browser |    27  100.0%         10     +  30971164  30971190              AB350025     1    27    27
browser |    27  100.0%         10     +  31630257  31630283              AB350025     1    27    27
browser |    27  100.0%         10     +  33766429  33766455              AB350025     1    27    27
browser |    27  100.0%         10     -  34618407  34618433              AB350025     1    27    27
browser |    27  100.0%         10     +  41723035  41723061              AB350025     1    27    27
browser |    27  100.0%         10     -  45431585  45431611              AB350025     1    27    27
browser |    27  100.0%         10     +  51763406  51763432              AB350025     1    27    27
browser |    27  100.0%         10     +  54468993  54469019              AB350025     1    27    27
browser |    27  100.0%         10     -  55592217  55592243              AB350025     1    27    27
browser |    27  100.0%         10     +  56603344  56603370              AB350025     1    27    27
browser |    27  100.0%         10     +  57020263  57020289              AB350025     1    27    27
browser |    27  100.0%         10     +  59222254  59222280              AB350025     1    27    27
browser |    27  100.0%         10     -  65787182  65787208              AB350025     1    27    27
browser |    27  100.0%         10     +  71533748  71533774              AB350025     1    27    27
browser |    27  100.0%         10     -  75217034  75217060              AB350025     1    27    27
browser |    27  100.0%         10     +  77793108  77793134              AB350025     1    27    27
browser |    27  100.0%         10     +  77860797  77860823              AB350025     1    27    27
browser |    27  100.0%         10     +  80816075  80816101              AB350025     1    27    27
browser |    27  100.0%         10     -  83507370  83507396              AB350025     1    27    27
browser |    27  100.0%         10     +  83627850  83627876              AB350025     1    27    27
browser |    27  100.0%         10     +  84585141  84585167              AB350025     1    27    27
browser |    27  100.0%         10     -  90161060  90161086              AB350025     1    27    27
browser |    27  100.0%         10     -  94199021  94199047              AB350025     1    27    27
browser |    27  100.0%         10     -  95993692  95993718              AB350025     1    27    27
browser |    27  100.0%         10     - 104655936 104655962              AB350025     1    27    27
browser |    27  100.0%         10     + 104677933 104677959              AB350025     1    27    27
browser |    27  100.0%         10     - 105509101 105509127              AB350025     1    27    27
browser |    27  100.0%         10     + 107841860 107841886              AB350025     1    27    27
browser |    27  100.0%         10     - 109151662 109151688              AB350025     1    27    27
browser |    27  100.0%         10     + 111893656 111893682              AB350025     1    27    27
browser |    27  100.0%         10     - 113559199 113559225              AB350025     1    27    27
browser |    27  100.0%         10     - 116442751 116442777              AB350025     1    27    27
browser |    27  100.0%         10     + 117911776 117911802              AB350025     1    27    27
browser |    27  100.0%         10     + 121004567 121004593              AB350025     1    27    27
browser |    27  100.0%         10     - 122202554 122202580              AB350025     1    27    27
browser |    27  100.0%         10     + 124418728 124418754              AB350025     1    27    27
browser |    27  100.0%         10     + 124446228 124446254              AB350025     1    27    27
browser |    27  100.0%         10     - 124516938 124516964              AB350025     1    27    27
browser |    27  100.0%         10     + 129764924 129764950              AB350025     1    27    27
browser |    27  100.0%         11     +   5312353   5312379              AB350025     1    27    27
browser |    27  100.0%         11     -   9658571   9658597              AB350025     1    27    27
browser |    27  100.0%         11     -  12457880  12457906              AB350025     1    27    27
browser |    27  100.0%         11     +  12518432  12518458              AB350025     1    27    27
browser |    27  100.0%         11     -  12904607  12904633              AB350025     1    27    27
browser |    27  100.0%         11     +  15184207  15184233              AB350025     1    27    27
browser |    27  100.0%         11     -  19516767  19516793              AB350025     1    27    27
browser |    27  100.0%         11     -  22285844  22285870              AB350025     1    27    27
browser |    27  100.0%         11     +  22532392  22532418              AB350025     1    27    27
browser |    27  100.0%         11     -  23169168  23169194              AB350025     1    27    27
browser |    27  100.0%         11     +  26510141  26510167              AB350025     1    27    27
browser |    27  100.0%         11     -  27901670  27901696              AB350025     1    27    27
browser |    27  100.0%         11     +  28053807  28053833              AB350025     1    27    27
browser |    27  100.0%         11     +  29079180  29079206              AB350025     1    27    27
browser |    27  100.0%         11     +  38377556  38377582              AB350025     1    27    27
browser |    27  100.0%         11     -  39955143  39955169              AB350025     1    27    27
browser |    27  100.0%         11     -  51556444  51556470              AB350025     1    27    27
browser |    27  100.0%         11     -  55132354  55132380              AB350025     1    27    27
browser |    27  100.0%         11     +  61317778  61317804              AB350025     1    27    27
browser |    27  100.0%         11     +  63365061  63365087              AB350025     1    27    27
browser |    27  100.0%         11     +  64687590  64687616              AB350025     1    27    27
browser |    27  100.0%         11     -  66839241  66839267              AB350025     1    27    27
browser |    27  100.0%         11     -  73627383  73627409              AB350025     1    27    27
browser |    27  100.0%         11     -  74111105  74111131              AB350025     1    27    27
browser |    27  100.0%         11     +  74435575  74435601              AB350025     1    27    27
browser |    27  100.0%         11     +  74781732  74781758              AB350025     1    27    27
browser |    27  100.0%         11     +  81442876  81442902              AB350025     1    27    27
browser |    27  100.0%         11     -  82225415  82225441              AB350025     1    27    27
browser |    27  100.0%         11     -  85176982  85177008              AB350025     1    27    27
browser |    27  100.0%         11     -  90721039  90721065              AB350025     1    27    27
browser |    27  100.0%         11     +  90798473  90798499              AB350025     1    27    27
browser |    27  100.0%         11     -  90851586  90851612              AB350025     1    27    27
browser |    27  100.0%         11     +  91996401  91996427              AB350025     1    27    27
browser |    27  100.0%         11     +  98510605  98510631              AB350025     1    27    27
browser |    27  100.0%         11     -  99604116  99604142              AB350025     1    27    27
browser |    27  100.0%         11     - 105919673 105919699              AB350025     1    27    27
browser |    27  100.0%         11     - 106184108 106184134              AB350025     1    27    27
browser |    27  100.0%         11     - 108290671 108290697              AB350025     1    27    27
browser |    27  100.0%         11     + 108545401 108545427              AB350025     1    27    27
browser |    27  100.0%         11     + 109914610 109914636              AB350025     1    27    27
browser |    27  100.0%         11     + 111079847 111079873              AB350025     1    27    27
browser |    27  100.0%         11     + 113809531 113809557              AB350025     1    27    27
browser |    27  100.0%         11     - 115646311 115646337              AB350025     1    27    27
browser |    27  100.0%         11     + 116284887 116284913              AB350025     1    27    27
browser |    27  100.0%         11     + 116682903 116682929              AB350025     1    27    27
browser |    27  100.0%         11     + 117395183 117395209              AB350025     1    27    27
browser |    27  100.0%         12     +   3058882   3058908              AB350025     1    27    27
browser |    27  100.0%         12     -   3381393   3381419              AB350025     1    27    27
browser |    27  100.0%         12     +   6573053   6573079              AB350025     1    27    27
browser |    27  100.0%         12     +   8457817   8457843              AB350025     1    27    27
browser |    27  100.0%         12     -  11154246  11154272              AB350025     1    27    27
browser |    27  100.0%         12     +  17178731  17178757              AB350025     1    27    27
browser |    27  100.0%         12     +  24451978  24452004              AB350025     1    27    27
browser |    27  100.0%         12     +  25644491  25644517              AB350025     1    27    27
browser |    27  100.0%         12     -  31408742  31408768              AB350025     1    27    27
browser |    27  100.0%         12     +  32081756  32081782              AB350025     1    27    27
browser |    27  100.0%         12     +  40458603  40458629              AB350025     1    27    27
browser |    27  100.0%         12     +  41420013  41420039              AB350025     1    27    27
browser |    27  100.0%         12     +  44831751  44831777              AB350025     1    27    27
browser |    27  100.0%         12     +  48585474  48585500              AB350025     1    27    27
browser |    27  100.0%         12     +  49048078  49048104              AB350025     1    27    27
browser |    27  100.0%         12     -  52777476  52777502              AB350025     1    27    27
browser |    27  100.0%         12     +  59493674  59493700              AB350025     1    27    27
browser |    27  100.0%         12     -  61336492  61336518              AB350025     1    27    27
browser |    27  100.0%         12     +  62585374  62585400              AB350025     1    27    27
browser |    27  100.0%         12     -  65074531  65074557              AB350025     1    27    27
browser |    27  100.0%         12     -  65848594  65848620              AB350025     1    27    27
browser |    27  100.0%         12     -  68669147  68669173              AB350025     1    27    27
browser |    27  100.0%         12     -  70708526  70708552              AB350025     1    27    27
browser |    27  100.0%         12     -  73358383  73358409              AB350025     1    27    27
browser |    27  100.0%         12     +  80470574  80470600              AB350025     1    27    27
browser |    27  100.0%         12     +  81634010  81634036              AB350025     1    27    27
browser |    27  100.0%         12     -  82508448  82508474              AB350025     1    27    27
browser |    27  100.0%         12     -  94003869  94003895              AB350025     1    27    27
browser |    27  100.0%         12     -  96197548  96197574              AB350025     1    27    27
browser |    27  100.0%         12     - 108046143 108046169              AB350025     1    27    27
browser |    27  100.0%         12     + 109874858 109874884              AB350025     1    27    27
browser |    27  100.0%         12     + 111359225 111359251              AB350025     1    27    27
browser |    27  100.0%         12     + 119561030 119561056              AB350025     1    27    27
browser |    27  100.0%         13     -   4116814   4116840              AB350025     1    27    27
browser |    27  100.0%         13     +   4394952   4394978              AB350025     1    27    27
browser |    27  100.0%         13     +   5333430   5333456              AB350025     1    27    27
browser |    27  100.0%         13     -   7999763   7999789              AB350025     1    27    27
browser |    27  100.0%         13     -   8520242   8520268              AB350025     1    27    27
browser |    27  100.0%         13     -   9483282   9483308              AB350025     1    27    27
browser |    27  100.0%         13     +  11522405  11522431              AB350025     1    27    27
browser |    27  100.0%         13     +  15612652  15612678              AB350025     1    27    27
browser |    27  100.0%         13     -  21814573  21814599              AB350025     1    27    27
browser |    27  100.0%         13     -  22413206  22413232              AB350025     1    27    27
browser |    27  100.0%         13     -  28308975  28309001              AB350025     1    27    27
browser |    27  100.0%         13     +  30560618  30560644              AB350025     1    27    27
browser |    27  100.0%         13     -  33132151  33132177              AB350025     1    27    27
browser |    27  100.0%         13     +  33628135  33628161              AB350025     1    27    27
browser |    27  100.0%         13     +  34052491  34052517              AB350025     1    27    27
browser |    27  100.0%         13     -  34351373  34351399              AB350025     1    27    27
browser |    27  100.0%         13     +  38298337  38298363              AB350025     1    27    27
browser |    27  100.0%         13     +  39696891  39696917              AB350025     1    27    27
browser |    27  100.0%         13     +  43437517  43437543              AB350025     1    27    27
browser |    27  100.0%         13     +  43546755  43546781              AB350025     1    27    27
browser |    27  100.0%         13     +  44424340  44424366              AB350025     1    27    27
browser |    27  100.0%         13     +  45171102  45171128              AB350025     1    27    27
browser |    27  100.0%         13     -  46530241  46530267              AB350025     1    27    27
browser |    27  100.0%         13     -  51420383  51420409              AB350025     1    27    27
browser |    27  100.0%         13     +  52144138  52144164              AB350025     1    27    27
browser |    27  100.0%         13     -  52444157  52444183              AB350025     1    27    27
browser |    27  100.0%         13     +  55930963  55930989              AB350025     1    27    27
browser |    27  100.0%         13     -  56861279  56861305              AB350025     1    27    27
browser |    27  100.0%         13     -  62621418  62621444              AB350025     1    27    27
browser |    27  100.0%         13     -  63305280  63305306              AB350025     1    27    27
browser |    27  100.0%         13     +  66166608  66166634              AB350025     1    27    27
browser |    27  100.0%         13     +  82045567  82045593              AB350025     1    27    27
browser |    27  100.0%         13     +  83573626  83573652              AB350025     1    27    27
browser |    27  100.0%         13     +  86867414  86867440              AB350025     1    27    27
browser |    27  100.0%         13     +  86925508  86925534              AB350025     1    27    27
browser |    27  100.0%         13     -  87318644  87318670              AB350025     1    27    27
browser |    27  100.0%         13     -  87497625  87497651              AB350025     1    27    27
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View details of parts of alignment within browser window
.
View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518