AB351824
 

Information on mRNA AB351824

Description: Mus musculus non-coding RNA, oocyte_piRNA2640, 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: AB351824
Position: chr12:56794829-56794853

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 |    25  100.0%         12     -  56794829  56794853              AB351824     1    25    25
browser |    25  100.0%          1     -   3101784   3101808              AB351824     1    25    25
browser |    25  100.0%          1     -   4202590   4202614              AB351824     1    25    25
browser |    25  100.0%          1     -   5874762   5874786              AB351824     1    25    25
browser |    25  100.0%          1     -   5881520   5881544              AB351824     1    25    25
browser |    25  100.0%          1     +   6238460   6238484              AB351824     1    25    25
browser |    25  100.0%          1     +   6242811   6242835              AB351824     1    25    25
browser |    25  100.0%          1     -   6500792   6500816              AB351824     1    25    25
browser |    25  100.0%          1     -   6507560   6507584              AB351824     1    25    25
browser |    25  100.0%          1     +   8064056   8064080              AB351824     1    25    25
browser |    25  100.0%          1     +   8070824   8070848              AB351824     1    25    25
browser |    25  100.0%          1     +   8226555   8226579              AB351824     1    25    25
browser |    25  100.0%          1     +   8233259   8233283              AB351824     1    25    25
browser |    25  100.0%          1     -  10800288  10800312              AB351824     1    25    25
browser |    25  100.0%          1     -  10807074  10807098              AB351824     1    25    25
browser |    25  100.0%          1     -  11957541  11957565              AB351824     1    25    25
browser |    25  100.0%          1     -  11961752  11961776              AB351824     1    25    25
browser |    25  100.0%          1     +  14068924  14068948              AB351824     1    25    25
browser |    25  100.0%          1     -  16275931  16275955              AB351824     1    25    25
browser |    25  100.0%          1     +  16808623  16808647              AB351824     1    25    25
browser |    25  100.0%          1     +  16815337  16815361              AB351824     1    25    25
browser |    25  100.0%          1     -  16918563  16918587              AB351824     1    25    25
browser |    25  100.0%          1     +  18587189  18587213              AB351824     1    25    25
browser |    25  100.0%          1     +  18591210  18591234              AB351824     1    25    25
browser |    25  100.0%          1     +  19692705  19692729              AB351824     1    25    25
browser |    25  100.0%          1     +  19699550  19699574              AB351824     1    25    25
browser |    25  100.0%          1     -  26388452  26388476              AB351824     1    25    25
browser |    25  100.0%          1     -  26393304  26393328              AB351824     1    25    25
browser |    25  100.0%          1     -  26509648  26509672              AB351824     1    25    25
browser |    25  100.0%          1     -  26515157  26515181              AB351824     1    25    25
browser |    25  100.0%          1     +  27219343  27219367              AB351824     1    25    25
browser |    25  100.0%          1     +  27226100  27226124              AB351824     1    25    25
browser |    25  100.0%          1     +  34386663  34386687              AB351824     1    25    25
browser |    25  100.0%          1     -  81542088  81542112              AB351824     1    25    25
browser |    25  100.0%          1     -  81548815  81548839              AB351824     1    25    25
browser |    25  100.0%          1     +  82478885  82478909              AB351824     1    25    25
browser |    25  100.0%          1     +  82483498  82483522              AB351824     1    25    25
browser |    25  100.0%          1     -  84973806  84973830              AB351824     1    25    25
browser |    25  100.0%          1     -  84978136  84978160              AB351824     1    25    25
browser |    25  100.0%          1     +  89126921  89126945              AB351824     1    25    25
browser |    25  100.0%          1     +  89130719  89130743              AB351824     1    25    25
browser |    25  100.0%          1     -  91405886  91405910              AB351824     1    25    25
browser |    25  100.0%          1     +  93884430  93884454              AB351824     1    25    25
browser |    25  100.0%          1     +  93888806  93888830              AB351824     1    25    25
browser |    25  100.0%          1     +  97100553  97100577              AB351824     1    25    25
browser |    25  100.0%          1     +  97108726  97108750              AB351824     1    25    25
browser |    25  100.0%          1     - 101454197 101454221              AB351824     1    25    25
browser |    25  100.0%          1     - 101906080 101906104              AB351824     1    25    25
browser |    25  100.0%          1     - 101912872 101912896              AB351824     1    25    25
browser |    25  100.0%          1     + 102959516 102959540              AB351824     1    25    25
browser |    25  100.0%          1     + 102966274 102966298              AB351824     1    25    25
browser |    25  100.0%          1     - 103133113 103133137              AB351824     1    25    25
browser |    25  100.0%          1     - 103139866 103139890              AB351824     1    25    25
browser |    25  100.0%          1     + 103516564 103516588              AB351824     1    25    25
browser |    25  100.0%          1     + 103521533 103521557              AB351824     1    25    25
browser |    25  100.0%          1     - 104217501 104217525              AB351824     1    25    25
browser |    25  100.0%          1     - 104222390 104222414              AB351824     1    25    25
browser |    25  100.0%          1     - 107966735 107966759              AB351824     1    25    25
browser |    25  100.0%          1     - 107968471 107968495              AB351824     1    25    25
browser |    25  100.0%          1     - 109056607 109056631              AB351824     1    25    25
browser |    25  100.0%          1     - 109061511 109061535              AB351824     1    25    25
browser |    25  100.0%          1     + 109541248 109541272              AB351824     1    25    25
browser |    25  100.0%          1     + 109548006 109548030              AB351824     1    25    25
browser |    25  100.0%          1     + 110256972 110256996              AB351824     1    25    25
browser |    25  100.0%          1     + 110261780 110261804              AB351824     1    25    25
browser |    25  100.0%          1     - 159797543 159797567              AB351824     1    25    25
browser |    25  100.0%          1     - 159804272 159804296              AB351824     1    25    25
browser |    25  100.0%          1     - 160643654 160643678              AB351824     1    25    25
browser |    25  100.0%          1     - 160648446 160648470              AB351824     1    25    25
browser |    25  100.0%          1     - 163296272 163296296              AB351824     1    25    25
browser |    25  100.0%          1     - 163300059 163300083              AB351824     1    25    25
browser |    25  100.0%          1     - 163520756 163520780              AB351824     1    25    25
browser |    25  100.0%          1     + 169370114 169370138              AB351824     1    25    25
browser |    25  100.0%          1     + 169376248 169376272              AB351824     1    25    25
browser |    25  100.0%          1     + 169943492 169943516              AB351824     1    25    25
browser |    25  100.0%          1     + 169950239 169950263              AB351824     1    25    25
browser |    25  100.0%          1     - 174869755 174869779              AB351824     1    25    25
browser |    25  100.0%          1     - 174875703 174875727              AB351824     1    25    25
browser |    25  100.0%          1     - 176370837 176370861              AB351824     1    25    25
browser |    25  100.0%          1     - 176377579 176377603              AB351824     1    25    25
browser |    25  100.0%          1     + 178001805 178001829              AB351824     1    25    25
browser |    25  100.0%          1     + 178008556 178008580              AB351824     1    25    25
browser |    25  100.0%          1     - 181091293 181091317              AB351824     1    25    25
browser |    25  100.0%          1     - 181098022 181098046              AB351824     1    25    25
browser |    25  100.0%          1     + 181320600 181320624              AB351824     1    25    25
browser |    25  100.0%          1     + 181326836 181326860              AB351824     1    25    25
browser |    25  100.0%          1     + 191839851 191839875              AB351824     1    25    25
browser |    25  100.0%          1     + 194336257 194336281              AB351824     1    25    25
browser |    25  100.0%         10     -   3551132   3551156              AB351824     1    25    25
browser |    25  100.0%         10     -   3557877   3557901              AB351824     1    25    25
browser |    25  100.0%         10     +  17900521  17900545              AB351824     1    25    25
browser |    25  100.0%         10     -  19414847  19414871              AB351824     1    25    25
browser |    25  100.0%         10     -  19421606  19421630              AB351824     1    25    25
browser |    25  100.0%         10     +  21087230  21087254              AB351824     1    25    25
browser |    25  100.0%         10     +  21092230  21092254              AB351824     1    25    25
browser |    25  100.0%         10     -  21518420  21518444              AB351824     1    25    25
browser |    25  100.0%         10     -  21525271  21525295              AB351824     1    25    25
browser |    25  100.0%         10     -  22559366  22559390              AB351824     1    25    25
browser |    25  100.0%         10     -  22566294  22566318              AB351824     1    25    25
browser |    25  100.0%         10     -  23744186  23744210              AB351824     1    25    25
browser |    25  100.0%         10     +  24562455  24562479              AB351824     1    25    25
browser |    25  100.0%         10     +  24567256  24567280              AB351824     1    25    25
browser |    25  100.0%         10     -  24977651  24977675              AB351824     1    25    25
browser |    25  100.0%         10     -  24982262  24982286              AB351824     1    25    25
browser |    25  100.0%         10     +  25844444  25844468              AB351824     1    25    25
browser |    25  100.0%         10     +  25848972  25848996              AB351824     1    25    25
browser |    25  100.0%         10     +  30690115  30690139              AB351824     1    25    25
browser |    25  100.0%         10     +  30696867  30696891              AB351824     1    25    25
browser |    25  100.0%         10     +  30964691  30964715              AB351824     1    25    25
browser |    25  100.0%         10     +  30971551  30971575              AB351824     1    25    25
browser |    25  100.0%         10     +  31358752  31358776              AB351824     1    25    25
browser |    25  100.0%         10     +  31365499  31365523              AB351824     1    25    25
browser |    25  100.0%         10     +  31626243  31626267              AB351824     1    25    25
browser |    25  100.0%         10     +  31630642  31630666              AB351824     1    25    25
browser |    25  100.0%         10     +  33762907  33762931              AB351824     1    25    25
browser |    25  100.0%         10     -  34618023  34618047              AB351824     1    25    25
browser |    25  100.0%         10     -  34624772  34624796              AB351824     1    25    25
browser |    25  100.0%         10     -  45431202  45431226              AB351824     1    25    25
browser |    25  100.0%         10     -  45436227  45436251              AB351824     1    25    25
browser |    25  100.0%         10     -  65474900  65474924              AB351824     1    25    25
browser |    25  100.0%         10     +  80811997  80812021              AB351824     1    25    25
browser |    25  100.0%         10     +  80816460  80816484              AB351824     1    25    25
browser |    25  100.0%         10     +  81803851  81803875              AB351824     1    25    25
browser |    25  100.0%         10     +  81810609  81810633              AB351824     1    25    25
browser |    25  100.0%         10     -  83506987  83507011              AB351824     1    25    25
browser |    25  100.0%         10     -  83513712  83513736              AB351824     1    25    25
browser |    25  100.0%         10     +  83623466  83623490              AB351824     1    25    25
browser |    25  100.0%         10     +  83628237  83628261              AB351824     1    25    25
browser |    25  100.0%         10     +  84580580  84580604              AB351824     1    25    25
browser |    25  100.0%         10     +  84585528  84585552              AB351824     1    25    25
browser |    25  100.0%         10     +  85551189  85551213              AB351824     1    25    25
browser |    25  100.0%         10     +  85556328  85556352              AB351824     1    25    25
browser |    25  100.0%         10     -  90160675  90160699              AB351824     1    25    25
browser |    25  100.0%         10     -  90165443  90165467              AB351824     1    25    25
browser |    25  100.0%         10     -  94198638  94198662              AB351824     1    25    25
browser |    25  100.0%         10     -  94204963  94204987              AB351824     1    25    25
browser |    25  100.0%         10     -  95993307  95993331              AB351824     1    25    25
browser |    25  100.0%         10     -  95998156  95998180              AB351824     1    25    25
browser |    25  100.0%         10     -  96028600  96028624              AB351824     1    25    25
browser |    25  100.0%         10     -  96035415  96035439              AB351824     1    25    25
browser |    25  100.0%         10     +  97377782  97377806              AB351824     1    25    25
browser |    25  100.0%         10     + 104391261 104391285              AB351824     1    25    25
browser |    25  100.0%         10     + 104398091 104398115              AB351824     1    25    25
browser |    25  100.0%         10     - 104655551 104655575              AB351824     1    25    25
browser |    25  100.0%         10     - 104660553 104660577              AB351824     1    25    25
browser |    25  100.0%         10     + 104671583 104671607              AB351824     1    25    25
browser |    25  100.0%         10     + 104678318 104678342              AB351824     1    25    25
browser |    25  100.0%         10     - 104857819 104857843              AB351824     1    25    25
browser |    25  100.0%         10     + 105013107 105013131              AB351824     1    25    25
browser |    25  100.0%         10     - 105508716 105508740              AB351824     1    25    25
browser |    25  100.0%         10     - 105513644 105513668              AB351824     1    25    25
browser |    25  100.0%         10     - 109151279 109151303              AB351824     1    25    25
browser |    25  100.0%         11     +   3999075   3999099              AB351824     1    25    25
browser |    25  100.0%         11     +   5312739   5312763              AB351824     1    25    25
browser |    25  100.0%         11     -   9658188   9658212              AB351824     1    25    25
browser |    25  100.0%         11     -   9664919   9664943              AB351824     1    25    25
browser |    25  100.0%         11     +  10710439  10710463              AB351824     1    25    25
browser |    25  100.0%         11     +  10717206  10717230              AB351824     1    25    25
browser |    25  100.0%         11     -  12457495  12457519              AB351824     1    25    25
browser |    25  100.0%         11     -  12462450  12462474              AB351824     1    25    25
browser |    25  100.0%         11     +  12512034  12512058              AB351824     1    25    25
browser |    25  100.0%         11     +  12518817  12518841              AB351824     1    25    25
browser |    25  100.0%         11     -  12904223  12904247              AB351824     1    25    25
browser |    25  100.0%         11     -  12909060  12909084              AB351824     1    25    25
browser |    25  100.0%         11     +  15177814  15177838              AB351824     1    25    25
browser |    25  100.0%         11     +  15184592  15184616              AB351824     1    25    25
browser |    25  100.0%         11     +  15833803  15833827              AB351824     1    25    25
browser |    25  100.0%         11     +  15837590  15837614              AB351824     1    25    25
browser |    25  100.0%         11     -  17102820  17102844              AB351824     1    25    25
browser |    25  100.0%         11     -  19516384  19516408              AB351824     1    25    25
browser |    25  100.0%         11     -  19520430  19520454              AB351824     1    25    25
browser |    25  100.0%         11     +  20466521  20466545              AB351824     1    25    25
browser |    25  100.0%         11     +  20470932  20470956              AB351824     1    25    25
browser |    25  100.0%         11     -  22285459  22285483              AB351824     1    25    25
browser |    25  100.0%         11     -  22290386  22290410              AB351824     1    25    25
browser |    25  100.0%         11     +  22527826  22527850              AB351824     1    25    25
browser |    25  100.0%         11     +  22532777  22532801              AB351824     1    25    25
browser |    25  100.0%         11     -  23168785  23168809              AB351824     1    25    25
browser |    25  100.0%         11     -  23175525  23175549              AB351824     1    25    25
browser |    25  100.0%         11     -  25562905  25562929              AB351824     1    25    25
browser |    25  100.0%         11     +  26505571  26505595              AB351824     1    25    25
browser |    25  100.0%         11     +  26510526  26510550              AB351824     1    25    25
browser |    25  100.0%         11     -  27901287  27901311              AB351824     1    25    25
browser |    25  100.0%         11     -  27906909  27906933              AB351824     1    25    25
browser |    25  100.0%         11     +  81436432  81436456              AB351824     1    25    25
browser |    25  100.0%         11     +  81443261  81443285              AB351824     1    25    25
browser |    25  100.0%         11     -  82225032  82225056              AB351824     1    25    25
browser |    25  100.0%         11     -  82229006  82229030              AB351824     1    25    25
browser |    25  100.0%         11     -  85176599  85176623              AB351824     1    25    25
browser |    25  100.0%         11     -  85183357  85183381              AB351824     1    25    25
browser |    25  100.0%         11     +  86736594  86736618              AB351824     1    25    25
browser |    25  100.0%         11     +  86740772  86740796              AB351824     1    25    25
browser |    25  100.0%         11     -  90201415  90201439              AB351824     1    25    25
browser |    25  100.0%         11     -  90203128  90203152              AB351824     1    25    25
browser |    25  100.0%         11     -  90720655  90720679              AB351824     1    25    25
browser |    25  100.0%         11     -  90725611  90725635              AB351824     1    25    25
browser |    25  100.0%         11     +  90792679  90792703              AB351824     1    25    25
browser |    25  100.0%         11     +  90798858  90798882              AB351824     1    25    25
browser |    25  100.0%         11     -  90851203  90851227              AB351824     1    25    25
browser |    25  100.0%         11     -  90857950  90857974              AB351824     1    25    25
browser |    25  100.0%         11     +  91989994  91990018              AB351824     1    25    25
browser |    25  100.0%         11     +  91996787  91996811              AB351824     1    25    25
browser |    25  100.0%         11     +  98504229  98504253              AB351824     1    25    25
browser |    25  100.0%         11     +  98510990  98511014              AB351824     1    25    25
browser |    25  100.0%         11     -  99603733  99603757              AB351824     1    25    25
browser |    25  100.0%         11     -  99607891  99607915              AB351824     1    25    25
browser |    25  100.0%         11     + 100553846 100553870              AB351824     1    25    25
browser |    25  100.0%         11     + 100560137 100560161              AB351824     1    25    25
browser |    25  100.0%         11     - 106183725 106183749              AB351824     1    25    25
browser |    25  100.0%         11     - 106188260 106188284              AB351824     1    25    25
browser |    25  100.0%         11     - 108290286 108290310              AB351824     1    25    25
browser |    25  100.0%         11     - 108295121 108295145              AB351824     1    25    25
browser |    25  100.0%         11     + 108540852 108540876              AB351824     1    25    25
browser |    25  100.0%         11     + 108545788 108545812              AB351824     1    25    25
browser |    25  100.0%         11     + 109910596 109910620              AB351824     1    25    25
browser |    25  100.0%         11     + 109914997 109915021              AB351824     1    25    25
browser |    25  100.0%         12     +   3052464   3052488              AB351824     1    25    25
browser |    25  100.0%         12     +   3059267   3059291              AB351824     1    25    25
browser |    25  100.0%         12     -   3381010   3381034              AB351824     1    25    25
browser |    25  100.0%         12     -   3387788   3387812              AB351824     1    25    25
browser |    25  100.0%         12     +   8453301   8453325              AB351824     1    25    25
browser |    25  100.0%         12     +   8458202   8458226              AB351824     1    25    25
browser |    25  100.0%         12     -  11153863  11153887              AB351824     1    25    25
browser |    25  100.0%         12     -  11160590  11160614              AB351824     1    25    25
browser |    25  100.0%         12     +  19831394  19831418              AB351824     1    25    25
browser |    25  100.0%         12     -  31408359  31408383              AB351824     1    25    25
browser |    25  100.0%         12     -  31415075  31415099              AB351824     1    25    25
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View details of parts of alignment within browser window
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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