AB350718
 

Information on mRNA AB350718

Description: Mus musculus non-coding RNA, oocyte_piRNA1534, 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: AB350718
Position: chr12:56797416-56797441

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 |    26  100.0%         12     -  56797416  56797441              AB350718     1    26    26
browser |    26  100.0%          1     -   5880101   5880126              AB350718     1    26    26
browser |    26  100.0%          1     -   6506130   6506155              AB350718     1    26    26
browser |    26  100.0%          1     +   8065493   8065518              AB350718     1    26    26
browser |    26  100.0%          1     +   8227934   8227959              AB350718     1    26    26
browser |    26  100.0%          1     -   8731141   8731166              AB350718     1    26    26
browser |    26  100.0%          1     -  10805617  10805642              AB350718     1    26    26
browser |    26  100.0%          1     -  12019441  12019466              AB350718     1    26    26
browser |    26  100.0%          1     +  13622358  13622383              AB350718     1    26    26
browser |    26  100.0%          1     +  16810004  16810029              AB350718     1    26    26
browser |    26  100.0%          1     +  18028598  18028623              AB350718     1    26    26
browser |    26  100.0%          1     +  18588628  18588653              AB350718     1    26    26
browser |    26  100.0%          1     +  19694212  19694237              AB350718     1    26    26
browser |    26  100.0%          1     -  22070994  22071019              AB350718     1    26    26
browser |    26  100.0%          1     +  23341769  23341794              AB350718     1    26    26
browser |    26  100.0%          1     -  26391890  26391915              AB350718     1    26    26
browser |    26  100.0%          1     +  26454620  26454645              AB350718     1    26    26
browser |    26  100.0%          1     -  26513706  26513731              AB350718     1    26    26
browser |    26  100.0%          1     +  27220768  27220793              AB350718     1    26    26
browser |    26  100.0%          1     -  29986836  29986861              AB350718     1    26    26
browser |    26  100.0%          1     +  34388101  34388126              AB350718     1    26    26
browser |    26  100.0%          1     +  35829097  35829122              AB350718     1    26    26
browser |    26  100.0%          1     +  38745486  38745511              AB350718     1    26    26
browser |    26  100.0%          1     +  40738777  40738802              AB350718     1    26    26
browser |    26  100.0%          1     +  45774850  45774875              AB350718     1    26    26
browser |    26  100.0%          1     -  47265550  47265575              AB350718     1    26    26
browser |    26  100.0%          1     +  48129784  48129809              AB350718     1    26    26
browser |    26  100.0%          1     -  48400891  48400916              AB350718     1    26    26
browser |    26  100.0%          1     -  53172381  53172406              AB350718     1    26    26
browser |    26  100.0%          1     -  58368056  58368081              AB350718     1    26    26
browser |    26  100.0%          1     -  58856364  58856389              AB350718     1    26    26
browser |    26  100.0%          1     -  60769550  60769575              AB350718     1    26    26
browser |    26  100.0%          1     -  62578814  62578839              AB350718     1    26    26
browser |    26  100.0%          1     -  81547425  81547450              AB350718     1    26    26
browser |    26  100.0%          1     +  82480347  82480372              AB350718     1    26    26
browser |    26  100.0%          1     -  83209029  83209054              AB350718     1    26    26
browser |    26  100.0%          1     -  87066907  87066932              AB350718     1    26    26
browser |    26  100.0%          1     +  87389424  87389449              AB350718     1    26    26
browser |    26  100.0%          1     +  89128352  89128377              AB350718     1    26    26
browser |    26  100.0%          1     -  91404480  91404505              AB350718     1    26    26
browser |    26  100.0%          1     +  93885834  93885859              AB350718     1    26    26
browser |    26  100.0%          1     +  95624422  95624447              AB350718     1    26    26
browser |    26  100.0%          1     +  97102033  97102058              AB350718     1    26    26
browser |    26  100.0%          1     -  98529677  98529702              AB350718     1    26    26
browser |    26  100.0%          1     - 101911415 101911440              AB350718     1    26    26
browser |    26  100.0%          1     + 102960935 102960960              AB350718     1    26    26
browser |    26  100.0%          1     - 103138444 103138469              AB350718     1    26    26
browser |    26  100.0%          1     + 103407566 103407591              AB350718     1    26    26
browser |    26  100.0%          1     + 103518097 103518122              AB350718     1    26    26
browser |    26  100.0%          1     - 104220940 104220965              AB350718     1    26    26
browser |    26  100.0%          1     - 108342132 108342157              AB350718     1    26    26
browser |    26  100.0%          1     - 109059991 109060016              AB350718     1    26    26
browser |    26  100.0%          1     + 109542677 109542702              AB350718     1    26    26
browser |    26  100.0%          1     + 110258342 110258367              AB350718     1    26    26
browser |    26  100.0%          1     - 111186901 111186926              AB350718     1    26    26
browser |    26  100.0%          1     + 111632645 111632670              AB350718     1    26    26
browser |    26  100.0%          1     - 112197621 112197646              AB350718     1    26    26
browser |    26  100.0%          1     + 112858754 112858779              AB350718     1    26    26
browser |    26  100.0%          1     + 112945352 112945377              AB350718     1    26    26
browser |    26  100.0%          1     + 114114559 114114584              AB350718     1    26    26
browser |    26  100.0%          1     - 115816742 115816767              AB350718     1    26    26
browser |    26  100.0%          1     - 116581549 116581574              AB350718     1    26    26
browser |    26  100.0%          1     - 117635207 117635232              AB350718     1    26    26
browser |    26  100.0%          1     - 120502225 120502250              AB350718     1    26    26
browser |    26  100.0%          1     + 125246140 125246165              AB350718     1    26    26
browser |    26  100.0%          1     - 159802875 159802900              AB350718     1    26    26
browser |    26  100.0%          1     - 160647092 160647117              AB350718     1    26    26
browser |    26  100.0%          1     + 162669665 162669690              AB350718     1    26    26
browser |    26  100.0%          1     - 166595748 166595773              AB350718     1    26    26
browser |    26  100.0%          1     - 174874280 174874305              AB350718     1    26    26
browser |    26  100.0%          1     - 176376174 176376199              AB350718     1    26    26
browser |    26  100.0%          1     + 177887164 177887189              AB350718     1    26    26
browser |    26  100.0%          1     + 178003217 178003242              AB350718     1    26    26
browser |    26  100.0%          1     + 179723112 179723137              AB350718     1    26    26
browser |    26  100.0%          1     - 181096631 181096656              AB350718     1    26    26
browser |    26  100.0%          1     + 181322006 181322031              AB350718     1    26    26
browser |    26  100.0%          1     + 183297824 183297849              AB350718     1    26    26
browser |    26  100.0%          1     + 191841222 191841247              AB350718     1    26    26
browser |    26  100.0%          1     + 195004201 195004226              AB350718     1    26    26
browser |    26  100.0%         10     -   3556471   3556496              AB350718     1    26    26
browser |    26  100.0%         10     +   8476590   8476615              AB350718     1    26    26
browser |    26  100.0%         10     +  11571569  11571594              AB350718     1    26    26
browser |    26  100.0%         10     -  19420184  19420209              AB350718     1    26    26
browser |    26  100.0%         10     +  19674604  19674629              AB350718     1    26    26
browser |    26  100.0%         10     -  19891911  19891936              AB350718     1    26    26
browser |    26  100.0%         10     +  21088789  21088814              AB350718     1    26    26
browser |    26  100.0%         10     -  21523757  21523782              AB350718     1    26    26
browser |    26  100.0%         10     -  22404649  22404674              AB350718     1    26    26
browser |    26  100.0%         10     -  22564703  22564728              AB350718     1    26    26
browser |    26  100.0%         10     -  23752758  23752783              AB350718     1    26    26
browser |    26  100.0%         10     +  24563817  24563842              AB350718     1    26    26
browser |    26  100.0%         10     -  24980830  24980855              AB350718     1    26    26
browser |    26  100.0%         10     +  25845862  25845887              AB350718     1    26    26
browser |    26  100.0%         10     +  30358934  30358959              AB350718     1    26    26
browser |    26  100.0%         10     +  30691530  30691555              AB350718     1    26    26
browser |    26  100.0%         10     +  30966215  30966240              AB350718     1    26    26
browser |    26  100.0%         10     +  31360157  31360182              AB350718     1    26    26
browser |    26  100.0%         10     +  33764484  33764509              AB350718     1    26    26
browser |    26  100.0%         10     -  34616583  34616608              AB350718     1    26    26
browser |    26  100.0%         10     -  34623361  34623386              AB350718     1    26    26
browser |    26  100.0%         10     +  41718084  41718109              AB350718     1    26    26
browser |    26  100.0%         10     +  47548234  47548259              AB350718     1    26    26
browser |    26  100.0%         10     +  51760642  51760667              AB350718     1    26    26
browser |    26  100.0%         10     -  65479164  65479189              AB350718     1    26    26
browser |    26  100.0%         10     -  65790238  65790263              AB350718     1    26    26
browser |    26  100.0%         10     -  66563779  66563804              AB350718     1    26    26
browser |    26  100.0%         10     +  77857741  77857766              AB350718     1    26    26
browser |    26  100.0%         10     -  78657328  78657353              AB350718     1    26    26
browser |    26  100.0%         10     -  81511912  81511937              AB350718     1    26    26
browser |    26  100.0%         10     -  81671040  81671065              AB350718     1    26    26
browser |    26  100.0%         10     +  81805274  81805299              AB350718     1    26    26
browser |    26  100.0%         10     -  83307269  83307294              AB350718     1    26    26
browser |    26  100.0%         10     -  83512324  83512349              AB350718     1    26    26
browser |    26  100.0%         10     +  83624852  83624877              AB350718     1    26    26
browser |    26  100.0%         10     +  85552608  85552633              AB350718     1    26    26
browser |    26  100.0%         10     +  86980028  86980053              AB350718     1    26    26
browser |    26  100.0%         10     +  88488395  88488420              AB350718     1    26    26
browser |    26  100.0%         10     -  90164059  90164084              AB350718     1    26    26
browser |    26  100.0%         10     -  94203472  94203497              AB350718     1    26    26
browser |    26  100.0%         10     -  95996748  95996773              AB350718     1    26    26
browser |    26  100.0%         10     -  96033932  96033957              AB350718     1    26    26
browser |    26  100.0%         10     -  97163851  97163876              AB350718     1    26    26
browser |    26  100.0%         10     +  99176534  99176559              AB350718     1    26    26
browser |    26  100.0%         10     -  99385624  99385649              AB350718     1    26    26
browser |    26  100.0%         10     + 104392761 104392786              AB350718     1    26    26
browser |    26  100.0%         10     + 104672978 104673003              AB350718     1    26    26
browser |    26  100.0%         10     + 105014497 105014522              AB350718     1    26    26
browser |    26  100.0%         10     - 113564144 113564169              AB350718     1    26    26
browser |    26  100.0%         10     + 121002186 121002211              AB350718     1    26    26
browser |    26  100.0%         10     - 122205314 122205339              AB350718     1    26    26
browser |    26  100.0%         10     + 122343232 122343257              AB350718     1    26    26
browser |    26  100.0%         10     - 122674191 122674216              AB350718     1    26    26
browser |    26  100.0%         10     + 123696799 123696824              AB350718     1    26    26
browser |    26  100.0%         10     + 124413773 124413798              AB350718     1    26    26
browser |    26  100.0%         10     + 124443194 124443219              AB350718     1    26    26
browser |    26  100.0%         10     - 124520385 124520410              AB350718     1    26    26
browser |    26  100.0%         10     + 129051213 129051238              AB350718     1    26    26
browser |    26  100.0%         10     - 129230230 129230255              AB350718     1    26    26
browser |    26  100.0%         10     + 129762721 129762746              AB350718     1    26    26
browser |    26  100.0%         10     - 130400439 130400464              AB350718     1    26    26
browser |    26  100.0%         11     -   6097032   6097057              AB350718     1    26    26
browser |    26  100.0%         11     -   9663523   9663548              AB350718     1    26    26
browser |    26  100.0%         11     +  10711874  10711899              AB350718     1    26    26
browser |    26  100.0%         11     +  12513484  12513509              AB350718     1    26    26
browser |    26  100.0%         11     -  12907660  12907685              AB350718     1    26    26
browser |    26  100.0%         11     +  15179254  15179279              AB350718     1    26    26
browser |    26  100.0%         11     -  15236398  15236423              AB350718     1    26    26
browser |    26  100.0%         11     -  18761996  18762021              AB350718     1    26    26
browser |    26  100.0%         11     -  19518965  19518990              AB350718     1    26    26
browser |    26  100.0%         11     +  20467940  20467965              AB350718     1    26    26
browser |    26  100.0%         11     -  22288897  22288922              AB350718     1    26    26
browser |    26  100.0%         11     +  22529342  22529367              AB350718     1    26    26
browser |    26  100.0%         11     -  23174123  23174148              AB350718     1    26    26
browser |    26  100.0%         11     +  26507084  26507109              AB350718     1    26    26
browser |    26  100.0%         11     -  27905509  27905534              AB350718     1    26    26
browser |    26  100.0%         11     +  28048857  28048882              AB350718     1    26    26
browser |    26  100.0%         11     +  29076122  29076147              AB350718     1    26    26
browser |    26  100.0%         11     -  29233139  29233164              AB350718     1    26    26
browser |    26  100.0%         11     -  31403103  31403128              AB350718     1    26    26
browser |    26  100.0%         11     +  38373886  38373911              AB350718     1    26    26
browser |    26  100.0%         11     -  39960092  39960117              AB350718     1    26    26
browser |    26  100.0%         11     -  51559497  51559522              AB350718     1    26    26
browser |    26  100.0%         11     +  61312825  61312850              AB350718     1    26    26
browser |    26  100.0%         11     +  63360114  63360139              AB350718     1    26    26
browser |    26  100.0%         11     +  64684540  64684565              AB350718     1    26    26
browser |    26  100.0%         11     +  74021322  74021347              AB350718     1    26    26
browser |    26  100.0%         11     -  74116019  74116044              AB350718     1    26    26
browser |    26  100.0%         11     +  74432517  74432542              AB350718     1    26    26
browser |    26  100.0%         11     +  74776784  74776809              AB350718     1    26    26
browser |    26  100.0%         11     -  79635106  79635131              AB350718     1    26    26
browser |    26  100.0%         11     +  81437928  81437953              AB350718     1    26    26
browser |    26  100.0%         11     -  82227613  82227638              AB350718     1    26    26
browser |    26  100.0%         11     -  85181936  85181961              AB350718     1    26    26
browser |    26  100.0%         11     +  86738000  86738025              AB350718     1    26    26
browser |    26  100.0%         11     -  90724091  90724116              AB350718     1    26    26
browser |    26  100.0%         11     +  90794077  90794102              AB350718     1    26    26
browser |    26  100.0%         11     -  90856540  90856565              AB350718     1    26    26
browser |    26  100.0%         11     +  91991447  91991472              AB350718     1    26    26
browser |    26  100.0%         11     +  98505651  98505676              AB350718     1    26    26
browser |    26  100.0%         11     + 100555307 100555332              AB350718     1    26    26
browser |    26  100.0%         11     - 105922725 105922750              AB350718     1    26    26
browser |    26  100.0%         11     - 106186867 106186892              AB350718     1    26    26
browser |    26  100.0%         11     - 108293601 108293626              AB350718     1    26    26
browser |    26  100.0%         11     + 108542345 108542370              AB350718     1    26    26
browser |    26  100.0%         11     + 111074893 111074918              AB350718     1    26    26
browser |    26  100.0%         11     - 111112012 111112037              AB350718     1    26    26
browser |    26  100.0%         11     + 113804583 113804608              AB350718     1    26    26
browser |    26  100.0%         11     - 115651266 115651291              AB350718     1    26    26
browser |    26  100.0%         11     + 116281834 116281859              AB350718     1    26    26
browser |    26  100.0%         11     + 116677950 116677975              AB350718     1    26    26
browser |    26  100.0%         11     + 117392245 117392270              AB350718     1    26    26
browser |    26  100.0%         11     + 120213544 120213569              AB350718     1    26    26
browser |    26  100.0%         11     + 120962296 120962321              AB350718     1    26    26
browser |    26  100.0%         12     +   3053931   3053956              AB350718     1    26    26
browser |    26  100.0%         12     -   3386349   3386374              AB350718     1    26    26
browser |    26  100.0%         12     +   6568099   6568124              AB350718     1    26    26
browser |    26  100.0%         12     +   8454884   8454909              AB350718     1    26    26
browser |    26  100.0%         12     -  11159197  11159222              AB350718     1    26    26
browser |    26  100.0%         12     +  14492430  14492455              AB350718     1    26    26
browser |    26  100.0%         12     -  14649697  14649722              AB350718     1    26    26
browser |    26  100.0%         12     +  17173778  17173803              AB350718     1    26    26
browser |    26  100.0%         12     +  18011367  18011392              AB350718     1    26    26
browser |    26  100.0%         12     +  18181805  18181830              AB350718     1    26    26
browser |    26  100.0%         12     -  18330629  18330654              AB350718     1    26    26
browser |    26  100.0%         12     -  19313780  19313805              AB350718     1    26    26
browser |    26  100.0%         12     +  19826068  19826093              AB350718     1    26    26
browser |    26  100.0%         12     +  24447034  24447059              AB350718     1    26    26
browser |    26  100.0%         12     -  31413688  31413713              AB350718     1    26    26
browser |    26  100.0%         12     +  32079558  32079583              AB350718     1    26    26
browser |    26  100.0%         12     +  40453648  40453673              AB350718     1    26    26
browser |    26  100.0%         12     +  41415065  41415090              AB350718     1    26    26
browser |    26  100.0%         12     -  44817467  44817492              AB350718     1    26    26
browser |    26  100.0%         12     +  48580520  48580545              AB350718     1    26    26
browser |    26  100.0%         12     +  49043130  49043155              AB350718     1    26    26
browser |    26  100.0%         12     -  52780528  52780553              AB350718     1    26    26
browser |    26  100.0%         12     +  54673392  54673417              AB350718     1    26    26
browser |    26  100.0%         12     -  65079484  65079509              AB350718     1    26    26
browser |    26  100.0%         12     -  65853542  65853567              AB350718     1    26    26
browser |    26  100.0%         12     -  66459342  66459367              AB350718     1    26    26
browser |    26  100.0%         12     -  70713475  70713500              AB350718     1    26    26
browser |    26  100.0%         12     -  70970324  70970349              AB350718     1    26    26
browser |    26  100.0%         12     -  79614154  79614179              AB350718     1    26    26
browser |    26  100.0%         12     +  80465627  80465652              AB350718     1    26    26
browser |    26  100.0%         12     -  82511505  82511530              AB350718     1    26    26
browser |    26  100.0%         12     -  85453336  85453361              AB350718     1    26    26
browser |    26  100.0%         12     +  93477889  93477914              AB350718     1    26    26
browser |    26  100.0%         12     -  94008823  94008848              AB350718     1    26    26
browser |    26  100.0%         12     -  94240345  94240370              AB350718     1    26    26
browser |    26  100.0%         12     -  96199746  96199771              AB350718     1    26    26
browser |    26  100.0%         12     +  98323050  98323075              AB350718     1    26    26
browser |    26  100.0%         12     - 105272022 105272047              AB350718     1    26    26
browser |    26  100.0%         12     - 108049202 108049227              AB350718     1    26    26
browser |    26  100.0%         12     + 109869911 109869936              AB350718     1    26    26
browser |    26  100.0%         12     + 111356168 111356193              AB350718     1    26    26
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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