AB349756
 

Information on mRNA AB349756

Description: Mus musculus non-coding RNA, oocyte_piRNA572, 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: AB349756
Position: chr12:57166751-57166773

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 |    23  100.0%         12     -  57166751  57166773              AB349756     2    24    24
browser |    23  100.0%          1     -   4961245   4961267              AB349756     2    24    24
browser |    24  100.0%          1     -   6187071   6187094              AB349756     1    24    24
browser |    24  100.0%          1     +   6214677   6214700              AB349756     1    24    24
browser |    23  100.0%          1     -   8967263   8967285              AB349756     2    24    24
browser |    24  100.0%          1     +   9611088   9611111              AB349756     1    24    24
browser |    23  100.0%          1     -  10823373  10823395              AB349756     2    24    24
browser |    24  100.0%          1     -  11608421  11608444              AB349756     1    24    24
browser |    24  100.0%          1     +  13180661  13180684              AB349756     1    24    24
browser |    22  100.0%          1     +  14393253  14393274              AB349756     2    23    24
browser |    24  100.0%          1     -  15145803  15145826              AB349756     1    24    24
browser |    23  100.0%          1     +  22549928  22549950              AB349756     2    24    24
browser |    24  100.0%          1     -  25948493  25948516              AB349756     1    24    24
browser |    23  100.0%          1     -  29440716  29440738              AB349756     2    24    24
browser |    24  100.0%          1     -  30045496  30045519              AB349756     1    24    24
browser |    23  100.0%          1     +  30368129  30368151              AB349756     2    24    24
browser |    23  100.0%          1     -  34833427  34833449              AB349756     2    24    24
browser |    23  100.0%          1     +  36633327  36633349              AB349756     2    24    24
browser |    23  100.0%          1     +  42764484  42764506              AB349756     2    24    24
browser |    24  100.0%          1     +  42823631  42823654              AB349756     1    24    24
browser |    24  100.0%          1     +  45741471  45741494              AB349756     1    24    24
browser |    24  100.0%          1     -  47293921  47293944              AB349756     1    24    24
browser |    24  100.0%          1     +  52552484  52552507              AB349756     1    24    24
browser |    23  100.0%          1     -  52706133  52706155              AB349756     2    24    24
browser |    24  100.0%          1     +  56212167  56212190              AB349756     1    24    24
browser |    24  100.0%          1     -  63781878  63781901              AB349756     1    24    24
browser |    23  100.0%          1     +  65013079  65013101              AB349756     2    24    24
browser |    23  100.0%          1     -  69778905  69778927              AB349756     2    24    24
browser |    24  100.0%          1     -  71754243  71754266              AB349756     1    24    24
browser |    24  100.0%          1     +  72065806  72065829              AB349756     1    24    24
browser |    24  100.0%          1     +  74425353  74425376              AB349756     1    24    24
browser |    24  100.0%          1     +  74805269  74805292              AB349756     1    24    24
browser |    23  100.0%          1     +  83836019  83836041              AB349756     2    24    24
browser |    24  100.0%          1     -  84062781  84062804              AB349756     1    24    24
browser |    24  100.0%          1     -  84839837  84839860              AB349756     1    24    24
browser |    24  100.0%          1     +  85239401  85239424              AB349756     1    24    24
browser |    24  100.0%          1     -  85536611  85536634              AB349756     1    24    24
browser |    23  100.0%          1     -  86123233  86123255              AB349756     2    24    24
browser |    24  100.0%          1     -  86413663  86413686              AB349756     1    24    24
browser |    23  100.0%          1     -  87248592  87248614              AB349756     2    24    24
browser |    24  100.0%          1     -  89458347  89458370              AB349756     1    24    24
browser |    24  100.0%          1     - 105478785 105478808              AB349756     1    24    24
browser |    23  100.0%          1     + 106192328 106192350              AB349756     2    24    24
browser |    23  100.0%          1     - 109172616 109172638              AB349756     2    24    24
browser |    23  100.0%          1     - 111378111 111378133              AB349756     2    24    24
browser |    24  100.0%          1     - 113124726 113124749              AB349756     1    24    24
browser |    23  100.0%          1     - 119467635 119467657              AB349756     2    24    24
browser |    23  100.0%          1     + 128195968 128195990              AB349756     2    24    24
browser |    22  100.0%          1     + 131377820 131377841              AB349756     2    23    24
browser |    24  100.0%          1     - 133270585 133270608              AB349756     1    24    24
browser |    24  100.0%          1     + 136562428 136562451              AB349756     1    24    24
browser |    24  100.0%          1     - 136579416 136579439              AB349756     1    24    24
browser |    23  100.0%          1     + 138855239 138855261              AB349756     2    24    24
browser |    24  100.0%          1     - 142789221 142789244              AB349756     1    24    24
browser |    24  100.0%          1     + 142882743 142882766              AB349756     1    24    24
browser |    23  100.0%          1     + 143082660 143082682              AB349756     2    24    24
browser |    24  100.0%          1     + 147380213 147380236              AB349756     1    24    24
browser |    22  100.0%          1     + 150996995 150997016              AB349756     2    23    24
browser |    23  100.0%          1     + 151301634 151301656              AB349756     2    24    24
browser |    24  100.0%          1     - 152133008 152133031              AB349756     1    24    24
browser |    24  100.0%          1     + 160529328 160529351              AB349756     1    24    24
browser |    23  100.0%          1     + 160826417 160826439              AB349756     2    24    24
browser |    22  100.0%          1     - 164194866 164194887              AB349756     2    23    24
browser |    23  100.0%          1     - 166230031 166230053              AB349756     2    24    24
browser |    23  100.0%          1     + 167151935 167151957              AB349756     2    24    24
browser |    23  100.0%          1     - 168204880 168204902              AB349756     2    24    24
browser |    23  100.0%          1     + 170392550 170392572              AB349756     2    24    24
browser |    24  100.0%          1     - 175475841 175475864              AB349756     1    24    24
browser |    24  100.0%          1     + 176871967 176871990              AB349756     1    24    24
browser |    23  100.0%          1     - 177495757 177495779              AB349756     2    24    24
browser |    23  100.0%          1     - 178167401 178167423              AB349756     1    23    24
browser |    23  100.0%          1     - 180485303 180485325              AB349756     2    24    24
browser |    23  100.0%          1     - 181752020 181752042              AB349756     2    24    24
browser |    23  100.0%          1     - 184197916 184197938              AB349756     2    24    24
browser |    23  100.0%          1     + 190593374 190593396              AB349756     2    24    24
browser |    23  100.0%          1     - 190842048 190842070              AB349756     2    24    24
browser |    24  100.0%          1     + 194470374 194470397              AB349756     1    24    24
browser |    24  100.0%         10     -   5039490   5039513              AB349756     1    24    24
browser |    24  100.0%         10     +   5815262   5815285              AB349756     1    24    24
browser |    23  100.0%         10     -   7138428   7138450              AB349756     2    24    24
browser |    23  100.0%         10     -  11161830  11161852              AB349756     2    24    24
browser |    24  100.0%         10     +  13858388  13858411              AB349756     1    24    24
browser |    24  100.0%         10     -  14614793  14614816              AB349756     1    24    24
browser |    23  100.0%         10     +  14850313  14850335              AB349756     2    24    24
browser |    24  100.0%         10     +  14910829  14910852              AB349756     1    24    24
browser |    23  100.0%         10     +  18160243  18160265              AB349756     2    24    24
browser |    24  100.0%         10     +  20435091  20435114              AB349756     1    24    24
browser |    24  100.0%         10     -  21216243  21216266              AB349756     1    24    24
browser |    24  100.0%         10     +  23648502  23648525              AB349756     1    24    24
browser |    23  100.0%         10     +  24530513  24530535              AB349756     2    24    24
browser |    24  100.0%         10     -  28557683  28557706              AB349756     1    24    24
browser |    23  100.0%         10     +  29137657  29137679              AB349756     2    24    24
browser |    23  100.0%         10     +  29614754  29614776              AB349756     2    24    24
browser |    24  100.0%         10     +  29963086  29963109              AB349756     1    24    24
browser |    24  100.0%         10     -  33137256  33137279              AB349756     1    24    24
browser |    24  100.0%         10     -  37689770  37689793              AB349756     1    24    24
browser |    24  100.0%         10     -  38876670  38876693              AB349756     1    24    24
browser |    24  100.0%         10     -  39172213  39172236              AB349756     1    24    24
browser |    24  100.0%         10     +  44459649  44459672              AB349756     1    24    24
browser |    24  100.0%         10     +  60980621  60980644              AB349756     1    24    24
browser |    24  100.0%         10     +  62260154  62260177              AB349756     1    24    24
browser |    24  100.0%         10     -  62398130  62398153              AB349756     1    24    24
browser |    24  100.0%         10     -  62609011  62609034              AB349756     1    24    24
browser |    24  100.0%         10     -  63223227  63223250              AB349756     1    24    24
browser |    24  100.0%         10     +  74066683  74066706              AB349756     1    24    24
browser |    24  100.0%         10     -  75455855  75455878              AB349756     1    24    24
browser |    24  100.0%         10     +  77010762  77010785              AB349756     1    24    24
browser |    24  100.0%         10     -  77896791  77896814              AB349756     1    24    24
browser |    24  100.0%         10     -  79947988  79948011              AB349756     1    24    24
browser |    23  100.0%         10     -  80285900  80285922              AB349756     2    24    24
browser |    24  100.0%         10     +  83847972  83847995              AB349756     1    24    24
browser |    24  100.0%         10     +  84330051  84330074              AB349756     1    24    24
browser |    23  100.0%         10     +  84686572  84686594              AB349756     2    24    24
browser |    23  100.0%         10     +  87251487  87251509              AB349756     1    23    24
browser |    24  100.0%         10     -  87307508  87307531              AB349756     1    24    24
browser |    23  100.0%         10     +  88005053  88005075              AB349756     2    24    24
browser |    23  100.0%         10     -  88846911  88846933              AB349756     2    24    24
browser |    23  100.0%         10     +  90822279  90822301              AB349756     2    24    24
browser |    24  100.0%         10     +  90972521  90972544              AB349756     1    24    24
browser |    23  100.0%         10     +  93599864  93599886              AB349756     2    24    24
browser |    23  100.0%         10     +  94242512  94242534              AB349756     2    24    24
browser |    23  100.0%         10     - 100970720 100970742              AB349756     2    24    24
browser |    24  100.0%         10     - 106583403 106583426              AB349756     1    24    24
browser |    24  100.0%         10     - 107788112 107788135              AB349756     1    24    24
browser |    24  100.0%         10     + 108134596 108134619              AB349756     1    24    24
browser |    23  100.0%         10     - 111806412 111806434              AB349756     2    24    24
browser |    23  100.0%         10     - 112595027 112595049              AB349756     2    24    24
browser |    23  100.0%         10     - 113438895 113438917              AB349756     2    24    24
browser |    24  100.0%         10     + 113740982 113741005              AB349756     1    24    24
browser |    23  100.0%         10     + 115387792 115387814              AB349756     2    24    24
browser |    24  100.0%         10     - 115773617 115773640              AB349756     1    24    24
browser |    23  100.0%         10     - 116845576 116845598              AB349756     2    24    24
browser |    23  100.0%         10     - 117971598 117971620              AB349756     2    24    24
browser |    23  100.0%         10     + 118940255 118940277              AB349756     2    24    24
browser |    23  100.0%         10     - 119286438 119286460              AB349756     2    24    24
browser |    23  100.0%         10     - 120393215 120393237              AB349756     2    24    24
browser |    23  100.0%         10     + 121571328 121571350              AB349756     2    24    24
browser |    24  100.0%         10     - 122832653 122832676              AB349756     1    24    24
browser |    24  100.0%         10     + 126316781 126316804              AB349756     1    24    24
browser |    23  100.0%         10     + 126883503 126883525              AB349756     2    24    24
browser |    24  100.0%         10     - 127835408 127835431              AB349756     1    24    24
browser |    24  100.0%         11     +   3178052   3178075              AB349756     1    24    24
browser |    23  100.0%         11     -   3271846   3271868              AB349756     1    23    24
browser |    23  100.0%         11     +   4780960   4780982              AB349756     2    24    24
browser |    23  100.0%         11     +   6409912   6409934              AB349756     2    24    24
browser |    24  100.0%         11     -  19062680  19062703              AB349756     1    24    24
browser |    23  100.0%         11     +  19200820  19200842              AB349756     2    24    24
browser |    24  100.0%         11     +  22857414  22857437              AB349756     1    24    24
browser |    23  100.0%         11     +  23020058  23020080              AB349756     2    24    24
browser |    24  100.0%         11     +  24085036  24085059              AB349756     1    24    24
browser |    23  100.0%         11     -  25913416  25913438              AB349756     2    24    24
browser |    24  100.0%         11     +  26192568  26192591              AB349756     1    24    24
browser |    24  100.0%         11     +  28521482  28521505              AB349756     1    24    24
browser |    24  100.0%         11     -  29353461  29353484              AB349756     1    24    24
browser |    24  100.0%         11     +  29706301  29706324              AB349756     1    24    24
browser |    23  100.0%         11     -  32154872  32154894              AB349756     2    24    24
browser |    24  100.0%         11     +  39581158  39581181              AB349756     1    24    24
browser |    23  100.0%         11     -  43892638  43892660              AB349756     2    24    24
browser |    23  100.0%         11     -  46080845  46080867              AB349756     2    24    24
browser |    23  100.0%         11     -  54537176  54537198              AB349756     2    24    24
browser |    23  100.0%         11     -  54848608  54848630              AB349756     2    24    24
browser |    24  100.0%         11     +  56233354  56233377              AB349756     1    24    24
browser |    23  100.0%         11     -  59405385  59405407              AB349756     2    24    24
browser |    24  100.0%         11     -  60230105  60230128              AB349756     1    24    24
browser |    24  100.0%         11     -  61438055  61438078              AB349756     1    24    24
browser |    24  100.0%         11     +  62278918  62278941              AB349756     1    24    24
browser |    24  100.0%         11     +  62472437  62472460              AB349756     1    24    24
browser |    24  100.0%         11     -  66838483  66838506              AB349756     1    24    24
browser |    24  100.0%         11     +  67994113  67994136              AB349756     1    24    24
browser |    24  100.0%         11     -  73769035  73769058              AB349756     1    24    24
browser |    24  100.0%         11     -  76001571  76001594              AB349756     1    24    24
browser |    24  100.0%         11     +  76964352  76964375              AB349756     1    24    24
browser |    24  100.0%         11     -  80051406  80051429              AB349756     1    24    24
browser |    23  100.0%         11     +  83652029  83652051              AB349756     2    24    24
browser |    24  100.0%         11     -  85259631  85259654              AB349756     1    24    24
browser |    23  100.0%         11     -  85594258  85594280              AB349756     2    24    24
browser |    23  100.0%         11     +  86146067  86146089              AB349756     2    24    24
browser |    23  100.0%         11     -  86544740  86544762              AB349756     2    24    24
browser |    23  100.0%         11     +  87430557  87430579              AB349756     2    24    24
browser |    22  100.0%         11     -  88012018  88012039              AB349756     3    24    24
browser |    23  100.0%         11     -  88794682  88794704              AB349756     2    24    24
browser |    24  100.0%         11     +  88797992  88798015              AB349756     1    24    24
browser |    23  100.0%         11     +  94619874  94619896              AB349756     2    24    24
browser |    23  100.0%         11     -  95613740  95613762              AB349756     2    24    24
browser |    24  100.0%         11     +  95651277  95651300              AB349756     1    24    24
browser |    24  100.0%         11     +  96948492  96948515              AB349756     1    24    24
browser |    24  100.0%         11     +  97954212  97954235              AB349756     1    24    24
browser |    23  100.0%         11     +  98201993  98202015              AB349756     2    24    24
browser |    24  100.0%         11     +  98333372  98333395              AB349756     1    24    24
browser |    23  100.0%         11     + 100487239 100487261              AB349756     2    24    24
browser |    23  100.0%         11     - 100820176 100820198              AB349756     2    24    24
browser |    23  100.0%         11     + 101441233 101441255              AB349756     2    24    24
browser |    23  100.0%         11     - 102082570 102082592              AB349756     2    24    24
browser |    23  100.0%         11     - 102152115 102152137              AB349756     2    24    24
browser |    24  100.0%         11     + 103165208 103165231              AB349756     1    24    24
browser |    23  100.0%         11     - 103648563 103648585              AB349756     2    24    24
browser |    23  100.0%         11     - 104262080 104262102              AB349756     2    24    24
browser |    23  100.0%         11     + 105577469 105577491              AB349756     2    24    24
browser |    23  100.0%         11     - 105973576 105973598              AB349756     2    24    24
browser |    23  100.0%         11     + 106544118 106544140              AB349756     2    24    24
browser |    24  100.0%         11     - 108038245 108038268              AB349756     1    24    24
browser |    23  100.0%         11     - 115170112 115170134              AB349756     2    24    24
browser |    23  100.0%         11     - 117872966 117872988              AB349756     2    24    24
browser |    24  100.0%         11     + 121178104 121178127              AB349756     1    24    24
browser |    23  100.0%         12     -   3818097   3818119              AB349756     2    24    24
browser |    24  100.0%         12     +   4284696   4284719              AB349756     1    24    24
browser |    23  100.0%         12     -   4542757   4542779              AB349756     2    24    24
browser |    23  100.0%         12     +   4869423   4869445              AB349756     2    24    24
browser |    24  100.0%         12     +  19283923  19283946              AB349756     1    24    24
browser |    24  100.0%         12     +  19497536  19497559              AB349756     1    24    24
browser |    24  100.0%         12     +  20071277  20071300              AB349756     1    24    24
browser |    24  100.0%         12     +  21348758  21348781              AB349756     1    24    24
browser |    23  100.0%         12     +  21404964  21404986              AB349756     2    24    24
browser |    24  100.0%         12     -  21764502  21764525              AB349756     1    24    24
browser |    24  100.0%         12     -  21991688  21991711              AB349756     1    24    24
browser |    23  100.0%         12     +  29341705  29341727              AB349756     2    24    24
browser |    23  100.0%         12     -  31812100  31812122              AB349756     2    24    24
browser |    24  100.0%         12     -  41446558  41446581              AB349756     1    24    24
browser |    23  100.0%         12     +  43396927  43396949              AB349756     2    24    24
browser |    23  100.0%         12     +  47132749  47132771              AB349756     2    24    24
browser |    23  100.0%         12     +  50051001  50051023              AB349756     1    23    24
browser |    24  100.0%         12     +  51907251  51907274              AB349756     1    24    24
browser |    24  100.0%         12     +  54679597  54679620              AB349756     1    24    24
browser |    24  100.0%         12     +  55165361  55165384              AB349756     1    24    24
browser |    24  100.0%         12     +  55314678  55314701              AB349756     1    24    24
browser |    22  100.0%         12     -  55497721  55497742              AB349756     2    23    24
browser |    24  100.0%         12     -  65124858  65124881              AB349756     1    24    24
browser |    23  100.0%         12     -  66953261  66953283              AB349756     1    23    24
browser |    23  100.0%         12     -  71060618  71060640              AB349756     2    24    24
browser |    24  100.0%         12     +  72617136  72617159              AB349756     1    24    24
browser |    23  100.0%         12     -  73038516  73038538              AB349756     2    24    24
browser |    23  100.0%         12     -  75715386  75715408              AB349756     2    24    24
browser |    23  100.0%         12     -  79348531  79348553              AB349756     2    24    24
browser |    24  100.0%         12     -  80933672  80933695              AB349756     1    24    24
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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