AB351911
 

Information on mRNA AB351911

Description: Mus musculus non-coding RNA, oocyte_piRNA2727, 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: AB351911
Position: chr12:56794915-56794941

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     +  56794915  56794941              AB351911     1    27    27
browser |    27  100.0%          1     +   3101870   3101896              AB351911     1    27    27
browser |    27  100.0%          1     +   4202676   4202702              AB351911     1    27    27
browser |    27  100.0%          1     -   5625323   5625349              AB351911     1    27    27
browser |    27  100.0%          1     +   5874848   5874874              AB351911     1    27    27
browser |    27  100.0%          1     +   5881606   5881632              AB351911     1    27    27
browser |    27  100.0%          1     -   6475153   6475179              AB351911     1    27    27
browser |    27  100.0%          1     +   6500878   6500904              AB351911     1    27    27
browser |    27  100.0%          1     +   6507646   6507672              AB351911     1    27    27
browser |    27  100.0%          1     -   8063968   8063994              AB351911     1    27    27
browser |    27  100.0%          1     -   8070736   8070762              AB351911     1    27    27
browser |    27  100.0%          1     -   8226467   8226493              AB351911     1    27    27
browser |    27  100.0%          1     -   8233171   8233197              AB351911     1    27    27
browser |    27  100.0%          1     +  10054984  10055010              AB351911     1    27    27
browser |    27  100.0%          1     +  10800374  10800400              AB351911     1    27    27
browser |    27  100.0%          1     +  10807160  10807186              AB351911     1    27    27
browser |    27  100.0%          1     +  11957627  11957653              AB351911     1    27    27
browser |    27  100.0%          1     +  11961838  11961864              AB351911     1    27    27
browser |    27  100.0%          1     +  12017135  12017161              AB351911     1    27    27
browser |    27  100.0%          1     +  12021069  12021095              AB351911     1    27    27
browser |    27  100.0%          1     -  12723454  12723480              AB351911     1    27    27
browser |    27  100.0%          1     -  14068836  14068862              AB351911     1    27    27
browser |    27  100.0%          1     +  16276017  16276043              AB351911     1    27    27
browser |    27  100.0%          1     -  16808535  16808561              AB351911     1    27    27
browser |    27  100.0%          1     -  16815249  16815275              AB351911     1    27    27
browser |    27  100.0%          1     +  16832745  16832771              AB351911     1    27    27
browser |    27  100.0%          1     +  16918649  16918675              AB351911     1    27    27
browser |    27  100.0%          1     -  18587101  18587127              AB351911     1    27    27
browser |    27  100.0%          1     -  18591122  18591148              AB351911     1    27    27
browser |    27  100.0%          1     -  19692617  19692643              AB351911     1    27    27
browser |    27  100.0%          1     -  19699462  19699488              AB351911     1    27    27
browser |    27  100.0%          1     -  22317875  22317901              AB351911     1    27    27
browser |    27  100.0%          1     -  26453123  26453149              AB351911     1    27    27
browser |    27  100.0%          1     +  81542174  81542200              AB351911     1    27    27
browser |    27  100.0%          1     +  81548901  81548927              AB351911     1    27    27
browser |    27  100.0%          1     -  81960316  81960342              AB351911     1    27    27
browser |    27  100.0%          1     -  81962577  81962603              AB351911     1    27    27
browser |    27  100.0%          1     -  82478797  82478823              AB351911     1    27    27
browser |    27  100.0%          1     -  82483410  82483436              AB351911     1    27    27
browser |    27  100.0%          1     -  83207569  83207595              AB351911     1    27    27
browser |    27  100.0%          1     +  86245764  86245790              AB351911     1    27    27
browser |    27  100.0%          1     +  86248589  86248615              AB351911     1    27    27
browser |    27  100.0%          1     +  87760982  87761008              AB351911     1    27    27
browser |    27  100.0%          1     -  88905174  88905200              AB351911     1    27    27
browser |    27  100.0%          1     -  89126833  89126859              AB351911     1    27    27
browser |    27  100.0%          1     -  89130631  89130657              AB351911     1    27    27
browser |    27  100.0%          1     +  91399231  91399257              AB351911     1    27    27
browser |    27  100.0%          1     +  91405972  91405998              AB351911     1    27    27
browser |    27  100.0%          1     -  93884342  93884368              AB351911     1    27    27
browser |    27  100.0%          1     -  93888718  93888744              AB351911     1    27    27
browser |    27  100.0%          1     -  95756154  95756180              AB351911     1    27    27
browser |    27  100.0%          1     +  96557902  96557928              AB351911     1    27    27
browser |    27  100.0%          1     -  97100465  97100491              AB351911     1    27    27
browser |    27  100.0%          1     -  97108638  97108664              AB351911     1    27    27
browser |    27  100.0%          1     +  98178925  98178951              AB351911     1    27    27
browser |    27  100.0%          1     -  98715080  98715106              AB351911     1    27    27
browser |    27  100.0%          1     + 100459425 100459451              AB351911     1    27    27
browser |    27  100.0%          1     + 101454283 101454309              AB351911     1    27    27
browser |    27  100.0%          1     + 101906166 101906192              AB351911     1    27    27
browser |    27  100.0%          1     + 101912958 101912984              AB351911     1    27    27
browser |    27  100.0%          1     + 102837360 102837386              AB351911     1    27    27
browser |    27  100.0%          1     - 102959428 102959454              AB351911     1    27    27
browser |    27  100.0%          1     - 102966186 102966212              AB351911     1    27    27
browser |    27  100.0%          1     + 103133199 103133225              AB351911     1    27    27
browser |    27  100.0%          1     + 103139952 103139978              AB351911     1    27    27
browser |    27  100.0%          1     + 159797629 159797655              AB351911     1    27    27
browser |    27  100.0%          1     + 159804358 159804384              AB351911     1    27    27
browser |    27  100.0%          1     + 163296358 163296384              AB351911     1    27    27
browser |    27  100.0%          1     + 163300145 163300171              AB351911     1    27    27
browser |    27  100.0%          1     + 163520842 163520868              AB351911     1    27    27
browser |    27  100.0%          1     + 166767987 166768013              AB351911     1    27    27
browser |    27  100.0%          1     - 169370026 169370052              AB351911     1    27    27
browser |    27  100.0%          1     - 169376160 169376186              AB351911     1    27    27
browser |    27  100.0%          1     - 169943404 169943430              AB351911     1    27    27
browser |    27  100.0%          1     - 169950151 169950177              AB351911     1    27    27
browser |    25  100.0%          1     - 171657318 171657342              AB351911     1    25    27
browser |    25  100.0%          1     - 171659779 171659803              AB351911     1    25    27
browser |    27  100.0%          1     + 174869841 174869867              AB351911     1    27    27
browser |    27  100.0%          1     + 174875789 174875815              AB351911     1    27    27
browser |    27  100.0%          1     + 176370923 176370949              AB351911     1    27    27
browser |    27  100.0%          1     + 176377665 176377691              AB351911     1    27    27
browser |    27  100.0%          1     - 178001717 178001743              AB351911     1    27    27
browser |    27  100.0%          1     - 178008468 178008494              AB351911     1    27    27
browser |    27  100.0%          1     + 178242337 178242363              AB351911     1    27    27
browser |    27  100.0%          1     + 181091379 181091405              AB351911     1    27    27
browser |    27  100.0%          1     + 181098108 181098134              AB351911     1    27    27
browser |    27  100.0%          1     - 181320512 181320538              AB351911     1    27    27
browser |    27  100.0%          1     - 181326748 181326774              AB351911     1    27    27
browser |    27  100.0%          1     - 185035733 185035759              AB351911     1    27    27
browser |    27  100.0%          1     - 185038263 185038289              AB351911     1    27    27
browser |    27  100.0%          1     - 194336169 194336195              AB351911     1    27    27
browser |    27  100.0%         10     +   3551218   3551244              AB351911     1    27    27
browser |    27  100.0%         10     +   3557963   3557989              AB351911     1    27    27
browser |    27  100.0%         10     +   4412503   4412529              AB351911     1    27    27
browser |    27  100.0%         10     +  15352709  15352735              AB351911     1    27    27
browser |    27  100.0%         10     -  15813288  15813314              AB351911     1    27    27
browser |    27  100.0%         10     -  17900433  17900459              AB351911     1    27    27
browser |    27  100.0%         10     +  19414933  19414959              AB351911     1    27    27
browser |    27  100.0%         10     +  19421692  19421718              AB351911     1    27    27
browser |    27  100.0%         10     +  19886669  19886695              AB351911     1    27    27
browser |    27  100.0%         10     +  19893470  19893496              AB351911     1    27    27
browser |    27  100.0%         10     -  21087142  21087168              AB351911     1    27    27
browser |    27  100.0%         10     -  21092142  21092168              AB351911     1    27    27
browser |    27  100.0%         10     +  21518506  21518532              AB351911     1    27    27
browser |    27  100.0%         10     +  21525357  21525383              AB351911     1    27    27
browser |    27  100.0%         10     +  22399416  22399442              AB351911     1    27    27
browser |    27  100.0%         10     +  22406324  22406350              AB351911     1    27    27
browser |    27  100.0%         10     +  22559452  22559478              AB351911     1    27    27
browser |    27  100.0%         10     +  22566380  22566406              AB351911     1    27    27
browser |    27  100.0%         10     +  23744272  23744298              AB351911     1    27    27
browser |    27  100.0%         10     -  24296681  24296707              AB351911     1    27    27
browser |    27  100.0%         10     +  24977737  24977763              AB351911     1    27    27
browser |    27  100.0%         10     -  25844356  25844382              AB351911     1    27    27
browser |    27  100.0%         10     -  25848884  25848910              AB351911     1    27    27
browser |    27  100.0%         10     -  29893365  29893391              AB351911     1    27    27
browser |    27  100.0%         10     -  30023838  30023864              AB351911     1    27    27
browser |    27  100.0%         10     -  30357277  30357303              AB351911     1    27    27
browser |    27  100.0%         10     -  30690027  30690053              AB351911     1    27    27
browser |    27  100.0%         10     -  30696779  30696805              AB351911     1    27    27
browser |    27  100.0%         10     -  31156050  31156076              AB351911     1    27    27
browser |    27  100.0%         10     -  31358664  31358690              AB351911     1    27    27
browser |    27  100.0%         10     -  31365411  31365437              AB351911     1    27    27
browser |    27  100.0%         10     -  31626155  31626181              AB351911     1    27    27
browser |    27  100.0%         10     -  80811909  80811935              AB351911     1    27    27
browser |    27  100.0%         10     -  80816372  80816398              AB351911     1    27    27
browser |    27  100.0%         10     +  81506676  81506702              AB351911     1    27    27
browser |    27  100.0%         10     +  81513540  81513566              AB351911     1    27    27
browser |    27  100.0%         10     +  81665804  81665830              AB351911     1    27    27
browser |    27  100.0%         10     +  81672668  81672694              AB351911     1    27    27
browser |    27  100.0%         10     -  81803763  81803789              AB351911     1    27    27
browser |    27  100.0%         10     -  81810521  81810547              AB351911     1    27    27
browser |    27  100.0%         10     -  82774966  82774992              AB351911     1    27    27
browser |    27  100.0%         10     -  82777437  82777463              AB351911     1    27    27
browser |    27  100.0%         10     +  83308828  83308854              AB351911     1    27    27
browser |    27  100.0%         10     +  83507073  83507099              AB351911     1    27    27
browser |    27  100.0%         10     +  83513798  83513824              AB351911     1    27    27
browser |    27  100.0%         10     -  85551101  85551127              AB351911     1    27    27
browser |    27  100.0%         10     -  85556240  85556266              AB351911     1    27    27
browser |    27  100.0%         10     +  91650614  91650640              AB351911     1    27    27
browser |    27  100.0%         10     +  91652910  91652936              AB351911     1    27    27
browser |    27  100.0%         10     +  92586675  92586701              AB351911     1    27    27
browser |    27  100.0%         10     +  92589950  92589976              AB351911     1    27    27
browser |    27  100.0%         10     +  94198724  94198750              AB351911     1    27    27
browser |    27  100.0%         10     +  94205049  94205075              AB351911     1    27    27
browser |    27  100.0%         10     +  96028686  96028712              AB351911     1    27    27
browser |    27  100.0%         10     +  96035501  96035527              AB351911     1    27    27
browser |    27  100.0%         10     -  97377695  97377721              AB351911     1    27    27
browser |    27  100.0%         10     - 104391173 104391199              AB351911     1    27    27
browser |    27  100.0%         10     - 104398003 104398029              AB351911     1    27    27
browser |    27  100.0%         10     + 104411251 104411277              AB351911     1    27    27
browser |    27  100.0%         10     - 104671495 104671521              AB351911     1    27    27
browser |    27  100.0%         10     - 104678230 104678256              AB351911     1    27    27
browser |    27  100.0%         10     - 105013019 105013045              AB351911     1    27    27
browser |    27  100.0%         10     - 105017355 105017381              AB351911     1    27    27
browser |    27  100.0%         10     - 107835398 107835424              AB351911     1    27    27
browser |    27  100.0%         11     -   3998987   3999013              AB351911     1    27    27
browser |    27  100.0%         11     -   5312651   5312677              AB351911     1    27    27
browser |    27  100.0%         11     +   7984143   7984169              AB351911     1    27    27
browser |    27  100.0%         11     +   7987586   7987612              AB351911     1    27    27
browser |    27  100.0%         11     +   9658274   9658300              AB351911     1    27    27
browser |    27  100.0%         11     +   9665005   9665031              AB351911     1    27    27
browser |    27  100.0%         11     -  10710351  10710377              AB351911     1    27    27
browser |    27  100.0%         11     -  10717118  10717144              AB351911     1    27    27
browser |    27  100.0%         11     -  12511946  12511972              AB351911     1    27    27
browser |    27  100.0%         11     -  12518729  12518755              AB351911     1    27    27
browser |    27  100.0%         11     -  12745574  12745600              AB351911     1    27    27
browser |    27  100.0%         11     -  12752403  12752429              AB351911     1    27    27
browser |    27  100.0%         11     +  12904309  12904335              AB351911     1    27    27
browser |    27  100.0%         11     +  12909146  12909172              AB351911     1    27    27
browser |    27  100.0%         11     -  13825399  13825425              AB351911     1    27    27
browser |    27  100.0%         11     -  13906067  13906093              AB351911     1    27    27
browser |    27  100.0%         11     -  15177726  15177752              AB351911     1    27    27
browser |    27  100.0%         11     -  15184504  15184530              AB351911     1    27    27
browser |    27  100.0%         11     -  15809853  15809879              AB351911     1    27    27
browser |    27  100.0%         11     -  15812383  15812409              AB351911     1    27    27
browser |    27  100.0%         11     -  15833715  15833741              AB351911     1    27    27
browser |    27  100.0%         11     -  15837502  15837528              AB351911     1    27    27
browser |    27  100.0%         11     +  17102906  17102932              AB351911     1    27    27
browser |    27  100.0%         11     +  19516470  19516496              AB351911     1    27    27
browser |    27  100.0%         11     +  19520516  19520542              AB351911     1    27    27
browser |    27  100.0%         11     +  20459495  20459521              AB351911     1    27    27
browser |    27  100.0%         11     +  20461819  20461845              AB351911     1    27    27
browser |    27  100.0%         11     +  23168871  23168897              AB351911     1    27    27
browser |    27  100.0%         11     +  23175611  23175637              AB351911     1    27    27
browser |    27  100.0%         11     +  25562991  25563017              AB351911     1    27    27
browser |    27  100.0%         11     +  27365395  27365421              AB351911     1    27    27
browser |    27  100.0%         11     +  27367661  27367687              AB351911     1    27    27
browser |    27  100.0%         11     -  81436344  81436370              AB351911     1    27    27
browser |    27  100.0%         11     -  81443173  81443199              AB351911     1    27    27
browser |    27  100.0%         11     +  82225118  82225144              AB351911     1    27    27
browser |    27  100.0%         11     +  82229092  82229118              AB351911     1    27    27
browser |    27  100.0%         11     +  85176685  85176711              AB351911     1    27    27
browser |    27  100.0%         11     +  85183443  85183469              AB351911     1    27    27
browser |    27  100.0%         11     +  85184928  85184954              AB351911     1    27    27
browser |    27  100.0%         11     -  86736506  86736532              AB351911     1    27    27
browser |    27  100.0%         11     -  86740684  86740710              AB351911     1    27    27
browser |    27  100.0%         11     +  88982701  88982727              AB351911     1    27    27
browser |    27  100.0%         11     +  90201501  90201527              AB351911     1    27    27
browser |    27  100.0%         11     +  90203214  90203240              AB351911     1    27    27
browser |    27  100.0%         11     +  90720741  90720767              AB351911     1    27    27
browser |    27  100.0%         11     +  90725697  90725723              AB351911     1    27    27
browser |    27  100.0%         11     -  90792591  90792617              AB351911     1    27    27
browser |    27  100.0%         11     -  90798770  90798796              AB351911     1    27    27
browser |    27  100.0%         11     +  90851289  90851315              AB351911     1    27    27
browser |    27  100.0%         11     +  90858036  90858062              AB351911     1    27    27
browser |    27  100.0%         11     -  98504141  98504167              AB351911     1    27    27
browser |    27  100.0%         11     -  98510902  98510928              AB351911     1    27    27
browser |    27  100.0%         11     - 100553758 100553784              AB351911     1    27    27
browser |    27  100.0%         11     - 100560049 100560075              AB351911     1    27    27
browser |    27  100.0%         11     - 108365891 108365917              AB351911     1    27    27
browser |    27  100.0%         11     + 108717171 108717197              AB351911     1    27    27
browser |    27  100.0%         11     - 111073374 111073400              AB351911     1    27    27
browser |    27  100.0%         11     + 111106759 111106785              AB351911     1    27    27
browser |    27  100.0%         11     + 111113553 111113579              AB351911     1    27    27
browser |    27  100.0%         11     - 120211939 120211965              AB351911     1    27    27
browser |    27  100.0%         11     - 120218789 120218815              AB351911     1    27    27
browser |    27  100.0%         11     - 120960776 120960802              AB351911     1    27    27
browser |    27  100.0%         11     - 120965357 120965383              AB351911     1    27    27
browser |    27  100.0%         11     + 121615651 121615677              AB351911     1    27    27
browser |    27  100.0%         12     -   3052376   3052402              AB351911     1    27    27
browser |    27  100.0%         12     -   3059179   3059205              AB351911     1    27    27
browser |    27  100.0%         12     +   3381096   3381122              AB351911     1    27    27
browser |    27  100.0%         12     +   3387874   3387900              AB351911     1    27    27
browser |    27  100.0%         12     -   6853060   6853086              AB351911     1    27    27
browser |    27  100.0%         12     -   6859827   6859853              AB351911     1    27    27
browser |    27  100.0%         12     -   7344609   7344635              AB351911     1    27    27
browser |    27  100.0%         12     -   7937161   7937187              AB351911     1    27    27
browser |    27  100.0%         12     -   8453213   8453239              AB351911     1    27    27
browser |    27  100.0%         12     -   8458114   8458140              AB351911     1    27    27
browser |    27  100.0%         12     +  11153949  11153975              AB351911     1    27    27
browser |    27  100.0%         12     +  11160676  11160702              AB351911     1    27    27
browser |    27  100.0%         12     +  14644463  14644489              AB351911     1    27    27
browser |    27  100.0%         12     +  14651388  14651414              AB351911     1    27    27
browser |    27  100.0%         12     +  16880665  16880691              AB351911     1    27    27
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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