AB350991
 

Information on mRNA AB350991

Description: Mus musculus non-coding RNA, oocyte_piRNA1807, 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: AB350991
Position: chr12:56794914-56794940

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     +  56794914  56794940              AB350991     1    27    27
browser |    27  100.0%          1     +   3101869   3101895              AB350991     1    27    27
browser |    27  100.0%          1     +   4202675   4202701              AB350991     1    27    27
browser |    27  100.0%          1     -   5625324   5625350              AB350991     1    27    27
browser |    27  100.0%          1     +   5874847   5874873              AB350991     1    27    27
browser |    27  100.0%          1     +   5881605   5881631              AB350991     1    27    27
browser |    27  100.0%          1     -   6475154   6475180              AB350991     1    27    27
browser |    27  100.0%          1     +   6500877   6500903              AB350991     1    27    27
browser |    27  100.0%          1     +   6507645   6507671              AB350991     1    27    27
browser |    27  100.0%          1     -   8063969   8063995              AB350991     1    27    27
browser |    27  100.0%          1     -   8070737   8070763              AB350991     1    27    27
browser |    27  100.0%          1     -   8226468   8226494              AB350991     1    27    27
browser |    27  100.0%          1     -   8233172   8233198              AB350991     1    27    27
browser |    27  100.0%          1     +  10054983  10055009              AB350991     1    27    27
browser |    27  100.0%          1     +  10800373  10800399              AB350991     1    27    27
browser |    27  100.0%          1     +  10807159  10807185              AB350991     1    27    27
browser |    27  100.0%          1     +  11957626  11957652              AB350991     1    27    27
browser |    27  100.0%          1     +  11961837  11961863              AB350991     1    27    27
browser |    27  100.0%          1     +  12017134  12017160              AB350991     1    27    27
browser |    27  100.0%          1     +  12021068  12021094              AB350991     1    27    27
browser |    27  100.0%          1     -  12723455  12723481              AB350991     1    27    27
browser |    27  100.0%          1     -  14068837  14068863              AB350991     1    27    27
browser |    27  100.0%          1     +  16276016  16276042              AB350991     1    27    27
browser |    27  100.0%          1     -  16808536  16808562              AB350991     1    27    27
browser |    27  100.0%          1     -  16815250  16815276              AB350991     1    27    27
browser |    27  100.0%          1     +  16832744  16832770              AB350991     1    27    27
browser |    27  100.0%          1     +  16918648  16918674              AB350991     1    27    27
browser |    27  100.0%          1     -  18587102  18587128              AB350991     1    27    27
browser |    27  100.0%          1     -  18591123  18591149              AB350991     1    27    27
browser |    27  100.0%          1     -  19692618  19692644              AB350991     1    27    27
browser |    27  100.0%          1     -  19699463  19699489              AB350991     1    27    27
browser |    27  100.0%          1     -  22317876  22317902              AB350991     1    27    27
browser |    27  100.0%          1     -  26453124  26453150              AB350991     1    27    27
browser |    27  100.0%          1     +  81542173  81542199              AB350991     1    27    27
browser |    27  100.0%          1     +  81548900  81548926              AB350991     1    27    27
browser |    27  100.0%          1     -  81960317  81960343              AB350991     1    27    27
browser |    27  100.0%          1     -  81962578  81962604              AB350991     1    27    27
browser |    27  100.0%          1     -  82478798  82478824              AB350991     1    27    27
browser |    27  100.0%          1     -  82483411  82483437              AB350991     1    27    27
browser |    27  100.0%          1     -  83207570  83207596              AB350991     1    27    27
browser |    27  100.0%          1     +  86245763  86245789              AB350991     1    27    27
browser |    27  100.0%          1     +  86248588  86248614              AB350991     1    27    27
browser |    27  100.0%          1     +  87760981  87761007              AB350991     1    27    27
browser |    27  100.0%          1     -  88905175  88905201              AB350991     1    27    27
browser |    27  100.0%          1     -  89126834  89126860              AB350991     1    27    27
browser |    27  100.0%          1     -  89130632  89130658              AB350991     1    27    27
browser |    27  100.0%          1     +  91399230  91399256              AB350991     1    27    27
browser |    27  100.0%          1     +  91405971  91405997              AB350991     1    27    27
browser |    27  100.0%          1     -  93884343  93884369              AB350991     1    27    27
browser |    27  100.0%          1     -  93888719  93888745              AB350991     1    27    27
browser |    27  100.0%          1     -  95756155  95756181              AB350991     1    27    27
browser |    27  100.0%          1     +  96557901  96557927              AB350991     1    27    27
browser |    27  100.0%          1     -  97100466  97100492              AB350991     1    27    27
browser |    27  100.0%          1     -  97108639  97108665              AB350991     1    27    27
browser |    27  100.0%          1     +  98178924  98178950              AB350991     1    27    27
browser |    27  100.0%          1     -  98715081  98715107              AB350991     1    27    27
browser |    27  100.0%          1     + 100459424 100459450              AB350991     1    27    27
browser |    27  100.0%          1     + 101454282 101454308              AB350991     1    27    27
browser |    27  100.0%          1     + 101906165 101906191              AB350991     1    27    27
browser |    27  100.0%          1     + 101912957 101912983              AB350991     1    27    27
browser |    27  100.0%          1     + 102837359 102837385              AB350991     1    27    27
browser |    27  100.0%          1     - 102959429 102959455              AB350991     1    27    27
browser |    27  100.0%          1     - 102966187 102966213              AB350991     1    27    27
browser |    27  100.0%          1     + 103133198 103133224              AB350991     1    27    27
browser |    27  100.0%          1     + 103139951 103139977              AB350991     1    27    27
browser |    27  100.0%          1     + 159797628 159797654              AB350991     1    27    27
browser |    27  100.0%          1     + 159804357 159804383              AB350991     1    27    27
browser |    27  100.0%          1     + 163296357 163296383              AB350991     1    27    27
browser |    27  100.0%          1     + 163300144 163300170              AB350991     1    27    27
browser |    27  100.0%          1     + 163520841 163520867              AB350991     1    27    27
browser |    25  100.0%          1     - 166179801 166179825              AB350991     1    25    27
browser |    25  100.0%          1     - 166183979 166184003              AB350991     1    25    27
browser |    27  100.0%          1     + 166767986 166768012              AB350991     1    27    27
browser |    27  100.0%          1     - 169370027 169370053              AB350991     1    27    27
browser |    27  100.0%          1     - 169376161 169376187              AB350991     1    27    27
browser |    27  100.0%          1     - 169943405 169943431              AB350991     1    27    27
browser |    27  100.0%          1     - 169950152 169950178              AB350991     1    27    27
browser |    26  100.0%          1     - 171657318 171657343              AB350991     1    26    27
browser |    26  100.0%          1     - 171659779 171659804              AB350991     1    26    27
browser |    27  100.0%          1     + 174869840 174869866              AB350991     1    27    27
browser |    27  100.0%          1     + 174875788 174875814              AB350991     1    27    27
browser |    27  100.0%          1     + 176370922 176370948              AB350991     1    27    27
browser |    27  100.0%          1     + 176377664 176377690              AB350991     1    27    27
browser |    27  100.0%          1     - 178001718 178001744              AB350991     1    27    27
browser |    27  100.0%          1     - 178008469 178008495              AB350991     1    27    27
browser |    27  100.0%          1     + 178242336 178242362              AB350991     1    27    27
browser |    27  100.0%          1     + 181091378 181091404              AB350991     1    27    27
browser |    27  100.0%          1     + 181098107 181098133              AB350991     1    27    27
browser |    27  100.0%          1     - 181320513 181320539              AB350991     1    27    27
browser |    27  100.0%          1     - 181326749 181326775              AB350991     1    27    27
browser |    27  100.0%          1     - 185035734 185035760              AB350991     1    27    27
browser |    27  100.0%          1     - 185038264 185038290              AB350991     1    27    27
browser |    27  100.0%          1     - 194336170 194336196              AB350991     1    27    27
browser |    27  100.0%         10     +   3551217   3551243              AB350991     1    27    27
browser |    27  100.0%         10     +   3557962   3557988              AB350991     1    27    27
browser |    27  100.0%         10     +   4412502   4412528              AB350991     1    27    27
browser |    27  100.0%         10     +  15352708  15352734              AB350991     1    27    27
browser |    27  100.0%         10     -  15813289  15813315              AB350991     1    27    27
browser |    27  100.0%         10     -  17900434  17900460              AB350991     1    27    27
browser |    27  100.0%         10     +  19414932  19414958              AB350991     1    27    27
browser |    27  100.0%         10     +  19421691  19421717              AB350991     1    27    27
browser |    27  100.0%         10     +  19886668  19886694              AB350991     1    27    27
browser |    27  100.0%         10     +  19893469  19893495              AB350991     1    27    27
browser |    27  100.0%         10     -  21087143  21087169              AB350991     1    27    27
browser |    27  100.0%         10     -  21092143  21092169              AB350991     1    27    27
browser |    27  100.0%         10     +  21518505  21518531              AB350991     1    27    27
browser |    27  100.0%         10     +  21525356  21525382              AB350991     1    27    27
browser |    27  100.0%         10     +  22399415  22399441              AB350991     1    27    27
browser |    27  100.0%         10     +  22406323  22406349              AB350991     1    27    27
browser |    27  100.0%         10     +  22559451  22559477              AB350991     1    27    27
browser |    27  100.0%         10     +  22566379  22566405              AB350991     1    27    27
browser |    27  100.0%         10     +  23744271  23744297              AB350991     1    27    27
browser |    27  100.0%         10     -  24296682  24296708              AB350991     1    27    27
browser |    27  100.0%         10     +  24977736  24977762              AB350991     1    27    27
browser |    27  100.0%         10     -  25844357  25844383              AB350991     1    27    27
browser |    27  100.0%         10     -  25848885  25848911              AB350991     1    27    27
browser |    27  100.0%         10     -  29893366  29893392              AB350991     1    27    27
browser |    27  100.0%         10     -  30023839  30023865              AB350991     1    27    27
browser |    27  100.0%         10     -  30357278  30357304              AB350991     1    27    27
browser |    27  100.0%         10     -  30690028  30690054              AB350991     1    27    27
browser |    27  100.0%         10     -  30696780  30696806              AB350991     1    27    27
browser |    27  100.0%         10     -  31156051  31156077              AB350991     1    27    27
browser |    27  100.0%         10     -  31358665  31358691              AB350991     1    27    27
browser |    27  100.0%         10     -  31365412  31365438              AB350991     1    27    27
browser |    27  100.0%         10     -  31626156  31626182              AB350991     1    27    27
browser |    27  100.0%         10     -  80811910  80811936              AB350991     1    27    27
browser |    27  100.0%         10     -  80816373  80816399              AB350991     1    27    27
browser |    27  100.0%         10     +  81506675  81506701              AB350991     1    27    27
browser |    27  100.0%         10     +  81513539  81513565              AB350991     1    27    27
browser |    27  100.0%         10     +  81665803  81665829              AB350991     1    27    27
browser |    27  100.0%         10     +  81672667  81672693              AB350991     1    27    27
browser |    27  100.0%         10     -  81803764  81803790              AB350991     1    27    27
browser |    27  100.0%         10     -  81810522  81810548              AB350991     1    27    27
browser |    27  100.0%         10     -  82774967  82774993              AB350991     1    27    27
browser |    27  100.0%         10     -  82777438  82777464              AB350991     1    27    27
browser |    27  100.0%         10     +  83308827  83308853              AB350991     1    27    27
browser |    27  100.0%         10     +  83507072  83507098              AB350991     1    27    27
browser |    27  100.0%         10     +  83513797  83513823              AB350991     1    27    27
browser |    27  100.0%         10     -  85551102  85551128              AB350991     1    27    27
browser |    27  100.0%         10     -  85556241  85556267              AB350991     1    27    27
browser |    27  100.0%         10     +  91650613  91650639              AB350991     1    27    27
browser |    27  100.0%         10     +  91652909  91652935              AB350991     1    27    27
browser |    27  100.0%         10     +  92586674  92586700              AB350991     1    27    27
browser |    27  100.0%         10     +  92589949  92589975              AB350991     1    27    27
browser |    27  100.0%         10     +  94198723  94198749              AB350991     1    27    27
browser |    27  100.0%         10     +  94205048  94205074              AB350991     1    27    27
browser |    27  100.0%         10     +  96028685  96028711              AB350991     1    27    27
browser |    27  100.0%         10     +  96035500  96035526              AB350991     1    27    27
browser |    27  100.0%         10     -  97377696  97377722              AB350991     1    27    27
browser |    27  100.0%         10     - 104391174 104391200              AB350991     1    27    27
browser |    27  100.0%         10     - 104398004 104398030              AB350991     1    27    27
browser |    27  100.0%         10     + 104411250 104411276              AB350991     1    27    27
browser |    27  100.0%         10     - 104671496 104671522              AB350991     1    27    27
browser |    27  100.0%         10     - 104678231 104678257              AB350991     1    27    27
browser |    27  100.0%         10     - 105013020 105013046              AB350991     1    27    27
browser |    27  100.0%         10     - 105017356 105017382              AB350991     1    27    27
browser |    27  100.0%         10     - 107835399 107835425              AB350991     1    27    27
browser |    27  100.0%         11     -   3998988   3999014              AB350991     1    27    27
browser |    27  100.0%         11     -   5312652   5312678              AB350991     1    27    27
browser |    27  100.0%         11     +   7984142   7984168              AB350991     1    27    27
browser |    27  100.0%         11     +   7987585   7987611              AB350991     1    27    27
browser |    27  100.0%         11     +   9658273   9658299              AB350991     1    27    27
browser |    27  100.0%         11     +   9665004   9665030              AB350991     1    27    27
browser |    27  100.0%         11     -  10710352  10710378              AB350991     1    27    27
browser |    27  100.0%         11     -  10717119  10717145              AB350991     1    27    27
browser |    27  100.0%         11     -  12511947  12511973              AB350991     1    27    27
browser |    27  100.0%         11     -  12518730  12518756              AB350991     1    27    27
browser |    27  100.0%         11     -  12745575  12745601              AB350991     1    27    27
browser |    27  100.0%         11     -  12752404  12752430              AB350991     1    27    27
browser |    27  100.0%         11     +  12904308  12904334              AB350991     1    27    27
browser |    27  100.0%         11     +  12909145  12909171              AB350991     1    27    27
browser |    27  100.0%         11     -  13825400  13825426              AB350991     1    27    27
browser |    27  100.0%         11     -  13906068  13906094              AB350991     1    27    27
browser |    27  100.0%         11     -  15177727  15177753              AB350991     1    27    27
browser |    27  100.0%         11     -  15184505  15184531              AB350991     1    27    27
browser |    27  100.0%         11     -  15809854  15809880              AB350991     1    27    27
browser |    27  100.0%         11     -  15812384  15812410              AB350991     1    27    27
browser |    27  100.0%         11     -  15833716  15833742              AB350991     1    27    27
browser |    27  100.0%         11     -  15837503  15837529              AB350991     1    27    27
browser |    27  100.0%         11     +  17102905  17102931              AB350991     1    27    27
browser |    27  100.0%         11     +  19516469  19516495              AB350991     1    27    27
browser |    27  100.0%         11     +  19520515  19520541              AB350991     1    27    27
browser |    27  100.0%         11     +  20459494  20459520              AB350991     1    27    27
browser |    27  100.0%         11     +  20461818  20461844              AB350991     1    27    27
browser |    27  100.0%         11     +  23168870  23168896              AB350991     1    27    27
browser |    27  100.0%         11     +  23175610  23175636              AB350991     1    27    27
browser |    27  100.0%         11     +  25562990  25563016              AB350991     1    27    27
browser |    27  100.0%         11     +  27365394  27365420              AB350991     1    27    27
browser |    27  100.0%         11     +  27367660  27367686              AB350991     1    27    27
browser |    27  100.0%         11     -  81436345  81436371              AB350991     1    27    27
browser |    27  100.0%         11     -  81443174  81443200              AB350991     1    27    27
browser |    27  100.0%         11     +  82225117  82225143              AB350991     1    27    27
browser |    27  100.0%         11     +  82229091  82229117              AB350991     1    27    27
browser |    27  100.0%         11     +  85176684  85176710              AB350991     1    27    27
browser |    27  100.0%         11     +  85183442  85183468              AB350991     1    27    27
browser |    27  100.0%         11     +  85184927  85184953              AB350991     1    27    27
browser |    27  100.0%         11     -  86736507  86736533              AB350991     1    27    27
browser |    27  100.0%         11     -  86740685  86740711              AB350991     1    27    27
browser |    27  100.0%         11     +  88982700  88982726              AB350991     1    27    27
browser |    27  100.0%         11     +  90201500  90201526              AB350991     1    27    27
browser |    27  100.0%         11     +  90203213  90203239              AB350991     1    27    27
browser |    27  100.0%         11     +  90720740  90720766              AB350991     1    27    27
browser |    27  100.0%         11     +  90725696  90725722              AB350991     1    27    27
browser |    27  100.0%         11     -  90792592  90792618              AB350991     1    27    27
browser |    27  100.0%         11     -  90798771  90798797              AB350991     1    27    27
browser |    27  100.0%         11     +  90851288  90851314              AB350991     1    27    27
browser |    27  100.0%         11     +  90858035  90858061              AB350991     1    27    27
browser |    27  100.0%         11     +  96727094  96727120              AB350991     1    27    27
browser |    27  100.0%         11     -  98504142  98504168              AB350991     1    27    27
browser |    27  100.0%         11     -  98510903  98510929              AB350991     1    27    27
browser |    27  100.0%         11     +  99603818  99603844              AB350991     1    27    27
browser |    27  100.0%         11     +  99607976  99608002              AB350991     1    27    27
browser |    27  100.0%         11     - 100553759 100553785              AB350991     1    27    27
browser |    27  100.0%         11     - 100560050 100560076              AB350991     1    27    27
browser |    27  100.0%         11     + 106183810 106183836              AB350991     1    27    27
browser |    27  100.0%         11     - 108365892 108365918              AB350991     1    27    27
browser |    27  100.0%         11     - 111073375 111073401              AB350991     1    27    27
browser |    27  100.0%         11     - 111080145 111080171              AB350991     1    27    27
browser |    27  100.0%         11     - 114835085 114835111              AB350991     1    27    27
browser |    27  100.0%         11     - 117390672 117390698              AB350991     1    27    27
browser |    27  100.0%         11     - 117395481 117395507              AB350991     1    27    27
browser |    27  100.0%         12     -   3052377   3052403              AB350991     1    27    27
browser |    27  100.0%         12     -   3059180   3059206              AB350991     1    27    27
browser |    27  100.0%         12     +   3381095   3381121              AB350991     1    27    27
browser |    27  100.0%         12     +   3387873   3387899              AB350991     1    27    27
browser |    27  100.0%         12     -   6853061   6853087              AB350991     1    27    27
browser |    27  100.0%         12     -   6859828   6859854              AB350991     1    27    27
browser |    27  100.0%         12     -   7344610   7344636              AB350991     1    27    27
browser |    27  100.0%         12     -   7937162   7937188              AB350991     1    27    27
browser |    27  100.0%         12     -   8453214   8453240              AB350991     1    27    27
browser |    27  100.0%         12     -   8458115   8458141              AB350991     1    27    27
browser |    27  100.0%         12     +  11153948  11153974              AB350991     1    27    27
browser |    27  100.0%         12     +  11160675  11160701              AB350991     1    27    27
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browser |    25  100.0%  X_GL456233v2_random     -    494599    494623              AB350991     1    25    27
browser |    25  100.0%  X_GL456233v2_random     -    498787    498811              AB350991     1    25    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