DQ719189
 

Information on mRNA DQ719189

Description: Mus musculus piRNA piR-134511, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2006-06-08
Version: 1
mRNA sequence: DQ719189
Position: chr12:56960142-56960171

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 |    30  100.0%         12     +  56960142  56960171              DQ719189     1    30    31
browser |    30  100.0%          1     +   7681958   7681987              DQ719189     1    30    31
browser |    30  100.0%          1     -   8248975   8249004              DQ719189     1    30    31
browser |    30  100.0%          1     -   8728984   8729013              DQ719189     1    30    31
browser |    30  100.0%          1     +   8860129   8860158              DQ719189     1    30    31
browser |    30  100.0%          1     -  11100197  11100226              DQ719189     1    30    31
browser |    30  100.0%          1     -  11438140  11438169              DQ719189     1    30    31
browser |    30  100.0%          1     -  12017269  12017298              DQ719189     1    30    31
browser |    30  100.0%          1     +  14033249  14033278              DQ719189     1    30    31
browser |    28  100.0%          1     -  17595218  17595245              DQ719189     3    30    31
browser |    30  100.0%          1     +  29697668  29697697              DQ719189     1    30    31
browser |    30  100.0%          1     -  30727280  30727309              DQ719189     1    30    31
browser |    30  100.0%          1     +  41129778  41129807              DQ719189     1    30    31
browser |    30  100.0%          1     -  47263019  47263048              DQ719189     1    30    31
browser |    30  100.0%          1     +  47829594  47829623              DQ719189     1    30    31
browser |    30  100.0%          1     -  58789083  58789112              DQ719189     1    30    31
browser |    30  100.0%          1     +  76595427  76595456              DQ719189     1    30    31
browser |    30  100.0%          1     +  77648057  77648086              DQ719189     1    30    31
browser |    29  100.0%          1     +  79000548  79000576              DQ719189     2    30    31
browser |    30  100.0%          1     +  95626930  95626959              DQ719189     1    30    31
browser |    30  100.0%          1     -  98528513  98528542              DQ719189     1    30    31
browser |    30  100.0%          1     - 108873410 108873439              DQ719189     1    30    31
browser |    30  100.0%          1     + 108887763 108887792              DQ719189     1    30    31
browser |    30  100.0%          1     - 112192508 112192537              DQ719189     1    30    31
browser |    30  100.0%          1     + 112289966 112289995              DQ719189     1    30    31
browser |    30  100.0%          1     - 117560403 117560432              DQ719189     1    30    31
browser |    30  100.0%          1     - 118069087 118069116              DQ719189     1    30    31
browser |    30  100.0%          1     + 128818980 128819009              DQ719189     1    30    31
browser |    30  100.0%          1     - 136736196 136736225              DQ719189     1    30    31
browser |    30  100.0%          1     + 161363168 161363197              DQ719189     1    30    31
browser |    30  100.0%          1     + 166411737 166411766              DQ719189     1    30    31
browser |    30  100.0%          1     + 192642053 192642082              DQ719189     1    30    31
browser |    30  100.0%         10     +   7193535   7193564              DQ719189     1    30    31
browser |    30  100.0%         10     +   8513114   8513143              DQ719189     1    30    31
browser |    30  100.0%         10     -  11776986  11777015              DQ719189     1    30    31
browser |    30  100.0%         10     +  18117048  18117077              DQ719189     1    30    31
browser |    30  100.0%         10     +  19676805  19676834              DQ719189     1    30    31
browser |    30  100.0%         10     -  22399550  22399579              DQ719189     1    30    31
browser |    30  100.0%         10     -  26607273  26607302              DQ719189     1    30    31
browser |    30  100.0%         10     -  34615418  34615447              DQ719189     1    30    31
browser |    30  100.0%         10     +  38469392  38469421              DQ719189     1    30    31
browser |    30  100.0%         10     +  43755552  43755581              DQ719189     1    30    31
browser |    30  100.0%         10     -  47512472  47512501              DQ719189     1    30    31
browser |    30  100.0%         10     +  47550224  47550253              DQ719189     1    30    31
browser |    30  100.0%         10     -  47557205  47557234              DQ719189     1    30    31
browser |    30  100.0%         10     +  74714792  74714821              DQ719189     1    30    31
browser |    30  100.0%         10     +  76759210  76759239              DQ719189     1    30    31
browser |    30  100.0%         10     -  81506810  81506839              DQ719189     1    30    31
browser |    30  100.0%         10     -  81665938  81665967              DQ719189     1    30    31
browser |    30  100.0%         10     -  82407681  82407710              DQ719189     1    30    31
browser |    30  100.0%         10     +  86981173  86981202              DQ719189     1    30    31
browser |    30  100.0%         10     + 103911935 103911964              DQ719189     1    30    31
browser |    30  100.0%         10     + 110536227 110536256              DQ719189     1    30    31
browser |    30  100.0%         10     + 121979046 121979075              DQ719189     1    30    31
browser |    30  100.0%         10     + 122348323 122348352              DQ719189     1    30    31
browser |    30  100.0%         11     +   6749689   6749718              DQ719189     1    30    31
browser |    30  100.0%         11     -   9035226   9035255              DQ719189     1    30    31
browser |    30  100.0%         11     +  14521091  14521120              DQ719189     1    30    31
browser |    30  100.0%         11     -  16154664  16154693              DQ719189     1    30    31
browser |    30  100.0%         11     -  23193204  23193233              DQ719189     1    30    31
browser |    30  100.0%         11     +  27087668  27087697              DQ719189     1    30    31
browser |    30  100.0%         11     -  29114472  29114501              DQ719189     1    30    31
browser |    30  100.0%         11     +  29232580  29232609              DQ719189     1    30    31
browser |    30  100.0%         11     -  70957010  70957039              DQ719189     1    30    31
browser |    30  100.0%         11     -  73837523  73837552              DQ719189     1    30    31
browser |    30  100.0%         11     -  79632722  79632751              DQ719189     1    30    31
browser |    30  100.0%         11     +  79767442  79767471              DQ719189     1    30    31
browser |    30  100.0%         11     -  85330734  85330763              DQ719189     1    30    31
browser |    30  100.0%         11     +  90400764  90400793              DQ719189     1    30    31
browser |    30  100.0%         11     - 104750857 104750886              DQ719189     1    30    31
browser |    30  100.0%         12     -   3084152   3084181              DQ719189     1    30    31
browser |    30  100.0%         12     +   6859690   6859719              DQ719189     1    30    31
browser |    30  100.0%         12     -  14644597  14644626              DQ719189     1    30    31
browser |    30  100.0%         12     +  18016473  18016502              DQ719189     1    30    31
browser |    30  100.0%         12     -  19864621  19864650              DQ719189     1    30    31
browser |    30  100.0%         12     +  21656477  21656506              DQ719189     1    30    31
browser |    30  100.0%         12     -  22425545  22425574              DQ719189     1    30    31
browser |    30  100.0%         12     -  23584557  23584586              DQ719189     1    30    31
browser |    30  100.0%         12     +  24745644  24745673              DQ719189     1    30    31
browser |    30  100.0%         12     -  26156906  26156935              DQ719189     1    30    31
browser |    30  100.0%         12     +  39485787  39485816              DQ719189     1    30    31
browser |    30  100.0%         12     -  52219977  52220006              DQ719189     1    30    31
browser |    30  100.0%         12     -  60754119  60754148              DQ719189     1    30    31
browser |    30  100.0%         12     +  63338631  63338660              DQ719189     1    30    31
browser |    30  100.0%         12     +  74747353  74747382              DQ719189     1    30    31
browser |    30  100.0%         12     +  96906710  96906739              DQ719189     1    30    31
browser |    30  100.0%         12     - 103686999 103687028              DQ719189     1    30    31
browser |    30  100.0%         12     - 103759709 103759738              DQ719189     1    30    31
browser |    30  100.0%         12     - 109787488 109787517              DQ719189     1    30    31
browser |    30  100.0%         12     + 115365814 115365843              DQ719189     1    30    31
browser |    30  100.0%         12     + 115528522 115528551              DQ719189     1    30    31
browser |    30  100.0%         13     +   3401565   3401594              DQ719189     1    30    31
browser |    30  100.0%         13     +   3668382   3668411              DQ719189     1    30    31
browser |    30  100.0%         13     -   4952138   4952167              DQ719189     1    30    31
browser |    30  100.0%         13     -   5295140   5295169              DQ719189     1    30    31
browser |    30  100.0%         13     -   8317699   8317728              DQ719189     1    30    31
browser |    30  100.0%         13     -   9903216   9903245              DQ719189     1    30    31
browser |    30  100.0%         13     +  12877986  12878015              DQ719189     1    30    31
browser |    30  100.0%         13     +  27474264  27474293              DQ719189     1    30    31
browser |    30  100.0%         13     +  32489533  32489562              DQ719189     1    30    31
browser |    30  100.0%         13     -  33958976  33959005              DQ719189     1    30    31
browser |    30  100.0%         13     -  50711562  50711591              DQ719189     1    30    31
browser |    30  100.0%         13     +  51189669  51189698              DQ719189     1    30    31
browser |    30  100.0%         13     -  59269849  59269878              DQ719189     1    30    31
browser |    30  100.0%         13     -  61095322  61095351              DQ719189     1    30    31
browser |    30  100.0%         13     -  64646852  64646881              DQ719189     1    30    31
browser |    30  100.0%         13     +  65668787  65668816              DQ719189     1    30    31
browser |    30  100.0%         13     +  68146449  68146478              DQ719189     1    30    31
browser |    30  100.0%         13     -  73291313  73291342              DQ719189     1    30    31
browser |    30  100.0%         13     -  81232304  81232333              DQ719189     1    30    31
browser |    30  100.0%         13     -  88308776  88308805              DQ719189     1    30    31
browser |    29  100.0%         13     +  93674064  93674092              DQ719189     1    29    31
browser |    30  100.0%         13     + 102101170 102101199              DQ719189     1    30    31
browser |    30  100.0%         13     - 104084056 104084085              DQ719189     1    30    31
browser |    30  100.0%         13     + 106924254 106924283              DQ719189     1    30    31
browser |    30  100.0%         13     - 114675985 114676014              DQ719189     1    30    31
browser |    30  100.0%         13     + 118287981 118288010              DQ719189     1    30    31
browser |    30  100.0%         14     -   5088189   5088218              DQ719189     1    30    31
browser |    30  100.0%         14     -   7002732   7002761              DQ719189     1    30    31
browser |    30  100.0%         14     -  11143925  11143954              DQ719189     1    30    31
browser |    30  100.0%         14     +  13342154  13342183              DQ719189     1    30    31
browser |    30  100.0%         14     -  23022208  23022237              DQ719189     1    30    31
browser |    30  100.0%         14     -  37223060  37223089              DQ719189     1    30    31
browser |    30  100.0%         14     +  37749450  37749479              DQ719189     1    30    31
browser |    30  100.0%         14     +  39218613  39218642              DQ719189     1    30    31
browser |    30  100.0%         14     +  39458735  39458764              DQ719189     1    30    31
browser |    30  100.0%         14     +  51559605  51559634              DQ719189     1    30    31
browser |    30  100.0%         14     -  52848325  52848354              DQ719189     1    30    31
browser |    30  100.0%         14     +  53351254  53351283              DQ719189     1    30    31
browser |    30  100.0%         14     -  55464380  55464409              DQ719189     1    30    31
browser |    30  100.0%         14     -  60801976  60802005              DQ719189     1    30    31
browser |    30  100.0%         14     -  62880465  62880494              DQ719189     1    30    31
browser |    30  100.0%         14     +  65177374  65177403              DQ719189     1    30    31
browser |    30  100.0%         14     +  66853950  66853979              DQ719189     1    30    31
browser |    30  100.0%         14     +  71459525  71459554              DQ719189     1    30    31
browser |    30  100.0%         14     +  72040943  72040972              DQ719189     1    30    31
browser |    30  100.0%         14     -  85415566  85415595              DQ719189     1    30    31
browser |    30  100.0%         14     +  86373043  86373072              DQ719189     1    30    31
browser |    30  100.0%         14     -  98992777  98992806              DQ719189     1    30    31
browser |    30  100.0%         14     + 101821056 101821085              DQ719189     1    30    31
browser |    28  100.0%         14     + 106590146 106590173              DQ719189     3    30    31
browser |    30  100.0%         14     - 107063587 107063616              DQ719189     1    30    31
browser |    30  100.0%         14     - 117316793 117316822              DQ719189     1    30    31
browser |    30  100.0%         15     +   3199329   3199358              DQ719189     1    30    31
browser |    30  100.0%         15     +  14731359  14731388              DQ719189     1    30    31
browser |    30  100.0%         15     +  16186050  16186079              DQ719189     1    30    31
browser |    30  100.0%         15     +  17581145  17581174              DQ719189     1    30    31
browser |    30  100.0%         15     +  19053348  19053377              DQ719189     1    30    31
browser |    30  100.0%         15     +  21721824  21721853              DQ719189     1    30    31
browser |    30  100.0%         15     -  22363155  22363184              DQ719189     1    30    31
browser |    30  100.0%         15     +  24325430  24325459              DQ719189     1    30    31
browser |    30  100.0%         15     -  29131857  29131886              DQ719189     1    30    31
browser |    30  100.0%         15     +  38617003  38617032              DQ719189     1    30    31
browser |    30  100.0%         15     -  39199503  39199532              DQ719189     1    30    31
browser |    30  100.0%         15     +  39581476  39581505              DQ719189     1    30    31
browser |    30  100.0%         15     +  46369635  46369664              DQ719189     1    30    31
browser |    30  100.0%         15     -  49597557  49597586              DQ719189     1    30    31
browser |    30  100.0%         15     +  51947617  51947646              DQ719189     1    30    31
browser |    30  100.0%         15     -  82489805  82489834              DQ719189     1    30    31
browser |    30  100.0%         15     +  97634072  97634101              DQ719189     1    30    31
browser |    30  100.0%         16     -   8881990   8882019              DQ719189     1    30    31
browser |    30  100.0%         16     -  13299990  13300019              DQ719189     1    30    31
browser |    30  100.0%         16     +  17813175  17813204              DQ719189     1    30    31
browser |    30  100.0%         16     -  19406995  19407024              DQ719189     1    30    31
browser |    30  100.0%         16     +  20927562  20927591              DQ719189     1    30    31
browser |    30  100.0%         16     +  22801382  22801411              DQ719189     1    30    31
browser |    30  100.0%         16     +  46944497  46944526              DQ719189     1    30    31
browser |    30  100.0%         16     +  51800107  51800136              DQ719189     1    30    31
browser |    30  100.0%         16     -  53400479  53400508              DQ719189     1    30    31
browser |    30  100.0%         16     -  54873499  54873528              DQ719189     1    30    31
browser |    30  100.0%         16     -  61133356  61133385              DQ719189     1    30    31
browser |    30  100.0%         16     -  61144996  61145025              DQ719189     1    30    31
browser |    30  100.0%         16     -  62199259  62199288              DQ719189     1    30    31
browser |    30  100.0%         16     +  64790434  64790463              DQ719189     1    30    31
browser |    30  100.0%         16     +  69762399  69762428              DQ719189     1    30    31
browser |    30  100.0%         16     -  71816720  71816749              DQ719189     1    30    31
browser |    30  100.0%         16     -  79339727  79339756              DQ719189     1    30    31
browser |    30  100.0%         16     +  88946229  88946258              DQ719189     1    30    31
browser |    30  100.0%         17     +  12506495  12506524              DQ719189     1    30    31
browser |    30  100.0%         17     +  15091333  15091362              DQ719189     1    30    31
browser |    30  100.0%         17     +  19187173  19187202              DQ719189     1    30    31
browser |    30  100.0%         17     +  20138912  20138941              DQ719189     1    30    31
browser |    30  100.0%         17     -  23338614  23338643              DQ719189     1    30    31
browser |    30  100.0%         17     +  32938672  32938701              DQ719189     1    30    31
browser |    30  100.0%         17     +  40021920  40021949              DQ719189     1    30    31
browser |    30  100.0%         17     +  50227653  50227682              DQ719189     1    30    31
browser |    30  100.0%         17     +  52257668  52257697              DQ719189     1    30    31
browser |    30  100.0%         17     +  52635581  52635610              DQ719189     1    30    31
browser |    30  100.0%         17     +  53678507  53678536              DQ719189     1    30    31
browser |    30  100.0%         17     -  66834492  66834521              DQ719189     1    30    31
browser |    30  100.0%         17     +  67736511  67736540              DQ719189     1    30    31
browser |    30  100.0%         17     -  72882449  72882478              DQ719189     1    30    31
browser |    30  100.0%         17     -  92556824  92556853              DQ719189     1    30    31
browser |    30  100.0%         17     -  94099332  94099361              DQ719189     1    30    31
browser |    30  100.0%         17     -  94535214  94535243              DQ719189     1    30    31
browser |    30  100.0%         18     -   4480013   4480042              DQ719189     1    30    31
browser |    30  100.0%         18     -   5110194   5110223              DQ719189     1    30    31
browser |    30  100.0%         18     -   6256422   6256451              DQ719189     1    30    31
browser |    30  100.0%         18     +   7062712   7062741              DQ719189     1    30    31
browser |    30  100.0%         18     -  11291551  11291580              DQ719189     1    30    31
browser |    30  100.0%         18     -  19638623  19638652              DQ719189     1    30    31
browser |    30  100.0%         18     -  23247414  23247443              DQ719189     1    30    31
browser |    30  100.0%         18     -  24166651  24166680              DQ719189     1    30    31
browser |    30  100.0%         18     +  24617250  24617279              DQ719189     1    30    31
browser |    30  100.0%         18     -  36956783  36956812              DQ719189     1    30    31
browser |    30  100.0%         18     -  44391829  44391858              DQ719189     1    30    31
browser |    30  100.0%         18     -  58418044  58418073              DQ719189     1    30    31
browser |    30  100.0%         18     +  63328450  63328479              DQ719189     1    30    31
browser |    30  100.0%         18     -  87100399  87100428              DQ719189     1    30    31
browser |    30  100.0%         19     -  11399922  11399951              DQ719189     1    30    31
browser |    30  100.0%         19     +  54880867  54880896              DQ719189     1    30    31
browser |    30  100.0%  1_GL456211v1_random     -    135459    135488              DQ719189     1    30    31
browser |    30  100.0%          2     +  14390793  14390822              DQ719189     1    30    31
browser |    30  100.0%          2     -  23809293  23809322              DQ719189     1    30    31
browser |    30  100.0%          2     -  24055435  24055464              DQ719189     1    30    31
browser |    30  100.0%          2     +  24088586  24088615              DQ719189     1    30    31
browser |    30  100.0%          2     +  32009497  32009526              DQ719189     1    30    31
browser |    30  100.0%          2     +  32367252  32367281              DQ719189     1    30    31
browser |    30  100.0%          2     +  39748592  39748621              DQ719189     1    30    31
browser |    30  100.0%          2     -  70710920  70710949              DQ719189     1    30    31
browser |    30  100.0%          2     -  81620809  81620838              DQ719189     1    30    31
browser |    30  100.0%          2     -  82948889  82948918              DQ719189     1    30    31
browser |    30  100.0%          2     -  88194190  88194219              DQ719189     1    30    31
browser |    30  100.0%          2     - 107877733 107877762              DQ719189     1    30    31
browser |    30  100.0%          2     + 108303518 108303547              DQ719189     1    30    31
browser |    30  100.0%          2     - 120466802 120466831              DQ719189     1    30    31
browser |    30  100.0%          2     - 129363707 129363736              DQ719189     1    30    31
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View details of parts of alignment within browser window
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Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518