DQ715339
 

Information on mRNA DQ715339

Description: Mus musculus piRNA piR-130661, 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: DQ715339
Position: chr12:56796595-56796621

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     +  56796595  56796621              DQ715339     1    27    27
browser |    27  100.0%          1     +   5879280   5879306              DQ715339     1    27    27
browser |    27  100.0%          1     -   8066313   8066339              DQ715339     1    27    27
browser |    27  100.0%          1     -   8228754   8228780              DQ715339     1    27    27
browser |    27  100.0%          1     +   8730320   8730346              DQ715339     1    27    27
browser |    27  100.0%          1     +  10804796  10804822              DQ715339     1    27    27
browser |    27  100.0%          1     -  13623178  13623204              DQ715339     1    27    27
browser |    27  100.0%          1     -  18029418  18029444              DQ715339     1    27    27
browser |    27  100.0%          1     -  18589448  18589474              DQ715339     1    27    27
browser |    27  100.0%          1     -  19695032  19695058              DQ715339     1    27    27
browser |    27  100.0%          1     +  22070173  22070199              DQ715339     1    27    27
browser |    27  100.0%          1     -  26455440  26455466              DQ715339     1    27    27
browser |    27  100.0%          1     +  26512885  26512911              DQ715339     1    27    27
browser |    27  100.0%          1     -  27221588  27221614              DQ715339     1    27    27
browser |    27  100.0%          1     +  29986015  29986041              DQ715339     1    27    27
browser |    27  100.0%          1     -  34388921  34388947              DQ715339     1    27    27
browser |    27  100.0%          1     -  35829917  35829943              DQ715339     1    27    27
browser |    27  100.0%          1     -  40739434  40739460              DQ715339     1    27    27
browser |    27  100.0%          1     +  47264729  47264755              DQ715339     1    27    27
browser |    27  100.0%          1     +  48400070  48400096              DQ715339     1    27    27
browser |    27  100.0%          1     -  55819871  55819897              DQ715339     1    27    27
browser |    27  100.0%          1     +  58855543  58855569              DQ715339     1    27    27
browser |    27  100.0%          1     +  60768729  60768755              DQ715339     1    27    27
browser |    27  100.0%          1     +  64222055  64222081              DQ715339     1    27    27
browser |    27  100.0%          1     +  65004191  65004217              DQ715339     1    27    27
browser |    27  100.0%          1     +  66061498  66061524              DQ715339     1    27    27
browser |    27  100.0%          1     -  70278606  70278632              DQ715339     1    27    27
browser |    27  100.0%          1     +  72169416  72169442              DQ715339     1    27    27
browser |    27  100.0%          1     +  74697311  74697337              DQ715339     1    27    27
browser |    27  100.0%          1     -  77646733  77646759              DQ715339     1    27    27
browser |    27  100.0%          1     -  79917131  79917157              DQ715339     1    27    27
browser |    27  100.0%          1     +  81546604  81546630              DQ715339     1    27    27
browser |    27  100.0%          1     -  82481167  82481193              DQ715339     1    27    27
browser |    27  100.0%          1     +  87066086  87066112              DQ715339     1    27    27
browser |    27  100.0%          1     +  91403659  91403685              DQ715339     1    27    27
browser |    27  100.0%          1     -  93886654  93886680              DQ715339     1    27    27
browser |    27  100.0%          1     -  95625242  95625268              DQ715339     1    27    27
browser |    27  100.0%          1     -  97102853  97102879              DQ715339     1    27    27
browser |    27  100.0%          1     + 101910594 101910620              DQ715339     1    27    27
browser |    26  100.0%          1     - 102961756 102961781              DQ715339     1    26    27
browser |    27  100.0%          1     + 103137623 103137649              DQ715339     1    27    27
browser |    27  100.0%          1     - 109543497 109543523              DQ715339     1    27    27
browser |    27  100.0%          1     + 111186080 111186106              DQ715339     1    27    27
browser |    27  100.0%          1     - 111633465 111633491              DQ715339     1    27    27
browser |    27  100.0%          1     + 112196789 112196815              DQ715339     1    27    27
browser |    27  100.0%          1     - 112859574 112859600              DQ715339     1    27    27
browser |    27  100.0%          1     - 112946172 112946198              DQ715339     1    27    27
browser |    27  100.0%          1     + 117634386 117634412              DQ715339     1    27    27
browser |    27  100.0%          1     - 125246960 125246986              DQ715339     1    27    27
browser |    27  100.0%          1     + 125275829 125275855              DQ715339     1    27    27
browser |    27  100.0%          1     + 127490722 127490748              DQ715339     1    27    27
browser |    27  100.0%          1     + 127807521 127807547              DQ715339     1    27    27
browser |    27  100.0%          1     - 130464419 130464445              DQ715339     1    27    27
browser |    27  100.0%          1     + 137203628 137203654              DQ715339     1    27    27
browser |    27  100.0%          1     - 140746915 140746941              DQ715339     1    27    27
browser |    27  100.0%          1     - 140965513 140965539              DQ715339     1    27    27
browser |    27  100.0%          1     + 144735151 144735177              DQ715339     1    27    27
browser |    27  100.0%          1     - 145999039 145999065              DQ715339     1    27    27
browser |    27  100.0%          1     + 146162361 146162387              DQ715339     1    27    27
browser |    27  100.0%          1     - 149271362 149271388              DQ715339     1    27    27
browser |    27  100.0%          1     - 149459672 149459698              DQ715339     1    27    27
browser |    27  100.0%          1     + 154779421 154779447              DQ715339     1    27    27
browser |    27  100.0%          1     + 159802054 159802080              DQ715339     1    27    27
browser |    26  100.0%          1     - 162670485 162670510              DQ715339     2    27    27
browser |    27  100.0%          1     - 166182123 166182149              DQ715339     1    27    27
browser |    27  100.0%          1     + 166594927 166594953              DQ715339     1    27    27
browser |    27  100.0%          1     - 169371732 169371758              DQ715339     1    27    27
browser |    27  100.0%          1     - 169945719 169945745              DQ715339     1    27    27
browser |    27  100.0%          1     + 174873459 174873485              DQ715339     1    27    27
browser |    27  100.0%          1     + 176375353 176375379              DQ715339     1    27    27
browser |    26  100.0%          1     - 177887984 177888009              DQ715339     2    27    27
browser |    27  100.0%          1     - 178004037 178004063              DQ715339     1    27    27
browser |    27  100.0%          1     + 181095810 181095836              DQ715339     1    27    27
browser |    27  100.0%          1     - 181322826 181322852              DQ715339     1    27    27
browser |    27  100.0%          1     - 183298644 183298670              DQ715339     1    27    27
browser |    27  100.0%          1     - 195005021 195005047              DQ715339     1    27    27
browser |    27  100.0%         10     +   3555650   3555676              DQ715339     1    27    27
browser |    27  100.0%         10     -   8477410   8477436              DQ715339     1    27    27
browser |    27  100.0%         10     -  11572389  11572415              DQ715339     1    27    27
browser |    27  100.0%         10     +  19419363  19419389              DQ715339     1    27    27
browser |    27  100.0%         10     -  19675261  19675287              DQ715339     1    27    27
browser |    27  100.0%         10     +  19891090  19891116              DQ715339     1    27    27
browser |    27  100.0%         10     +  21522936  21522962              DQ715339     1    27    27
browser |    27  100.0%         10     +  22403827  22403853              DQ715339     1    27    27
browser |    27  100.0%         10     +  22563882  22563908              DQ715339     1    27    27
browser |    27  100.0%         10     +  24980009  24980035              DQ715339     1    27    27
browser |    27  100.0%         10     -  25846682  25846708              DQ715339     1    27    27
browser |    27  100.0%         10     -  30692350  30692376              DQ715339     1    27    27
browser |    26  100.0%         10     -  30967035  30967060              DQ715339     2    27    27
browser |    27  100.0%         10     -  31360978  31361004              DQ715339     1    27    27
browser |    26  100.0%         10     +  34622541  34622566              DQ715339     2    27    27
browser |    27  100.0%         10     -  41718904  41718930              DQ715339     1    27    27
browser |    27  100.0%         10     +  43647812  43647838              DQ715339     1    27    27
browser |    27  100.0%         10     -  51761462  51761488              DQ715339     1    27    27
browser |    27  100.0%         10     -  56599210  56599236              DQ715339     1    27    27
browser |    27  100.0%         10     -  57016130  57016156              DQ715339     1    27    27
browser |    27  100.0%         10     -  62942132  62942158              DQ715339     1    27    27
browser |    27  100.0%         10     +  65478343  65478369              DQ715339     1    27    27
browser |    27  100.0%         10     +  66562958  66562984              DQ715339     1    27    27
browser |    26  100.0%         10     -  70629623  70629648              DQ715339     2    27    27
browser |    27  100.0%         10     -  71529616  71529642              DQ715339     1    27    27
browser |    26  100.0%         10     -  77788974  77788999              DQ715339     2    27    27
browser |    27  100.0%         10     +  78656507  78656533              DQ715339     1    27    27
browser |    27  100.0%         10     +  81511092  81511118              DQ715339     1    27    27
browser |    27  100.0%         10     +  81670220  81670246              DQ715339     1    27    27
browser |    27  100.0%         10     -  81806094  81806120              DQ715339     1    27    27
browser |    27  100.0%         10     +  83306448  83306474              DQ715339     1    27    27
browser |    27  100.0%         10     +  83511503  83511529              DQ715339     1    27    27
browser |    27  100.0%         10     -  85553428  85553454              DQ715339     1    27    27
browser |    27  100.0%         10     -  88489215  88489241              DQ715339     1    27    27
browser |    27  100.0%         10     +  94202651  94202677              DQ715339     1    27    27
browser |    27  100.0%         10     +  96033111  96033137              DQ715339     1    27    27
browser |    27  100.0%         10     +  97163030  97163056              DQ715339     1    27    27
browser |    27  100.0%         10     -  99177354  99177380              DQ715339     1    27    27
browser |    27  100.0%         10     - 104393581 104393607              DQ715339     1    27    27
browser |    27  100.0%         10     - 104673798 104673824              DQ715339     1    27    27
browser |    27  100.0%         10     - 105015317 105015343              DQ715339     1    27    27
browser |    27  100.0%         10     - 107837727 107837753              DQ715339     1    27    27
browser |    27  100.0%         10     + 109155797 109155823              DQ715339     1    27    27
browser |    27  100.0%         10     - 110534498 110534524              DQ715339     1    27    27
browser |    27  100.0%         10     + 113563323 113563349              DQ715339     1    27    27
browser |    26  100.0%         10     + 116446885 116446910              DQ715339     2    27    27
browser |    27  100.0%         10     - 117908921 117908947              DQ715339     1    27    27
browser |    27  100.0%         10     - 121003006 121003032              DQ715339     1    27    27
browser |    27  100.0%         10     + 122204493 122204519              DQ715339     1    27    27
browser |    27  100.0%         10     - 122344041 122344067              DQ715339     1    27    27
browser |    27  100.0%         10     + 122673370 122673396              DQ715339     1    27    27
browser |    27  100.0%         10     - 123697618 123697644              DQ715339     1    27    27
browser |    27  100.0%         10     - 124414593 124414619              DQ715339     1    27    27
browser |    27  100.0%         10     + 124519564 124519590              DQ715339     1    27    27
browser |    27  100.0%         10     + 129229409 129229435              DQ715339     1    27    27
browser |    27  100.0%         10     - 129763541 129763567              DQ715339     1    27    27
browser |    27  100.0%         10     + 130399618 130399644              DQ715339     1    27    27
browser |    27  100.0%         11     +   7530403   7530429              DQ715339     1    27    27
browser |    26  100.0%         11     +   9662703   9662728              DQ715339     2    27    27
browser |    27  100.0%         11     -  10712694  10712720              DQ715339     1    27    27
browser |    26  100.0%         11     -  12747977  12748002              DQ715339     1    26    27
browser |    27  100.0%         11     -  15180074  15180100              DQ715339     1    27    27
browser |    27  100.0%         11     +  18761175  18761201              DQ715339     1    27    27
browser |    27  100.0%         11     +  19518144  19518170              DQ715339     1    27    27
browser |    27  100.0%         11     -  20468760  20468786              DQ715339     1    27    27
browser |    27  100.0%         11     +  23173302  23173328              DQ715339     1    27    27
browser |    27  100.0%         11     +  23194915  23194941              DQ715339     1    27    27
browser |    27  100.0%         11     -  27085981  27086007              DQ715339     1    27    27
browser |    27  100.0%         11     +  27904688  27904714              DQ715339     1    27    27
browser |    27  100.0%         11     -  28049677  28049703              DQ715339     1    27    27
browser |    27  100.0%         11     +  31402282  31402308              DQ715339     1    27    27
browser |    27  100.0%         11     -  38374706  38374732              DQ715339     1    27    27
browser |    27  100.0%         11     +  39959271  39959297              DQ715339     1    27    27
browser |    27  100.0%         11     -  51330892  51330918              DQ715339     1    27    27
browser |    27  100.0%         11     +  54472119  54472145              DQ715339     1    27    27
browser |    27  100.0%         11     +  55136482  55136508              DQ715339     1    27    27
browser |    27  100.0%         11     -  61313645  61313671              DQ715339     1    27    27
browser |    27  100.0%         11     -  63360934  63360960              DQ715339     1    27    27
browser |    27  100.0%         11     +  65347329  65347355              DQ715339     1    27    27
browser |    27  100.0%         11     +  66842788  66842814              DQ715339     1    27    27
browser |    27  100.0%         11     -  74022142  74022168              DQ715339     1    27    27
browser |    26  100.0%         11     +  74115199  74115224              DQ715339     2    27    27
browser |    26  100.0%         11     -  74777604  74777629              DQ715339     2    27    27
browser |    27  100.0%         11     +  79634448  79634474              DQ715339     1    27    27
browser |    27  100.0%         11     -  79765755  79765781              DQ715339     1    27    27
browser |    27  100.0%         11     -  81438748  81438774              DQ715339     1    27    27
browser |    27  100.0%         11     +  82226792  82226818              DQ715339     1    27    27
browser |    27  100.0%         11     -  84953910  84953936              DQ715339     1    27    27
browser |    27  100.0%         11     +  85181115  85181141              DQ715339     1    27    27
browser |    27  100.0%         11     -  86738820  86738846              DQ715339     1    27    27
browser |    27  100.0%         11     +  88806502  88806528              DQ715339     1    27    27
browser |    27  100.0%         11     -  90794897  90794923              DQ715339     1    27    27
browser |    27  100.0%         11     +  90855719  90855745              DQ715339     1    27    27
browser |    27  100.0%         11     -  91992267  91992293              DQ715339     1    27    27
browser |    27  100.0%         11     -  98506471  98506497              DQ715339     1    27    27
browser |    27  100.0%         11     +  99605665  99605691              DQ715339     1    27    27
browser |    27  100.0%         11     - 100556127 100556153              DQ715339     1    27    27
browser |    27  100.0%         11     + 106186046 106186072              DQ715339     1    27    27
browser |    27  100.0%         11     - 111075713 111075739              DQ715339     1    27    27
browser |    27  100.0%         11     + 111111191 111111217              DQ715339     1    27    27
browser |    26  100.0%         11     - 113805403 113805428              DQ715339     2    27    27
browser |    27  100.0%         11     + 115650445 115650471              DQ715339     1    27    27
browser |    27  100.0%         11     - 116678770 116678796              DQ715339     1    27    27
browser |    27  100.0%         11     - 117393065 117393091              DQ715339     1    27    27
browser |    27  100.0%         11     - 120214364 120214390              DQ715339     1    27    27
browser |    27  100.0%         11     - 120963116 120963142              DQ715339     1    27    27
browser |    27  100.0%         12     -   3054751   3054777              DQ715339     1    27    27
browser |    27  100.0%         12     +   3085884   3085910              DQ715339     1    27    27
browser |    27  100.0%         12     +   3385528   3385554              DQ715339     1    27    27
browser |    27  100.0%         12     -   6568919   6568945              DQ715339     1    27    27
browser |    27  100.0%         12     -   6855410   6855436              DQ715339     1    27    27
browser |    27  100.0%         12     +  11158376  11158402              DQ715339     1    27    27
browser |    27  100.0%         12     +  14648877  14648903              DQ715339     1    27    27
browser |    27  100.0%         12     -  17174598  17174624              DQ715339     1    27    27
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browser |    27  100.0%         12     +  19312959  19312985              DQ715339     1    27    27
browser |    27  100.0%         12     +  19850194  19850220              DQ715339     1    27    27
browser |    27  100.0%         12     -  24447854  24447880              DQ715339     1    27    27
browser |    27  100.0%         12     +  31412867  31412893              DQ715339     1    27    27
browser |    26  100.0%         12     -  32080378  32080403              DQ715339     2    27    27
browser |    27  100.0%         12     -  40454468  40454494              DQ715339     1    27    27
browser |    26  100.0%         12     -  41415885  41415910              DQ715339     2    27    27
browser |    27  100.0%         12     +  44816645  44816671              DQ715339     1    27    27
browser |    27  100.0%         12     -  48581340  48581366              DQ715339     1    27    27
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browser |    27  100.0%         12     +  61338060  61338086              DQ715339     1    27    27
browser |    27  100.0%         12     -  62583997  62584023              DQ715339     1    27    27
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browser |    27  100.0%         12     -  65682431  65682457              DQ715339     1    27    27
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browser |    27  100.0%         12     +  66458521  66458547              DQ715339     1    27    27
browser |    27  100.0%         12     +  68673274  68673300              DQ715339     1    27    27
browser |    26  100.0%         12     -  76793747  76793772              DQ715339     2    27    27
browser |    26  100.0%         12     -  80466447  80466472              DQ715339     2    27    27
browser |    27  100.0%         12     +  85452515  85452541              DQ715339     1    27    27
browser |    27  100.0%         12     -  93478709  93478735              DQ715339     1    27    27
browser |    27  100.0%         12     +  94239524  94239550              DQ715339     1    27    27
browser |    27  100.0%         12     +  96198925  96198951              DQ715339     1    27    27
browser |    27  100.0%         12     -  98323870  98323896              DQ715339     1    27    27
browser |    27  100.0%         12     + 105271201 105271227              DQ715339     1    27    27
browser |    27  100.0%         12     - 109870731 109870757              DQ715339     1    27    27
browser |    27  100.0%         12     - 114599421 114599447              DQ715339     1    27    27
browser |    27  100.0%         12     - 115524229 115524255              DQ715339     1    27    27
browser |    27  100.0%         12     - 119556903 119556929              DQ715339     1    27    27
browser |    27  100.0%         13     -   3666728   3666754              DQ715339     1    27    27
browser |    27  100.0%         13     -   4390828   4390854              DQ715339     1    27    27
browser |    27  100.0%         13     -   5330407   5330433              DQ715339     1    27    27
browser |    27  100.0%         13     +   7327181   7327207              DQ715339     1    27    27
browser |    27  100.0%         13     -  11518340  11518366              DQ715339     1    27    27
browser |    27  100.0%         13     -  15608525  15608551              DQ715339     1    27    27
browser |    27  100.0%         13     +  19182755  19182781              DQ715339     1    27    27
browser |    27  100.0%         13     +  21818698  21818724              DQ715339     1    27    27
browser |    27  100.0%         13     -  22301543  22301569              DQ715339     1    27    27
browser |    27  100.0%         13     +  22414589  22414615              DQ715339     1    27    27
browser |    27  100.0%         13     +  23827653  23827679              DQ715339     1    27    27
browser |    27  100.0%         13     -  26553513  26553539              DQ715339     1    27    27
browser |    27  100.0%         13     +  30068279  30068305              DQ715339     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