DQ689735
 

Information on mRNA DQ689735

Description: Mus musculus piRNA piR-105057, 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: DQ689735
Position: chr12:56795000-56795028

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 |    29  100.0%         12     -  56795000  56795028              DQ689735     1    29    29
browser |    29  100.0%          1     -   4627700   4627728              DQ689735     1    29    29
browser |    29  100.0%          1     -   5874933   5874961              DQ689735     1    29    29
browser |    29  100.0%          1     +   6242634   6242662              DQ689735     1    29    29
browser |    29  100.0%          1     -   6500963   6500991              DQ689735     1    29    29
browser |    29  100.0%          1     +   8070649   8070677              DQ689735     1    29    29
browser |    29  100.0%          1     +   8233084   8233112              DQ689735     1    29    29
browser |    29  100.0%          1     -  10800459  10800487              DQ689735     1    29    29
browser |    29  100.0%          1     -  11957712  11957740              DQ689735     1    29    29
browser |    29  100.0%          1     +  16815162  16815190              DQ689735     1    29    29
browser |    29  100.0%          1     +  18033750  18033778              DQ689735     1    29    29
browser |    29  100.0%          1     +  18591035  18591063              DQ689735     1    29    29
browser |    29  100.0%          1     +  19699375  19699403              DQ689735     1    29    29
browser |    29  100.0%          1     +  21654742  21654770              DQ689735     1    29    29
browser |    29  100.0%          1     +  23345037  23345065              DQ689735     1    29    29
browser |    29  100.0%          1     -  26388625  26388653              DQ689735     1    29    29
browser |    29  100.0%          1     +  26459777  26459805              DQ689735     1    29    29
browser |    29  100.0%          1     -  26509819  26509847              DQ689735     1    29    29
browser |    29  100.0%          1     +  27225925  27225953              DQ689735     1    29    29
browser |    29  100.0%          1     -  29982178  29982206              DQ689735     1    29    29
browser |    29  100.0%          1     +  34390048  34390076              DQ689735     1    29    29
browser |    29  100.0%          1     +  34957875  34957903              DQ689735     1    29    29
browser |    29  100.0%          1     +  35834261  35834289              DQ689735     1    29    29
browser |    29  100.0%          1     +  37817303  37817331              DQ689735     1    29    29
browser |    29  100.0%          1     +  38747636  38747664              DQ689735     1    29    29
browser |    29  100.0%          1     -  48841393  48841421              DQ689735     1    29    29
browser |    29  100.0%          1     -  53169157  53169185              DQ689735     1    29    29
browser |    29  100.0%          1     -  58362896  58362924              DQ689735     1    29    29
browser |    29  100.0%          1     -  58851205  58851233              DQ689735     1    29    29
browser |    29  100.0%          1     -  60764383  60764411              DQ689735     1    29    29
browser |    29  100.0%          1     -  62573652  62573680              DQ689735     1    29    29
browser |    29  100.0%          1     -  64217718  64217746              DQ689735     1    29    29
browser |    29  100.0%          1     -  64999846  64999874              DQ689735     1    29    29
browser |    29  100.0%          1     -  81542259  81542287              DQ689735     1    29    29
browser |    29  100.0%          1     +  82483323  82483351              DQ689735     1    29    29
browser |    29  100.0%          1     -  84973977  84974005              DQ689735     1    29    29
browser |    29  100.0%          1     +  87394582  87394610              DQ689735     1    29    29
browser |    29  100.0%          1     +  89130544  89130572              DQ689735     1    29    29
browser |    29  100.0%          1     -  91399316  91399344              DQ689735     1    29    29
browser |    29  100.0%          1     -  93035583  93035611              DQ689735     1    29    29
browser |    29  100.0%          1     +  93888631  93888659              DQ689735     1    29    29
browser |    29  100.0%          1     +  97108551  97108579              DQ689735     1    29    29
browser |    29  100.0%          1     - 101906251 101906279              DQ689735     1    29    29
browser |    29  100.0%          1     + 102966099 102966127              DQ689735     1    29    29
browser |    29  100.0%          1     - 103133284 103133312              DQ689735     1    29    29
browser |    29  100.0%          1     + 103521357 103521385              DQ689735     1    29    29
browser |    29  100.0%          1     - 104217674 104217702              DQ689735     1    29    29
browser |    29  100.0%          1     - 107966906 107966934              DQ689735     1    29    29
browser |    29  100.0%          1     - 108336971 108336999              DQ689735     1    29    29
browser |    29  100.0%          1     - 109056780 109056808              DQ689735     1    29    29
browser |    29  100.0%          1     + 109547831 109547859              DQ689735     1    29    29
browser |    29  100.0%          1     + 110261603 110261631              DQ689735     1    29    29
browser |    29  100.0%          1     - 110865713 110865741              DQ689735     1    29    29
browser |    29  100.0%          1     - 111181738 111181766              DQ689735     1    29    29
browser |    29  100.0%          1     + 111637795 111637823              DQ689735     1    29    29
browser |    29  100.0%          1     + 112862795 112862823              DQ689735     1    29    29
browser |    29  100.0%          1     + 112950510 112950538              DQ689735     1    29    29
browser |    29  100.0%          1     + 114117819 114117847              DQ689735     1    29    29
browser |    29  100.0%          1     - 115813479 115813507              DQ689735     1    29    29
browser |    29  100.0%          1     - 116576382 116576410              DQ689735     1    29    29
browser |    29  100.0%          1     - 117630040 117630068              DQ689735     1    29    29
browser |    29  100.0%          1     - 120498960 120498988              DQ689735     1    29    29
browser |    29  100.0%          1     + 125251294 125251322              DQ689735     1    29    29
browser |    29  100.0%          1     + 126356995 126357023              DQ689735     1    29    29
browser |    29  100.0%          1     + 126871715 126871743              DQ689735     1    29    29
browser |    29  100.0%          1     - 159797714 159797742              DQ689735     1    29    29
browser |    29  100.0%          1     - 160643827 160643855              DQ689735     1    29    29
browser |    29  100.0%          1     + 162674823 162674851              DQ689735     1    29    29
browser |    29  100.0%          1     - 163296443 163296471              DQ689735     1    29    29
browser |    29  100.0%          1     - 166591086 166591114              DQ689735     1    29    29
browser |    29  100.0%          1     + 169376073 169376101              DQ689735     1    29    29
browser |    29  100.0%          1     + 169950064 169950092              DQ689735     1    29    29
browser |    29  100.0%          1     - 174869926 174869954              DQ689735     1    29    29
browser |    29  100.0%          1     - 176371008 176371036              DQ689735     1    29    29
browser |    29  100.0%          1     + 177892292 177892320              DQ689735     1    29    29
browser |    29  100.0%          1     + 178008381 178008409              DQ689735     1    29    29
browser |    29  100.0%          1     + 180443568 180443596              DQ689735     1    29    29
browser |    29  100.0%          1     - 181091464 181091492              DQ689735     1    29    29
browser |    29  100.0%          1     + 181326661 181326689              DQ689735     1    29    29
browser |    29  100.0%          1     + 191844484 191844512              DQ689735     1    29    29
browser |    29  100.0%          1     + 195009349 195009377              DQ689735     1    29    29
browser |    29  100.0%         10     -   3266723   3266751              DQ689735     1    29    29
browser |    29  100.0%         10     -   3551303   3551331              DQ689735     1    29    29
browser |    29  100.0%         10     +   8481741   8481769              DQ689735     1    29    29
browser |    29  100.0%         10     +   9727124   9727152              DQ689735     1    29    29
browser |    29  100.0%         10     +  11576719  11576747              DQ689735     1    29    29
browser |    29  100.0%         10     -  19415018  19415046              DQ689735     1    29    29
browser |    29  100.0%         10     +  21092055  21092083              DQ689735     1    29    29
browser |    29  100.0%         10     -  21518591  21518619              DQ689735     1    29    29
browser |    29  100.0%         10     -  22559537  22559565              DQ689735     1    29    29
browser |    29  100.0%         10     -  23747604  23747632              DQ689735     1    29    29
browser |    29  100.0%         10     +  24567079  24567107              DQ689735     1    29    29
browser |    29  100.0%         10     -  24977822  24977850              DQ689735     1    29    29
browser |    29  100.0%         10     +  25848797  25848825              DQ689735     1    29    29
browser |    29  100.0%         10     +  30696692  30696720              DQ689735     1    29    29
browser |    29  100.0%         10     +  30971374  30971402              DQ689735     1    29    29
browser |    29  100.0%         10     +  31365324  31365352              DQ689735     1    29    29
browser |    29  100.0%         10     +  31630467  31630495              DQ689735     1    29    29
browser |    29  100.0%         10     +  32814756  32814784              DQ689735     1    29    29
browser |    29  100.0%         10     +  33766639  33766667              DQ689735     1    29    29
browser |    29  100.0%         10     -  34618195  34618223              DQ689735     1    29    29
browser |    29  100.0%         10     +  41723245  41723273              DQ689735     1    29    29
browser |    29  100.0%         10     -  45431373  45431401              DQ689735     1    29    29
browser |    29  100.0%         10     +  50371166  50371194              DQ689735     1    29    29
browser |    29  100.0%         10     +  51763616  51763644              DQ689735     1    29    29
browser |    29  100.0%         10     +  54469203  54469231              DQ689735     1    29    29
browser |    29  100.0%         10     -  55592005  55592033              DQ689735     1    29    29
browser |    29  100.0%         10     -  65475071  65475099              DQ689735     1    29    29
browser |    29  100.0%         10     -  65786970  65786998              DQ689735     1    29    29
browser |    29  100.0%         10     -  66558621  66558649              DQ689735     1    29    29
browser |    29  100.0%         10     -  75216822  75216850              DQ689735     1    29    29
browser |    29  100.0%         10     -  78652664  78652692              DQ689735     1    29    29
browser |    29  100.0%         10     +  80816285  80816313              DQ689735     1    29    29
browser |    29  100.0%         10     +  81810434  81810462              DQ689735     1    29    29
browser |    29  100.0%         10     -  83507158  83507186              DQ689735     1    29    29
browser |    29  100.0%         10     +  83628060  83628088              DQ689735     1    29    29
browser |    29  100.0%         10     +  84585351  84585379              DQ689735     1    29    29
browser |    29  100.0%         10     +  85556153  85556181              DQ689735     1    29    29
browser |    29  100.0%         10     -  85604669  85604697              DQ689735     1    29    29
browser |    29  100.0%         10     +  88493527  88493555              DQ689735     1    29    29
browser |    29  100.0%         10     -  90160848  90160876              DQ689735     1    29    29
browser |    29  100.0%         10     -  94198809  94198837              DQ689735     1    29    29
browser |    29  100.0%         10     -  95993480  95993508              DQ689735     1    29    29
browser |    29  100.0%         10     -  96028771  96028799              DQ689735     1    29    29
browser |    29  100.0%         10     -  97156806  97156834              DQ689735     1    29    29
browser |    29  100.0%         10     -  98934431  98934459              DQ689735     1    29    29
browser |    29  100.0%         10     +  99181694  99181722              DQ689735     1    29    29
browser |    29  100.0%         10     + 100419218 100419246              DQ689735     1    29    29
browser |    29  100.0%         10     + 104397916 104397944              DQ689735     1    29    29
browser |    29  100.0%         10     - 104655724 104655752              DQ689735     1    29    29
browser |    29  100.0%         10     + 104678143 104678171              DQ689735     1    29    29
browser |    29  100.0%         10     + 105017268 105017296              DQ689735     1    29    29
browser |    29  100.0%         10     - 105508889 105508917              DQ689735     1    29    29
browser |    29  100.0%         10     + 107842070 107842098              DQ689735     1    29    29
browser |    29  100.0%         10     - 109151450 109151478              DQ689735     1    29    29
browser |    29  100.0%         10     + 111893866 111893894              DQ689735     1    29    29
browser |    29  100.0%         10     - 113558987 113559015              DQ689735     1    29    29
browser |    29  100.0%         10     - 116442539 116442567              DQ689735     1    29    29
browser |    29  100.0%         10     + 117911986 117912014              DQ689735     1    29    29
browser |    29  100.0%         10     + 121004777 121004805              DQ689735     1    29    29
browser |    29  100.0%         10     - 122139914 122139942              DQ689735     1    29    29
browser |    29  100.0%         10     - 122202342 122202370              DQ689735     1    29    29
browser |    29  100.0%         10     - 122669148 122669176              DQ689735     1    29    29
browser |    29  100.0%         10     + 124418938 124418966              DQ689735     1    29    29
browser |    29  100.0%         11     +   5312564   5312592              DQ689735     1    29    29
browser |    29  100.0%         11     -   9658359   9658387              DQ689735     1    29    29
browser |    29  100.0%         11     +  10717031  10717059              DQ689735     1    29    29
browser |    29  100.0%         11     -  12457668  12457696              DQ689735     1    29    29
browser |    29  100.0%         11     +  12518642  12518670              DQ689735     1    29    29
browser |    29  100.0%         11     -  12904395  12904423              DQ689735     1    29    29
browser |    29  100.0%         11     +  15184417  15184445              DQ689735     1    29    29
browser |    29  100.0%         11     +  15837415  15837443              DQ689735     1    29    29
browser |    29  100.0%         11     +  16182259  16182287              DQ689735     1    29    29
browser |    29  100.0%         11     -  18756842  18756870              DQ689735     1    29    29
browser |    29  100.0%         11     -  19516555  19516583              DQ689735     1    29    29
browser |    29  100.0%         11     -  19739111  19739139              DQ689735     1    29    29
browser |    29  100.0%         11     +  20470757  20470785              DQ689735     1    29    29
browser |    29  100.0%         11     -  22285632  22285660              DQ689735     1    29    29
browser |    29  100.0%         11     +  22532602  22532630              DQ689735     1    29    29
browser |    29  100.0%         11     -  23168956  23168984              DQ689735     1    29    29
browser |    29  100.0%         11     +  26510351  26510379              DQ689735     1    29    29
browser |    29  100.0%         11     -  27901458  27901486              DQ689735     1    29    29
browser |    29  100.0%         11     +  28054017  28054045              DQ689735     1    29    29
browser |    29  100.0%         11     +  29079390  29079418              DQ689735     1    29    29
browser |    29  100.0%         11     -  31397945  31397973              DQ689735     1    29    29
browser |    29  100.0%         11     +  38377766  38377794              DQ689735     1    29    29
browser |    29  100.0%         11     +  51332480  51332508              DQ689735     1    29    29
browser |    29  100.0%         11     -  51556232  51556260              DQ689735     1    29    29
browser |    29  100.0%         11     -  54467786  54467814              DQ689735     1    29    29
browser |    29  100.0%         11     -  55132142  55132170              DQ689735     1    29    29
browser |    29  100.0%         11     +  61317988  61318016              DQ689735     1    29    29
browser |    29  100.0%         11     +  63365271  63365299              DQ689735     1    29    29
browser |    29  100.0%         11     +  64687800  64687828              DQ689735     1    29    29
browser |    29  100.0%         11     -  65342992  65343020              DQ689735     1    29    29
browser |    29  100.0%         11     -  66839029  66839057              DQ689735     1    29    29
browser |    29  100.0%         11     -  70931587  70931615              DQ689735     1    29    29
browser |    29  100.0%         11     +  81443086  81443114              DQ689735     1    29    29
browser |    29  100.0%         11     -  82225203  82225231              DQ689735     1    29    29
browser |    29  100.0%         11     -  85176770  85176798              DQ689735     1    29    29
browser |    29  100.0%         11     +  86740597  86740625              DQ689735     1    29    29
browser |    29  100.0%         11     -  90201586  90201614              DQ689735     1    29    29
browser |    29  100.0%         11     -  90720827  90720855              DQ689735     1    29    29
browser |    29  100.0%         11     +  90798683  90798711              DQ689735     1    29    29
browser |    29  100.0%         11     -  90851374  90851402              DQ689735     1    29    29
browser |    29  100.0%         11     +  91996611  91996639              DQ689735     1    29    29
browser |    29  100.0%         11     +  98510815  98510843              DQ689735     1    29    29
browser |    29  100.0%         11     -  99603904  99603932              DQ689735     1    29    29
browser |    29  100.0%         11     + 100559962 100559990              DQ689735     1    29    29
browser |    29  100.0%         11     - 105919461 105919489              DQ689735     1    29    29
browser |    29  100.0%         11     - 106183896 106183924              DQ689735     1    29    29
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browser |    29  100.0%         11     - 111106844 111106872              DQ689735     1    29    29
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browser |    29  100.0%         11     - 115646099 115646127              DQ689735     1    29    29
browser |    29  100.0%         11     + 116683113 116683141              DQ689735     1    29    29
browser |    29  100.0%         11     + 117395393 117395421              DQ689735     1    29    29
browser |    29  100.0%         11     + 120218702 120218730              DQ689735     1    29    29
browser |    29  100.0%         11     + 120965270 120965298              DQ689735     1    29    29
browser |    29  100.0%         12     +   3059092   3059120              DQ689735     1    29    29
browser |    29  100.0%         12     +   3112853   3112881              DQ689735     1    29    29
browser |    29  100.0%         12     -   3381181   3381209              DQ689735     1    29    29
browser |    29  100.0%         12     +   6573263   6573291              DQ689735     1    29    29
browser |    29  100.0%         12     +   8458027   8458055              DQ689735     1    29    29
browser |    29  100.0%         12     -  11154034  11154062              DQ689735     1    29    29
browser |    29  100.0%         12     +  17178941  17178969              DQ689735     1    29    29
browser |    29  100.0%         12     -  19308620  19308648              DQ689735     1    29    29
browser |    29  100.0%         12     +  24452188  24452216              DQ689735     1    29    29
browser |    29  100.0%         12     +  25644701  25644729              DQ689735     1    29    29
browser |    29  100.0%         12     -  31408530  31408558              DQ689735     1    29    29
browser |    29  100.0%         12     +  32081966  32081994              DQ689735     1    29    29
browser |    29  100.0%         12     +  32650167  32650195              DQ689735     1    29    29
browser |    29  100.0%         12     +  32956045  32956073              DQ689735     1    29    29
browser |    29  100.0%         12     +  40458813  40458841              DQ689735     1    29    29
browser |    29  100.0%         12     +  41420223  41420251              DQ689735     1    29    29
browser |    29  100.0%         12     -  44812862  44812890              DQ689735     1    29    29
browser |    29  100.0%         12     +  44831961  44831989              DQ689735     1    29    29
browser |    29  100.0%         12     +  48585684  48585712              DQ689735     1    29    29
browser |    29  100.0%         12     +  49048288  49048316              DQ689735     1    29    29
browser |    29  100.0%         12     -  52777264  52777292              DQ689735     1    29    29
browser |    29  100.0%         12     +  54407895  54407923              DQ689735     1    29    29
browser |    29  100.0%         12     -  61336280  61336308              DQ689735     1    29    29
browser |    29  100.0%         12     -  65074319  65074347              DQ689735     1    29    29
browser |    29  100.0%         12     -  65848382  65848410              DQ689735     1    29    29
browser |    29  100.0%         12     -  66454181  66454209              DQ689735     1    29    29
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browser |    29  100.0%          Y     +  81110864  81110892              DQ689735     1    29    29
browser |    29  100.0%          Y     -  82266618  82266646              DQ689735     1    29    29
browser |    29  100.0%          Y     +  84726988  84727016              DQ689735     1    29    29
browser |    29  100.0%          Y     -  85100342  85100370              DQ689735     1    29    29
browser |    29  100.0%          Y     +  87791830  87791858              DQ689735     1    29    29
browser |    29  100.0%          Y     +  88476521  88476549              DQ689735     1    29    29
browser |    29  100.0%          Y     +  89143033  89143061              DQ689735     1    29    29

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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