DQ705661
 

Information on mRNA DQ705661

Description: Mus musculus piRNA piR-120983, 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: DQ705661
Position: chr12:56798428-56798455

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 |    28  100.0%         12     +  56798428  56798455              DQ705661     1    28    28
browser |    27  100.0%          1     +   4629732   4629758              DQ705661     2    28    28
browser |    28  100.0%          1     -   8064434   8064461              DQ705661     1    28    28
browser |    28  100.0%          1     +   8732180   8732207              DQ705661     1    28    28
browser |    28  100.0%          1     +  10806671  10806698              DQ705661     1    28    28
browser |    28  100.0%          1     -  16809002  16809029              DQ705661     1    28    28
browser |    28  100.0%          1     -  18587599  18587626              DQ705661     1    28    28
browser |    28  100.0%          1     -  19693210  19693237              DQ705661     1    28    28
browser |    28  100.0%          1     -  21652534  21652561              DQ705661     1    28    28
browser |    28  100.0%          1     +  26514760  26514787              DQ705661     1    28    28
browser |    28  100.0%          1     -  27219751  27219778              DQ705661     1    28    28
browser |    28  100.0%          1     +  29987860  29987887              DQ705661     1    28    28
browser |    28  100.0%          1     -  34387057  34387084              DQ705661     1    28    28
browser |    28  100.0%          1     -  35828104  35828131              DQ705661     1    28    28
browser |    28  100.0%          1     +  47266589  47266616              DQ705661     1    28    28
browser |    28  100.0%          1     +  53173381  53173408              DQ705661     1    28    28
browser |    28  100.0%          1     -  55818057  55818084              DQ705661     1    28    28
browser |    28  100.0%          1     -  56811911  56811938              DQ705661     1    28    28
browser |    28  100.0%          1     +  58369068  58369095              DQ705661     1    28    28
browser |    28  100.0%          1     +  60770574  60770601              DQ705661     1    28    28
browser |    28  100.0%          1     +  65006000  65006027              DQ705661     1    28    28
browser |    28  100.0%          1     +  66063451  66063478              DQ705661     1    28    28
browser |    28  100.0%          1     +  67797166  67797193              DQ705661     1    28    28
browser |    28  100.0%          1     -  70276760  70276787              DQ705661     1    28    28
browser |    28  100.0%          1     +  81548416  81548443              DQ705661     1    28    28
browser |    28  100.0%          1     -  82479264  82479291              DQ705661     1    28    28
browser |    28  100.0%          1     +  84977754  84977781              DQ705661     1    28    28
browser |    28  100.0%          1     +  87068009  87068036              DQ705661     1    28    28
browser |    28  100.0%          1     -  89127350  89127377              DQ705661     1    28    28
browser |    28  100.0%          1     +  91405504  91405531              DQ705661     1    28    28
browser |    28  100.0%          1     -  97100947  97100974              DQ705661     1    28    28
browser |    28  100.0%          1     - 102959927 102959954              DQ705661     1    28    28
browser |    28  100.0%          1     + 103139450 103139477              DQ705661     1    28    28
browser |    28  100.0%          1     - 104292764 104292791              DQ705661     1    28    28
browser |    28  100.0%          1     - 109541672 109541699              DQ705661     1    28    28
browser |    28  100.0%          1     - 111631574 111631601              DQ705661     1    28    28
browser |    28  100.0%          1     - 112857629 112857656              DQ705661     1    28    28
browser |    28  100.0%          1     + 116582564 116582591              DQ705661     1    28    28
browser |    28  100.0%          1     + 125277533 125277560              DQ705661     1    28    28
browser |    28  100.0%          1     - 126352316 126352343              DQ705661     1    28    28
browser |    28  100.0%          1     + 127492660 127492687              DQ705661     1    28    28
browser |    28  100.0%          1     + 127809378 127809405              DQ705661     1    28    28
browser |    28  100.0%          1     - 130462546 130462573              DQ705661     1    28    28
browser |    28  100.0%          1     + 137205476 137205503              DQ705661     1    28    28
browser |    28  100.0%          1     + 141301245 141301272              DQ705661     1    28    28
browser |    28  100.0%          1     + 142288414 142288441              DQ705661     1    28    28
browser |    28  100.0%          1     - 145997226 145997253              DQ705661     1    28    28
browser |    28  100.0%          1     + 146164233 146164260              DQ705661     1    28    28
browser |    28  100.0%          1     + 146279479 146279506              DQ705661     1    28    28
browser |    28  100.0%          1     - 148150550 148150577              DQ705661     1    28    28
browser |    28  100.0%          1     - 148361812 148361839              DQ705661     1    28    28
browser |    28  100.0%          1     - 149269549 149269576              DQ705661     1    28    28
browser |    28  100.0%          1     - 149457796 149457823              DQ705661     1    28    28
browser |    28  100.0%          1     + 154781281 154781308              DQ705661     1    28    28
browser |    28  100.0%          1     + 159803866 159803893              DQ705661     1    28    28
browser |    28  100.0%          1     + 163299641 163299668              DQ705661     1    28    28
browser |    27  100.0%          1     + 166596845 166596871              DQ705661     2    28    28
browser |    28  100.0%          1     - 169943870 169943897              DQ705661     1    28    28
browser |    28  100.0%          1     + 176377198 176377225              DQ705661     1    28    28
browser |    28  100.0%          1     + 181097625 181097652              DQ705661     1    28    28
browser |    28  100.0%          1     - 181320977 181321004              DQ705661     1    28    28
browser |    28  100.0%         10     -   8475519   8475546              DQ705661     1    28    28
browser |    27  100.0%         10     -   9723339   9723365              DQ705661     2    28    28
browser |    28  100.0%         10     +  19421223  19421250              DQ705661     1    28    28
browser |    28  100.0%         10     +  21524751  21524778              DQ705661     1    28    28
browser |    28  100.0%         10     +  22565694  22565721              DQ705661     1    28    28
browser |    28  100.0%         10     +  24981881  24981908              DQ705661     1    28    28
browser |    28  100.0%         10     -  32813277  32813304              DQ705661     1    28    28
browser |    28  100.0%         10     +  34624376  34624403              DQ705661     1    28    28
browser |    28  100.0%         10     -  41717031  41717058              DQ705661     1    28    28
browser |    28  100.0%         10     -  56597394  56597421              DQ705661     1    28    28
browser |    28  100.0%         10     +  78658355  78658382              DQ705661     1    28    28
browser |    28  100.0%         10     +  83513315  83513342              DQ705661     1    28    28
browser |    28  100.0%         10     +  94204580  94204607              DQ705661     1    28    28
browser |    28  100.0%         10     +  96035019  96035046              DQ705661     1    28    28
browser |    28  100.0%         10     - 104391654 104391681              DQ705661     1    28    28
browser |    28  100.0%         10     - 104671976 104672003              DQ705661     1    28    28
browser |    28  100.0%         10     - 105013486 105013513              DQ705661     1    28    28
browser |    28  100.0%         10     - 107835914 107835941              DQ705661     1    28    28
browser |    28  100.0%         10     + 109157645 109157672              DQ705661     1    28    28
browser |    28  100.0%         10     + 113565153 113565180              DQ705661     1    28    28
browser |    28  100.0%         10     + 116448720 116448747              DQ705661     1    28    28
browser |    28  100.0%         10     - 121001157 121001184              DQ705661     1    28    28
browser |    28  100.0%         10     + 122206350 122206377              DQ705661     1    28    28
browser |    28  100.0%         10     + 122675245 122675272              DQ705661     1    28    28
browser |    28  100.0%         10     + 124521421 124521448              DQ705661     1    28    28
browser |    27  100.0%         10     + 129231375 129231401              DQ705661     2    28    28
browser |    27  100.0%         10     + 130401455 130401481              DQ705661     2    28    28
browser |    28  100.0%         11     +   9664523   9664550              DQ705661     1    28    28
browser |    28  100.0%         11     -  15178252  15178279              DQ705661     1    28    28
browser |    28  100.0%         11     -  15834197  15834224              DQ705661     1    28    28
browser |    28  100.0%         11     -  16179071  16179098              DQ705661     1    28    28
browser |    28  100.0%         11     -  20466947  20466974              DQ705661     1    28    28
browser |    28  100.0%         11     -  22528337  22528364              DQ705661     1    28    28
browser |    28  100.0%         11     +  23175129  23175156              DQ705661     1    28    28
browser |    28  100.0%         11     +  27906494  27906521              DQ705661     1    28    28
browser |    28  100.0%         11     -  38372866  38372893              DQ705661     1    28    28
browser |    28  100.0%         11     +  39961119  39961146              DQ705661     1    28    28
browser |    28  100.0%         11     -  51329061  51329088              DQ705661     1    28    28
browser |    28  100.0%         11     +  55138294  55138321              DQ705661     1    28    28
browser |    28  100.0%         11     -  63359121  63359148              DQ705661     1    28    28
browser |    28  100.0%         11     -  64683559  64683586              DQ705661     1    28    28
browser |    28  100.0%         11     +  66844636  66844663              DQ705661     1    28    28
browser |    28  100.0%         11     +  70934849  70934876              DQ705661     1    28    28
browser |    28  100.0%         11     -  81436935  81436962              DQ705661     1    28    28
browser |    28  100.0%         11     +  82228625  82228652              DQ705661     1    28    28
browser |    28  100.0%         11     -  90793072  90793099              DQ705661     1    28    28
browser |    28  100.0%         11     -  98504625  98504652              DQ705661     1    28    28
browser |    28  100.0%         11     +  99607510  99607537              DQ705661     1    28    28
browser |    28  100.0%         11     + 106187879 106187906              DQ705661     1    28    28
browser |    28  100.0%         11     - 111073840 111073867              DQ705661     1    28    28
browser |    28  100.0%         11     - 116676954 116676981              DQ705661     1    28    28
browser |    28  100.0%         12     -   3052844   3052871              DQ705661     1    28    28
browser |    28  100.0%         12     +   3087581   3087608              DQ705661     1    28    28
browser |    28  100.0%         12     +   3387406   3387433              DQ705661     1    28    28
browser |    28  100.0%         12     -   6567007   6567034              DQ705661     1    28    28
browser |    28  100.0%         12     -   6853525   6853552              DQ705661     1    28    28
browser |    28  100.0%         12     +  11160191  11160218              DQ705661     1    28    28
browser |    28  100.0%         12     -  17172689  17172716              DQ705661     1    28    28
browser |    28  100.0%         12     +  31414679  31414706              DQ705661     1    28    28
browser |    28  100.0%         12     -  32078556  32078583              DQ705661     1    28    28
browser |    28  100.0%         12     -  40452595  40452622              DQ705661     1    28    28
browser |    28  100.0%         12     -  41414064  41414091              DQ705661     1    28    28
browser |    28  100.0%         12     -  48579515  48579542              DQ705661     1    28    28
browser |    28  100.0%         12     -  49042077  49042104              DQ705661     1    28    28
browser |    28  100.0%         12     +  61339960  61339987              DQ705661     1    28    28
browser |    28  100.0%         12     -  62582166  62582193              DQ705661     1    28    28
browser |    28  100.0%         12     -  65680486  65680513              DQ705661     1    28    28
browser |    28  100.0%         12     +  65854566  65854593              DQ705661     1    28    28
browser |    28  100.0%         12     +  68675101  68675128              DQ705661     1    28    28
browser |    28  100.0%         12     -  76791925  76791952              DQ705661     1    28    28
browser |    28  100.0%         12     -  90734344  90734371              DQ705661     1    28    28
browser |    28  100.0%         12     +  94241366  94241393              DQ705661     1    28    28
browser |    28  100.0%         12     +  96200731  96200758              DQ705661     1    28    28
browser |    28  100.0%         12     -  98322024  98322051              DQ705661     1    28    28
browser |    28  100.0%         12     - 111355175 111355202              DQ705661     1    28    28
browser |    28  100.0%         12     - 119554991 119555018              DQ705661     1    28    28
browser |    28  100.0%         13     -   4388982   4389009              DQ705661     1    28    28
browser |    27  100.0%         13     +   4513985   4514011              DQ705661     2    28    28
browser |    28  100.0%         13     -   5328594   5328621              DQ705661     1    28    28
browser |    28  100.0%         13     +   9489225   9489252              DQ705661     1    28    28
browser |    28  100.0%         13     +  21820534  21820561              DQ705661     1    28    28
browser |    28  100.0%         13     +  22416434  22416461              DQ705661     1    28    28
browser |    28  100.0%         13     +  23829558  23829585              DQ705661     1    28    28
browser |    28  100.0%         13     +  30070211  30070238              DQ705661     1    28    28
browser |    28  100.0%         13     +  31781138  31781165              DQ705661     1    28    28
browser |    28  100.0%         13     -  32534977  32535004              DQ705661     1    28    28
browser |    28  100.0%         13     +  33126740  33126767              DQ705661     1    28    28
browser |    28  100.0%         13     +  33138098  33138125              DQ705661     1    28    28
browser |    28  100.0%         13     -  33622152  33622179              DQ705661     1    28    28
browser |    28  100.0%         13     -  34046535  34046562              DQ705661     1    28    28
browser |    28  100.0%         13     -  43431540  43431567              DQ705661     1    28    28
browser |    28  100.0%         13     -  43540774  43540801              DQ705661     1    28    28
browser |    28  100.0%         13     -  45165147  45165174              DQ705661     1    28    28
browser |    28  100.0%         13     +  46536205  46536232              DQ705661     1    28    28
browser |    28  100.0%         13     +  51424416  51424443              DQ705661     1    28    28
browser |    28  100.0%         13     +  52542690  52542717              DQ705661     1    28    28
browser |    28  100.0%         13     -  55927379  55927406              DQ705661     1    28    28
browser |    28  100.0%         13     +  60175985  60176012              DQ705661     1    28    28
browser |    27  100.0%         13     +  60351115  60351141              DQ705661     2    28    28
browser |    28  100.0%         13     +  62627389  62627416              DQ705661     1    28    28
browser |    28  100.0%         13     +  63311006  63311033              DQ705661     1    28    28
browser |    27  100.0%         13     -  65026441  65026467              DQ705661     2    28    28
browser |    28  100.0%         13     -  66160615  66160642              DQ705661     1    28    28
browser |    28  100.0%         13     -  66377542  66377569              DQ705661     1    28    28
browser |    28  100.0%         13     -  82039615  82039642              DQ705661     1    28    28
browser |    28  100.0%         13     -  83567665  83567692              DQ705661     1    28    28
browser |    28  100.0%         13     -  85747532  85747559              DQ705661     1    28    28
browser |    28  100.0%         13     -  86861471  86861498              DQ705661     1    28    28
browser |    28  100.0%         13     +  87218603  87218630              DQ705661     1    28    28
browser |    25  100.0%         13     +  87322053  87322077              DQ705661     1    25    28
browser |    28  100.0%         13     -  87704934  87704961              DQ705661     1    28    28
browser |    28  100.0%         13     -  94872502  94872529              DQ705661     1    28    28
browser |    27  100.0%         13     -  98219880  98219906              DQ705661     2    28    28
browser |    28  100.0%         13     +  98466364  98466391              DQ705661     1    28    28
browser |    28  100.0%         13     - 104067177 104067204              DQ705661     1    28    28
browser |    28  100.0%         13     - 111636912 111636939              DQ705661     1    28    28
browser |    28  100.0%         13     - 116102246 116102273              DQ705661     1    28    28
browser |    28  100.0%         13     + 116721196 116721223              DQ705661     1    28    28
browser |    28  100.0%         13     + 119271409 119271436              DQ705661     1    28    28
browser |    28  100.0%         14     -   3603624   3603651              DQ705661     1    28    28
browser |    27  100.0%         14     +   6651799   6651825              DQ705661     2    28    28
browser |    28  100.0%         14     +   8136098   8136125              DQ705661     1    28    28
browser |    28  100.0%         14     -  12284431  12284458              DQ705661     1    28    28
browser |    28  100.0%         14     -  13338745  13338772              DQ705661     1    28    28
browser |    28  100.0%         14     +  13424263  13424290              DQ705661     1    28    28
browser |    27  100.0%         14     -  14768069  14768095              DQ705661     2    28    28
browser |    28  100.0%         14     -  14876292  14876319              DQ705661     1    28    28
browser |    28  100.0%         14     -  19591772  19591799              DQ705661     1    28    28
browser |    28  100.0%         14     -  20330499  20330526              DQ705661     1    28    28
browser |    28  100.0%         14     +  24433594  24433621              DQ705661     1    28    28
browser |    28  100.0%         14     +  32121768  32121795              DQ705661     1    28    28
browser |    28  100.0%         14     +  34110365  34110392              DQ705661     1    28    28
browser |    28  100.0%         14     -  35614382  35614409              DQ705661     1    28    28
browser |    28  100.0%         14     -  35921217  35921244              DQ705661     1    28    28
browser |    28  100.0%         14     -  39453997  39454024              DQ705661     1    28    28
browser |    28  100.0%         14     -  51118172  51118199              DQ705661     1    28    28
browser |    28  100.0%         14     +  53716601  53716628              DQ705661     1    28    28
browser |    28  100.0%         14     -  58290566  58290593              DQ705661     1    28    28
browser |    27  100.0%         14     +  63886435  63886461              DQ705661     2    28    28
browser |    28  100.0%         14     +  68250863  68250890              DQ705661     1    28    28
browser |    28  100.0%         14     +  68919959  68919986              DQ705661     1    28    28
browser |    28  100.0%         14     -  71359159  71359186              DQ705661     1    28    28
browser |    28  100.0%         14     -  75663266  75663293              DQ705661     1    28    28
browser |    28  100.0%         14     +  80036748  80036775              DQ705661     1    28    28
browser |    28  100.0%         14     +  85762415  85762442              DQ705661     1    28    28
browser |    28  100.0%         14     -  86127071  86127098              DQ705661     1    28    28
browser |    28  100.0%         14     -  86828462  86828489              DQ705661     1    28    28
browser |    27  100.0%         14     +  88277695  88277721              DQ705661     2    28    28
browser |    28  100.0%         14     -  96521864  96521891              DQ705661     1    28    28
browser |    28  100.0%         14     + 104348859 104348886              DQ705661     1    28    28
browser |    28  100.0%         14     + 105451118 105451145              DQ705661     1    28    28
browser |    28  100.0%         14     - 106209044 106209071              DQ705661     1    28    28
browser |    28  100.0%         14     + 110599881 110599908              DQ705661     1    28    28
browser |    28  100.0%         14     + 112871724 112871751              DQ705661     1    28    28
browser |    28  100.0%         14     - 113256471 113256498              DQ705661     1    28    28
browser |    28  100.0%         14     + 114447688 114447715              DQ705661     1    28    28
browser |    28  100.0%         14     - 114743755 114743782              DQ705661     1    28    28
browser |    27  100.0%         14     + 118100207 118100233              DQ705661     2    28    28
browser |    28  100.0%         14     + 119720423 119720450              DQ705661     1    28    28
browser |    28  100.0%         14     - 123962377 123962404              DQ705661     1    28    28
browser |    28  100.0%         15     +   4888110   4888137              DQ705661     1    28    28
browser |    28  100.0%         15     -   5408304   5408331              DQ705661     1    28    28
browser |    28  100.0%         15     +  17163525  17163552              DQ705661     1    28    28
browser |    28  100.0%         15     +  23247005  23247032              DQ705661     1    28    28
browser |    28  100.0%         15     -  25052062  25052089              DQ705661     1    28    28
browser |    28  100.0%         15     -  38479556  38479583              DQ705661     1    28    28
browser |    28  100.0%         15     -  43194632  43194659              DQ705661     1    28    28
browser |    28  100.0%         15     -  44587021  44587048              DQ705661     1    28    28
browser |    28  100.0%         15     -  46767371  46767398              DQ705661     1    28    28
browser |    28  100.0%         15     -  60673474  60673501              DQ705661     1    28    28
browser |    28  100.0%         15     -  65539040  65539067              DQ705661     1    28    28
browser |    28  100.0%         15     +  71108886  71108913              DQ705661     1    28    28
browser |    28  100.0%         15     +  72959256  72959283              DQ705661     1    28    28
browser |    25  100.0%         15     +  92515468  92515492              DQ705661     1    25    28
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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