DQ684736
 

Information on mRNA DQ684736

Description: Mus musculus piRNA piR-100058, 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: DQ684736
Position: chr12:57084558-57084586

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     +  57084558  57084586              DQ684736     1    29    29
browser |    28  100.0%          1     +   3639822   3639849              DQ684736     2    29    29
browser |    27  100.0%          1     +  14720803  14720829              DQ684736     1    27    29
browser |    29  100.0%          1     -  17994526  17994554              DQ684736     1    29    29
browser |    26  100.0%          1     -  23977032  23977057              DQ684736     1    26    29
browser |    29  100.0%          1     +  25455485  25455513              DQ684736     1    29    29
browser |    27  100.0%          1     +  26290277  26290303              DQ684736     1    27    29
browser |    29  100.0%          1     +  26292854  26292882              DQ684736     1    29    29
browser |    29  100.0%          1     -  30341111  30341139              DQ684736     1    29    29
browser |    29  100.0%          1     -  35206862  35206890              DQ684736     1    29    29
browser |    29  100.0%          1     +  49559189  49559217              DQ684736     1    29    29
browser |    28  100.0%          1     -  62346531  62346558              DQ684736     1    28    29
browser |    29  100.0%          1     +  65762328  65762356              DQ684736     1    29    29
browser |    29  100.0%          1     -  66160263  66160291              DQ684736     1    29    29
browser |    26  100.0%          1     +  72684939  72684964              DQ684736     1    26    29
browser |    28  100.0%          1     +  75198640  75198667              DQ684736     1    28    29
browser |    29  100.0%          1     +  94534962  94534990              DQ684736     1    29    29
browser |    29  100.0%          1     -  95658287  95658315              DQ684736     1    29    29
browser |    29  100.0%          1     +  95795092  95795120              DQ684736     1    29    29
browser |    27  100.0%          1     -  96972750  96972776              DQ684736     1    27    29
browser |    29  100.0%          1     -  97229075  97229103              DQ684736     1    29    29
browser |    29  100.0%          1     +  97921094  97921122              DQ684736     1    29    29
browser |    29  100.0%          1     -  98617002  98617030              DQ684736     1    29    29
browser |    29  100.0%          1     - 101802919 101802947              DQ684736     1    29    29
browser |    29  100.0%          1     - 103696627 103696655              DQ684736     1    29    29
browser |    29  100.0%          1     + 106373623 106373651              DQ684736     1    29    29
browser |    29  100.0%          1     + 109818361 109818389              DQ684736     1    29    29
browser |    29  100.0%          1     - 111538702 111538730              DQ684736     1    29    29
browser |    28  100.0%          1     - 111897174 111897201              DQ684736     2    29    29
browser |    28  100.0%          1     - 112646000 112646027              DQ684736     1    28    29
browser |    29  100.0%          1     - 113547051 113547079              DQ684736     1    29    29
browser |    29  100.0%          1     + 114220737 114220765              DQ684736     1    29    29
browser |    29  100.0%          1     + 119509299 119509327              DQ684736     1    29    29
browser |    29  100.0%          1     + 128859796 128859824              DQ684736     1    29    29
browser |    29  100.0%          1     - 130706687 130706715              DQ684736     1    29    29
browser |    29  100.0%          1     + 138831426 138831454              DQ684736     1    29    29
browser |    29  100.0%          1     - 140381408 140381436              DQ684736     1    29    29
browser |    29  100.0%          1     - 141535334 141535362              DQ684736     1    29    29
browser |    29  100.0%          1     - 141950216 141950244              DQ684736     1    29    29
browser |    29  100.0%          1     - 145210003 145210031              DQ684736     1    29    29
browser |    29  100.0%          1     + 149337507 149337535              DQ684736     1    29    29
browser |    29  100.0%          1     + 156330496 156330524              DQ684736     1    29    29
browser |    29  100.0%          1     - 161391287 161391315              DQ684736     1    29    29
browser |    27  100.0%          1     + 168313502 168313528              DQ684736     1    27    29
browser |    29  100.0%          1     + 169369087 169369115              DQ684736     1    29    29
browser |    29  100.0%          1     + 169755119 169755147              DQ684736     1    29    29
browser |    27  100.0%          1     + 173881539 173881565              DQ684736     1    27    29
browser |    29  100.0%          1     - 179887386 179887414              DQ684736     1    29    29
browser |    29  100.0%          1     + 181773132 181773160              DQ684736     1    29    29
browser |    28  100.0%          1     + 181775918 181775945              DQ684736     1    28    29
browser |    29  100.0%          1     + 182021481 182021509              DQ684736     1    29    29
browser |    29  100.0%          1     + 182025074 182025102              DQ684736     1    29    29
browser |    29  100.0%          1     + 184580422 184580450              DQ684736     1    29    29
browser |    26  100.0%          1     + 184906938 184906963              DQ684736     4    29    29
browser |    29  100.0%          1     - 186547764 186547792              DQ684736     1    29    29
browser |    29  100.0%          1     + 194055075 194055103              DQ684736     1    29    29
browser |    27  100.0%         10     +  15702099  15702125              DQ684736     1    27    29
browser |    26  100.0%         10     -  27906672  27906697              DQ684736     1    26    29
browser |    29  100.0%         10     -  28052050  28052078              DQ684736     1    29    29
browser |    29  100.0%         10     -  28201941  28201969              DQ684736     1    29    29
browser |    29  100.0%         10     +  29781138  29781166              DQ684736     1    29    29
browser |    29  100.0%         10     +  31305521  31305549              DQ684736     1    29    29
browser |    29  100.0%         10     +  31574475  31574503              DQ684736     1    29    29
browser |    28  100.0%         10     +  32863647  32863674              DQ684736     2    29    29
browser |    29  100.0%         10     -  35080184  35080212              DQ684736     1    29    29
browser |    29  100.0%         10     +  35380105  35380133              DQ684736     1    29    29
browser |    29  100.0%         10     +  36726450  36726478              DQ684736     1    29    29
browser |    29  100.0%         10     -  36876997  36877025              DQ684736     1    29    29
browser |    29  100.0%         10     +  47037202  47037230              DQ684736     1    29    29
browser |    29  100.0%         10     +  47358726  47358754              DQ684736     1    29    29
browser |    29  100.0%         10     -  49537793  49537821              DQ684736     1    29    29
browser |    29  100.0%         10     +  49790718  49790746              DQ684736     1    29    29
browser |    29  100.0%         10     -  55166798  55166826              DQ684736     1    29    29
browser |    28  100.0%         10     +  57281500  57281527              DQ684736     2    29    29
browser |    28  100.0%         10     -  57452077  57452104              DQ684736     2    29    29
browser |    29  100.0%         10     +  57491702  57491730              DQ684736     1    29    29
browser |    29  100.0%         10     +  58640738  58640766              DQ684736     1    29    29
browser |    29  100.0%         10     +  78823511  78823539              DQ684736     1    29    29
browser |    29  100.0%         10     -  93658098  93658126              DQ684736     1    29    29
browser |    29  100.0%         10     +  98158518  98158546              DQ684736     1    29    29
browser |    29  100.0%         10     + 101410049 101410078              DQ684736     1    29    29
browser |    29  100.0%         10     + 103179279 103179307              DQ684736     1    29    29
browser |    29  100.0%         10     + 104054659 104054687              DQ684736     1    29    29
browser |    26  100.0%         10     + 104363945 104363970              DQ684736     1    26    29
browser |    29  100.0%         10     - 106751997 106752025              DQ684736     1    29    29
browser |    29  100.0%         10     + 110279118 110279146              DQ684736     1    29    29
browser |    26  100.0%         10     - 110632618 110632643              DQ684736     1    26    29
browser |    27  100.0%         10     - 118201956 118201982              DQ684736     1    27    29
browser |    29  100.0%         10     + 123660890 123660918              DQ684736     1    29    29
browser |    29  100.0%         10     + 124578693 124578721              DQ684736     1    29    29
browser |    29  100.0%         11     +   8184648   8184676              DQ684736     1    29    29
browser |    29  100.0%         11     -  14416254  14416282              DQ684736     1    29    29
browser |    29  100.0%         11     +  14909202  14909230              DQ684736     1    29    29
browser |    29  100.0%         11     +  15495589  15495617              DQ684736     1    29    29
browser |    29  100.0%         11     +  16295545  16295573              DQ684736     1    29    29
browser |    29  100.0%         11     -  16448571  16448599              DQ684736     1    29    29
browser |    29  100.0%         11     -  17854632  17854660              DQ684736     1    29    29
browser |    29  100.0%         11     -  20345574  20345602              DQ684736     1    29    29
browser |    29  100.0%         11     -  23455445  23455473              DQ684736     1    29    29
browser |    29  100.0%         11     +  23471331  23471359              DQ684736     1    29    29
browser |    29  100.0%         11     -  26840014  26840042              DQ684736     1    29    29
browser |    28  100.0%         11     -  27146208  27146235              DQ684736     1    28    29
browser |    29  100.0%         11     -  28596718  28596746              DQ684736     1    29    29
browser |    29  100.0%         11     +  29634515  29634543              DQ684736     1    29    29
browser |    29  100.0%         11     -  30649219  30649247              DQ684736     1    29    29
browser |    29  100.0%         11     -  47950985  47951013              DQ684736     1    29    29
browser |    27  100.0%         11     +  48250801  48250827              DQ684736     3    29    29
browser |    26  100.0%         11     +  71253002  71253027              DQ684736     1    26    29
browser |    29  100.0%         11     -  71519559  71519587              DQ684736     1    29    29
browser |    29  100.0%         11     -  79867178  79867206              DQ684736     1    29    29
browser |    29  100.0%         11     -  83666442  83666470              DQ684736     1    29    29
browser |    29  100.0%         11     -  87740376  87740404              DQ684736     1    29    29
browser |    27  100.0%         11     -  91442668  91442694              DQ684736     3    29    29
browser |    29  100.0%         11     -  91609345  91609373              DQ684736     1    29    29
browser |    29  100.0%         11     - 118364992 118365020              DQ684736     1    29    29
browser |    29  100.0%         12     -  10653981  10654009              DQ684736     1    29    29
browser |    26  100.0%         12     +  13922521  13922546              DQ684736     1    26    29
browser |    29  100.0%         12     +  38375744  38375772              DQ684736     1    29    29
browser |    29  100.0%         12     +  48861979  48862007              DQ684736     1    29    29
browser |    29  100.0%         12     +  52262524  52262552              DQ684736     1    29    29
browser |    29  100.0%         12     +  55714269  55714297              DQ684736     1    29    29
browser |    29  100.0%         12     +  56397698  56397726              DQ684736     1    29    29
browser |    29  100.0%         12     -  58492298  58492326              DQ684736     1    29    29
browser |    29  100.0%         12     -  62773926  62773954              DQ684736     1    29    29
browser |    29  100.0%         12     -  68288585  68288613              DQ684736     1    29    29
browser |    29  100.0%         12     -  69317955  69317983              DQ684736     1    29    29
browser |    28  100.0%         12     -  72128857  72128884              DQ684736     1    28    29
browser |    29  100.0%         12     -  89381964  89381992              DQ684736     1    29    29
browser |    29  100.0%         12     -  92719356  92719384              DQ684736     1    29    29
browser |    29  100.0%         12     +  99732465  99732493              DQ684736     1    29    29
browser |    29  100.0%         12     - 106995309 106995337              DQ684736     1    29    29
browser |    29  100.0%         12     + 114918557 114918585              DQ684736     1    29    29
browser |    29  100.0%         12     - 115091921 115091949              DQ684736     1    29    29
browser |    29  100.0%         12     - 115305069 115305097              DQ684736     1    29    29
browser |    29  100.0%         12     - 115594301 115594329              DQ684736     1    29    29
browser |    29  100.0%         13     -   4132059   4132087              DQ684736     1    29    29
browser |    29  100.0%         13     -   4135810   4135838              DQ684736     1    29    29
browser |    29  100.0%         13     +  15220272  15220300              DQ684736     1    29    29
browser |    26  100.0%         13     -  25517343  25517368              DQ684736     1    26    29
browser |    29  100.0%         13     +  41894709  41894737              DQ684736     1    29    29
browser |    29  100.0%         13     -  43233950  43233978              DQ684736     1    29    29
browser |    29  100.0%         13     -  58236122  58236150              DQ684736     1    29    29
browser |    29  100.0%         13     +  64709431  64709459              DQ684736     1    29    29
browser |    29  100.0%         13     -  65003009  65003037              DQ684736     1    29    29
browser |    29  100.0%         13     +  73606260  73606288              DQ684736     1    29    29
browser |    29  100.0%         13     +  79639916  79639944              DQ684736     1    29    29
browser |    29  100.0%         13     -  81752405  81752433              DQ684736     1    29    29
browser |    29  100.0%         13     -  82347501  82347529              DQ684736     1    29    29
browser |    29  100.0%         13     +  84814903  84814931              DQ684736     1    29    29
browser |    29  100.0%         13     -  86042335  86042363              DQ684736     1    29    29
browser |    27  100.0%         13     -  86060129  86060155              DQ684736     1    27    29
browser |    29  100.0%         13     +  91398102  91398130              DQ684736     1    29    29
browser |    29  100.0%         13     + 100181592 100181620              DQ684736     1    29    29
browser |    29  100.0%         13     - 102426389 102426417              DQ684736     1    29    29
browser |    29  100.0%         13     + 103987721 103987749              DQ684736     1    29    29
browser |    29  100.0%         13     + 104320011 104320039              DQ684736     1    29    29
browser |    26  100.0%         13     + 107140349 107140374              DQ684736     1    26    29
browser |    29  100.0%         14     +   3624156   3624184              DQ684736     1    29    29
browser |    29  100.0%         14     -   5590159   5590187              DQ684736     1    29    29
browser |    29  100.0%         14     -   8636682   8636710              DQ684736     1    29    29
browser |    29  100.0%         14     +   9318047   9318075              DQ684736     1    29    29
browser |    29  100.0%         14     -  13917288  13917316              DQ684736     1    29    29
browser |    29  100.0%         14     -  19911376  19911404              DQ684736     1    29    29
browser |    29  100.0%         14     +  27240733  27240761              DQ684736     1    29    29
browser |    29  100.0%         14     +  31235940  31235968              DQ684736     1    29    29
browser |    29  100.0%         14     +  33980695  33980723              DQ684736     1    29    29
browser |    29  100.0%         14     -  34780631  34780659              DQ684736     1    29    29
browser |    28  100.0%         14     -  35528021  35528048              DQ684736     1    28    29
browser |    29  100.0%         14     +  41085252  41085280              DQ684736     1    29    29
browser |    29  100.0%         14     +  41254019  41254047              DQ684736     1    29    29
browser |    29  100.0%         14     +  41308619  41308647              DQ684736     1    29    29
browser |    29  100.0%         14     +  41325036  41325064              DQ684736     1    29    29
browser |    29  100.0%         14     +  41705678  41705706              DQ684736     1    29    29
browser |    29  100.0%         14     +  41761407  41761435              DQ684736     1    29    29
browser |    29  100.0%         14     +  42300516  42300544              DQ684736     1    29    29
browser |    29  100.0%         14     +  42984032  42984060              DQ684736     1    29    29
browser |    29  100.0%         14     +  43793834  43793862              DQ684736     1    29    29
browser |    29  100.0%         14     +  43931971  43931999              DQ684736     1    29    29
browser |    29  100.0%         14     -  44391158  44391186              DQ684736     1    29    29
browser |    29  100.0%         14     -  44454019  44454047              DQ684736     1    29    29
browser |    29  100.0%         14     -  44553045  44553073              DQ684736     1    29    29
browser |    29  100.0%         14     -  44625237  44625265              DQ684736     1    29    29
browser |    29  100.0%         14     -  44776172  44776200              DQ684736     1    29    29
browser |    29  100.0%         14     -  44947801  44947829              DQ684736     1    29    29
browser |    29  100.0%         14     -  50281919  50281947              DQ684736     1    29    29
browser |    29  100.0%         14     -  50331458  50331486              DQ684736     1    29    29
browser |    29  100.0%         14     +  50502480  50502508              DQ684736     1    29    29
browser |    29  100.0%         14     -  76974204  76974232              DQ684736     1    29    29
browser |    29  100.0%         14     -  82293039  82293067              DQ684736     1    29    29
browser |    28  100.0%         14     -  91306281  91306308              DQ684736     1    28    29
browser |    29  100.0%         14     +  97706842  97706870              DQ684736     1    29    29
browser |    29  100.0%         14     +  99150940  99150968              DQ684736     1    29    29
browser |    29  100.0%         14     - 101921035 101921063              DQ684736     1    29    29
browser |    28  100.0%         14     + 107260565 107260592              DQ684736     1    28    29
browser |    29  100.0%         14     - 108893542 108893570              DQ684736     1    29    29
browser |    29  100.0%         14     + 110973739 110973767              DQ684736     1    29    29
browser |    29  100.0%         14     - 113116992 113117020              DQ684736     1    29    29
browser |    27  100.0%         14     - 116834597 116834623              DQ684736     1    27    29
browser |    28  100.0%         14     + 118028647 118028674              DQ684736     1    28    29
browser |    29  100.0%         14     + 119234276 119234304              DQ684736     1    29    29
browser |    29  100.0%         14     - 119342302 119342330              DQ684736     1    29    29
browser |    29  100.0%         14     + 123957081 123957109              DQ684736     1    29    29
browser |    29  100.0%         14     + 124231272 124231300              DQ684736     1    29    29
browser |    29  100.0%         15     -   6776204   6776232              DQ684736     1    29    29
browser |    29  100.0%         15     -   8191510   8191538              DQ684736     1    29    29
browser |    29  100.0%         15     -  10977299  10977327              DQ684736     1    29    29
browser |    29  100.0%         15     -  18088072  18088100              DQ684736     1    29    29
browser |    28  100.0%         15     +  19934400  19934427              DQ684736     1    28    29
browser |    29  100.0%         15     +  19937569  19937597              DQ684736     1    29    29
browser |    29  100.0%         15     +  20040936  20040964              DQ684736     1    29    29
browser |    29  100.0%         15     -  20763314  20763342              DQ684736     1    29    29
browser |    29  100.0%         15     -  21176976  21177004              DQ684736     1    29    29
browser |    29  100.0%         15     -  24434493  24434521              DQ684736     1    29    29
browser |    26  100.0%         15     +  29243360  29243385              DQ684736     4    29    29
browser |    29  100.0%         15     -  29506839  29506867              DQ684736     1    29    29
browser |    29  100.0%         15     +  42811045  42811073              DQ684736     1    29    29
browser |    28  100.0%         15     -  43846344  43846371              DQ684736     1    28    29
browser |    29  100.0%         15     -  45765043  45765071              DQ684736     1    29    29
browser |    28  100.0%         15     -  49434809  49434836              DQ684736     1    28    29
browser |    29  100.0%         15     +  50455798  50455826              DQ684736     1    29    29
browser |    29  100.0%         15     -  63181938  63181966              DQ684736     1    29    29
browser |    29  100.0%         15     +  63233837  63233865              DQ684736     1    29    29
browser |    28  100.0%         15     -  64961745  64961772              DQ684736     2    29    29
browser |    29  100.0%         15     -  74950995  74951023              DQ684736     1    29    29
browser |    29  100.0%         15     -  79753253  79753281              DQ684736     1    29    29
browser |    29  100.0%         15     -  90105596  90105624              DQ684736     1    29    29
browser |    26  100.0%         15     +  90920041  90920066              DQ684736     1    26    29
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View details of parts of alignment within browser window
.
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