DQ722040
 

Information on mRNA DQ722040

Description: Mus musculus piRNA piR-137362, 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: DQ722040
Position: chr12:56885359-56885388

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    30  100.0%         12     +  56885359  56885388              DQ722040     1    30    31
browser |    30  100.0%          1     -   4499094   4499123              DQ722040     1    30    31
browser |    31  100.0%          1     +   5789311   5789341              DQ722040     1    31    31
browser |    31  100.0%          1     -  21619051  21619081              DQ722040     1    31    31
browser |    30  100.0%          1     +  21707114  21707143              DQ722040     1    30    31
browser |    30  100.0%          1     +  22178289  22178318              DQ722040     1    30    31
browser |    31  100.0%          1     -  23858786  23858816              DQ722040     1    31    31
browser |    31  100.0%          1     +  26043924  26043954              DQ722040     1    31    31
browser |    30  100.0%          1     +  28505814  28505843              DQ722040     1    30    31
browser |    30  100.0%          1     +  42226499  42226528              DQ722040     1    30    31
browser |    28  100.0%          1     +  49063940  49063967              DQ722040     3    30    31
browser |    30  100.0%          1     +  54677709  54677738              DQ722040     1    30    31
browser |    30  100.0%          1     -  55359064  55359093              DQ722040     1    30    31
browser |    30  100.0%          1     +  94988934  94988963              DQ722040     1    30    31
browser |    29  100.0%          1     -  96178479  96178507              DQ722040     2    30    31
browser |    28  100.0%          1     -  97196031  97196058              DQ722040     4    31    31
browser |    30  100.0%          1     +  99412393  99412422              DQ722040     1    30    31
browser |    31  100.0%          1     + 100915808 100915838              DQ722040     1    31    31
browser |    31  100.0%          1     - 101024703 101024733              DQ722040     1    31    31
browser |    31  100.0%          1     + 107473133 107473163              DQ722040     1    31    31
browser |    29  100.0%          1     - 107797204 107797232              DQ722040     2    30    31
browser |    30  100.0%          1     + 109023724 109023753              DQ722040     1    30    31
browser |    29  100.0%          1     + 109302884 109302912              DQ722040     2    30    31
browser |    30  100.0%          1     - 111108454 111108483              DQ722040     1    30    31
browser |    30  100.0%          1     - 112438939 112438968              DQ722040     1    30    31
browser |    30  100.0%          1     + 112822681 112822712              DQ722040     1    30    31
browser |    30  100.0%          1     + 115275139 115275168              DQ722040     1    30    31
browser |    29  100.0%          1     - 116978104 116978132              DQ722040     2    30    31
browser |    30  100.0%          1     + 123242609 123242638              DQ722040     1    30    31
browser |    30  100.0%          1     + 141079543 141079572              DQ722040     1    30    31
browser |    30  100.0%          1     - 142868969 142868998              DQ722040     1    30    31
browser |    30  100.0%          1     + 145338698 145338727              DQ722040     1    30    31
browser |    30  100.0%          1     + 160974259 160974288              DQ722040     1    30    31
browser |    31  100.0%          1     + 165571869 165571899              DQ722040     1    31    31
browser |    30  100.0%          1     - 172776974 172777003              DQ722040     1    30    31
browser |    31  100.0%          1     - 179707548 179707578              DQ722040     1    31    31
browser |    30  100.0%          1     + 179887063 179887092              DQ722040     1    30    31
browser |    30  100.0%          1     + 184257159 184257188              DQ722040     1    30    31
browser |    30  100.0%         10     +   6616938   6616967              DQ722040     1    30    31
browser |    29  100.0%         10     +  12893250  12893278              DQ722040     3    31    31
browser |    31  100.0%         10     +  17767538  17767568              DQ722040     1    31    31
browser |    31  100.0%         10     -  50005156  50005186              DQ722040     1    31    31
browser |    30  100.0%         10     +  71372609  71372638              DQ722040     1    30    31
browser |    30  100.0%         10     -  73697434  73697463              DQ722040     1    30    31
browser |    30  100.0%         10     +  74173934  74173963              DQ722040     1    30    31
browser |    31  100.0%         10     +  84650148  84650178              DQ722040     1    31    31
browser |    30  100.0%         10     +  94592259  94592288              DQ722040     2    31    31
browser |    30  100.0%         10     - 101511174 101511203              DQ722040     1    30    31
browser |    28  100.0%         10     + 103129785 103129812              DQ722040     3    30    31
browser |    28  100.0%         10     + 119210626 119210653              DQ722040     4    31    31
browser |    28  100.0%         10     - 122302634 122302661              DQ722040     3    30    31
browser |    30  100.0%         10     + 125454024 125454053              DQ722040     1    30    31
browser |    30  100.0%         11     +   7772358   7772387              DQ722040     1    30    31
browser |    30  100.0%         11     +   9119814   9119843              DQ722040     1    30    31
browser |    30  100.0%         11     +  13228319  13228348              DQ722040     1    30    31
browser |    28  100.0%         11     -  14809953  14809980              DQ722040     4    31    31
browser |    28  100.0%         11     +  17794134  17794161              DQ722040     1    28    31
browser |    30  100.0%         11     -  17973244  17973273              DQ722040     1    30    31
browser |    30  100.0%         11     -  18689204  18689233              DQ722040     1    30    31
browser |    30  100.0%         11     +  21845849  21845878              DQ722040     1    30    31
browser |    28  100.0%         11     +  48419534  48419561              DQ722040     1    28    31
browser |    31  100.0%         11     -  56507076  56507106              DQ722040     1    31    31
browser |    30  100.0%         11     +  73509064  73509093              DQ722040     1    30    31
browser |    30  100.0%         12     +  14430603  14430632              DQ722040     1    30    31
browser |    30  100.0%         12     -  24790749  24790778              DQ722040     1    30    31
browser |    28  100.0%         12     -  28142496  28142523              DQ722040     4    31    31
browser |    30  100.0%         12     -  32514174  32514203              DQ722040     1    30    31
browser |    30  100.0%         12     +  32564794  32564823              DQ722040     1    30    31
browser |    30  100.0%         12     +  37326004  37326033              DQ722040     1    30    31
browser |    28  100.0%         12     +  37368790  37368817              DQ722040     3    30    31
browser |    31  100.0%         12     -  39044193  39044223              DQ722040     1    31    31
browser |    30  100.0%         12     -  44552854  44552883              DQ722040     1    30    31
browser |    28  100.0%         12     +  49065436  49065463              DQ722040     3    30    31
browser |    30  100.0%         12     +  57604283  57604312              DQ722040     1    30    31
browser |    30  100.0%         12     +  57608413  57608442              DQ722040     1    30    31
browser |    30  100.0%         12     +  61737933  61737962              DQ722040     1    30    31
browser |    30  100.0%         12     -  62897774  62897803              DQ722040     1    30    31
browser |    30  100.0%         12     +  66466698  66466727              DQ722040     1    30    31
browser |    30  100.0%         12     -  83393459  83393488              DQ722040     1    30    31
browser |    30  100.0%         12     +  92389698  92389727              DQ722040     1    30    31
browser |    31  100.0%         12     - 115125161 115125191              DQ722040     1    31    31
browser |    31  100.0%         12     - 115325858 115325888              DQ722040     1    31    31
browser |    30  100.0%         12     - 115338764 115338793              DQ722040     1    30    31
browser |    31  100.0%         12     - 115427753 115427783              DQ722040     1    31    31
browser |    30  100.0%         13     -  15245584  15245613              DQ722040     1    30    31
browser |    29  100.0%         13     -  17774449  17774477              DQ722040     2    30    31
browser |    30  100.0%         13     +  19045774  19045803              DQ722040     1    30    31
browser |    30  100.0%         13     -  19176739  19176768              DQ722040     1    30    31
browser |    30  100.0%         13     +  24104114  24104143              DQ722040     1    30    31
browser |    30  100.0%         13     +  26190878  26190907              DQ722040     1    30    31
browser |    30  100.0%         13     -  31940054  31940083              DQ722040     1    30    31
browser |    29  100.0%         13     +  35273494  35273522              DQ722040     2    30    31
browser |    30  100.0%         13     +  40245808  40245837              DQ722040     1    30    31
browser |    31  100.0%         13     +  49989681  49989711              DQ722040     1    31    31
browser |    30  100.0%         13     +  61113283  61113312              DQ722040     1    30    31
browser |    30  100.0%         13     +  61136159  61136188              DQ722040     1    30    31
browser |    30  100.0%         13     +  63973618  63973647              DQ722040     1    30    31
browser |    30  100.0%         13     +  75566399  75566428              DQ722040     1    30    31
browser |    31  100.0%         13     +  84611466  84611496              DQ722040     1    31    31
browser |    29  100.0%         13     +  86255339  86255367              DQ722040     2    30    31
browser |    30  100.0%         13     +  87346854  87346883              DQ722040     1    30    31
browser |    28  100.0%         13     -  89920626  89920653              DQ722040     1    28    31
browser |    30  100.0%         13     + 106400763 106400792              DQ722040     1    30    31
browser |    29  100.0%         13     + 113565604 113565632              DQ722040     2    30    31
browser |    31  100.0%         13     + 115703661 115703691              DQ722040     1    31    31
browser |    30  100.0%         14     -   4425689   4425718              DQ722040     1    30    31
browser |    30  100.0%         14     +   7228869   7228898              DQ722040     1    30    31
browser |    31  100.0%         14     +  11471561  11471591              DQ722040     1    31    31
browser |    30  100.0%         14     +  11541544  11541573              DQ722040     1    30    31
browser |    30  100.0%         14     -  38133944  38133973              DQ722040     1    30    31
browser |    30  100.0%         14     -  45034409  45034438              DQ722040     1    30    31
browser |    31  100.0%         14     -  53044871  53044901              DQ722040     1    31    31
browser |    30  100.0%         14     -  54535774  54535968              DQ722040     1    30    31
browser |    30  100.0%         14     +  62163778  62163807              DQ722040     1    30    31
browser |    31  100.0%         14     -  66304551  66304581              DQ722040     1    31    31
browser |    30  100.0%         14     -  66870619  66870648              DQ722040     1    30    31
browser |    29  100.0%         14     -  81463751  81463779              DQ722040     3    31    31
browser |    30  100.0%         14     +  86340383  86340412              DQ722040     1    30    31
browser |    28  100.0%         14     +  89186049  89186076              DQ722040     1    28    31
browser |    30  100.0%         14     +  97376934  97376963              DQ722040     1    30    31
browser |    30  100.0%         14     +  97661408  97661437              DQ722040     1    30    31
browser |    28  100.0%         14     + 108145341 108145368              DQ722040     3    30    31
browser |    30  100.0%         14     - 113486774 113486803              DQ722040     1    30    31
browser |    30  100.0%         14     + 113774583 113774612              DQ722040     1    30    31
browser |    29  100.0%         14     - 114613364 114613392              DQ722040     2    30    31
browser |    30  100.0%         15     -   9358324   9358353              DQ722040     1    30    31
browser |    30  100.0%         15     +  11499334  11499363              DQ722040     1    30    31
browser |    30  100.0%         15     +  19416652  19416681              DQ722040     2    31    31
browser |    30  100.0%         15     +  22181018  22181047              DQ722040     1    30    31
browser |    31  100.0%         15     +  33930259  33930289              DQ722040     1    31    31
browser |    31  100.0%         15     -  35050091  35050121              DQ722040     1    31    31
browser |    30  100.0%         15     +  41343419  41343448              DQ722040     1    30    31
browser |    30  100.0%         15     -  43706639  43706668              DQ722040     1    30    31
browser |    30  100.0%         15     +  46883584  46883613              DQ722040     1    30    31
browser |    29  100.0%         15     -  61830459  61830487              DQ722040     2    30    31
browser |    30  100.0%         15     +  70399528  70399557              DQ722040     1    30    31
browser |    29  100.0%         15     +  93843088  93843116              DQ722040     1    29    31
browser |    29  100.0%         16     -   6379010   6379038              DQ722040     1    29    31
browser |    30  100.0%         16     -   9308824   9308853              DQ722040     1    30    31
browser |    30  100.0%         16     +  14355139  14355168              DQ722040     1    30    31
browser |    30  100.0%         16     +  16420939  16420968              DQ722040     1    30    31
browser |    29  100.0%         16     -  24957450  24957478              DQ722040     1    29    31
browser |    30  100.0%         16     +  25218383  25218412              DQ722040     1    30    31
browser |    28  100.0%         16     -  26019554  26019581              DQ722040     3    30    31
browser |    29  100.0%         16     +  36901775  36901803              DQ722040     2    30    31
browser |    31  100.0%         16     -  42645718  42645748              DQ722040     1    31    31
browser |    28  100.0%         16     -  43082631  43082658              DQ722040     1    28    31
browser |    30  100.0%         16     +  44675678  44675707              DQ722040     1    30    31
browser |    30  100.0%         16     +  47030663  47030692              DQ722040     1    30    31
browser |    30  100.0%         16     +  63515033  63515062              DQ722040     1    30    31
browser |    31  100.0%         16     +  65786001  65786031              DQ722040     1    31    31
browser |    30  100.0%         16     +  67116633  67116662              DQ722040     1    30    31
browser |    31  100.0%         16     -  68602816  68602846              DQ722040     1    31    31
browser |    28  100.0%         16     +  70600979  70601006              DQ722040     1    28    31
browser |    31  100.0%         16     +  72086084  72086114              DQ722040     1    31    31
browser |    30  100.0%         16     -  74162939  74162968              DQ722040     1    30    31
browser |    30  100.0%         16     +  79042979  79043008              DQ722040     1    30    31
browser |    28  100.0%         16     +  86482544  86482571              DQ722040     1    28    31
browser |    31  100.0%         16     -  96458711  96458741              DQ722040     1    31    31
browser |    29  100.0%         17     +   8493706   8493734              DQ722040     3    31    31
browser |    28  100.0%         17     +  20729394  20729421              DQ722040     1    28    31
browser |    30  100.0%         17     +  38621538  38621567              DQ722040     1    30    31
browser |    29  100.0%         17     +  41979110  41979138              DQ722040     2    30    31
browser |    30  100.0%         17     +  52506078  52506107              DQ722040     1    30    31
browser |    31  100.0%         17     +  53214338  53214368              DQ722040     1    31    31
browser |    30  100.0%         17     -  62287934  62287963              DQ722040     1    30    31
browser |    30  100.0%         17     +  76108898  76108927              DQ722040     1    30    31
browser |    30  100.0%         17     -  77738584  77738613              DQ722040     1    30    31
browser |    30  100.0%         18     +   7055573   7055602              DQ722040     1    30    31
browser |    30  100.0%         18     +   7082133   7082162              DQ722040     1    30    31
browser |    28  100.0%         18     +  10657221  10657248              DQ722040     3    30    31
browser |    30  100.0%         18     +  14580454  14580483              DQ722040     1    30    31
browser |    30  100.0%         18     +  26457984  26458013              DQ722040     1    30    31
browser |    31  100.0%         18     +  31494134  31494166              DQ722040     1    31    31
browser |    31  100.0%         18     +  45822579  45822609              DQ722040     1    31    31
browser |    30  100.0%         18     +  54445914  54445943              DQ722040     1    30    31
browser |    31  100.0%         18     -  65540983  65541013              DQ722040     1    31    31
browser |    30  100.0%         18     -  71374424  71374453              DQ722040     1    30    31
browser |    31  100.0%         18     +  83807061  83807091              DQ722040     1    31    31
browser |    30  100.0%         18     +  89581254  89581283              DQ722040     1    30    31
browser |    30  100.0%         18     -  89765434  89765463              DQ722040     1    30    31
browser |    30  100.0%         19     +   7993868   7993897              DQ722040     1    30    31
browser |    30  100.0%         19     +   8287928   8287957              DQ722040     1    30    31
browser |    30  100.0%         19     +  38002079  38002108              DQ722040     1    30    31
browser |    30  100.0%         19     +  53577639  53577668              DQ722040     1    30    31
browser |    30  100.0%         19     +  54991059  54991088              DQ722040     1    30    31
browser |    30  100.0%          2     -  12851699  12851728              DQ722040     1    30    31
browser |    28  100.0%          2     +  13037999  13038026              DQ722040     1    28    31
browser |    30  100.0%          2     -  15258689  15258718              DQ722040     1    30    31
browser |    30  100.0%          2     -  16686889  16686918              DQ722040     1    30    31
browser |    31  100.0%          2     +  18508121  18508151              DQ722040     1    31    31
browser |    30  100.0%          2     +  39172289  39172318              DQ722040     1    30    31
browser |    29  100.0%          2     +  40470933  40470961              DQ722040     1    29    31
browser |    30  100.0%          2     +  41508933  41508962              DQ722040     1    30    31
browser |    29  100.0%          2     +  52910513  52910541              DQ722040     1    29    31
browser |    30  100.0%          2     +  53455694  53455723              DQ722040     1    30    31
browser |    31  100.0%          2     +  55856919  55856949              DQ722040     1    31    31
browser |    30  100.0%          2     +  56387804  56387833              DQ722040     1    30    31
browser |    31  100.0%          2     +  60866381  60866411              DQ722040     1    31    31
browser |    31  100.0%          2     +  61670006  61670036              DQ722040     1    31    31
browser |    31  100.0%          2     -  61690141  61690171              DQ722040     1    31    31
browser |    30  100.0%          2     -  74161459  74161488              DQ722040     1    30    31
browser |    31  100.0%          2     -  79440133  79440163              DQ722040     1    31    31
browser |    30  100.0%          2     +  82365479  82365508              DQ722040     1    30    31
browser |    29  100.0%          2     +  86116454  86116482              DQ722040     1    29    31
browser |    30  100.0%          2     -  88996819  88996848              DQ722040     1    30    31
browser |    30  100.0%          2     +  89857549  89857578              DQ722040     1    30    31
browser |    28  100.0%          2     +  94622919  94622946              DQ722040     4    31    31
browser |    28  100.0%          2     +  94628119  94628146              DQ722040     1    28    31
browser |    30  100.0%          2     +  95770554  95770583              DQ722040     1    30    31
browser |    30  100.0%          2     - 105460266 105460295              DQ722040     2    31    31
browser |    30  100.0%          2     + 111572364 111572393              DQ722040     1    30    31
browser |    30  100.0%          2     + 112615763 112615792              DQ722040     1    30    31
browser |    30  100.0%          2     + 122329048 122329077              DQ722040     1    30    31
browser |    28  100.0%          2     + 122409700 122409727              DQ722040     3    30    31
browser |    30  100.0%          2     - 123475184 123475213              DQ722040     1    30    31
browser |    30  100.0%          2     + 141940573 141940602              DQ722040     1    30    31
browser |    29  100.0%          2     - 159612303 159612331              DQ722040     3    31    31
browser |    30  100.0%          3     +   6006173   6006202              DQ722040     1    30    31
browser |    30  100.0%          3     +   7033984   7034013              DQ722040     1    30    31
browser |    30  100.0%          3     -   8903879   8903908              DQ722040     1    30    31
browser |    30  100.0%          3     +   9575983   9576012              DQ722040     1    30    31
browser |    28  100.0%          3     -  10916466  10916493              DQ722040     1    28    31
browser |    30  100.0%          3     +  12907674  12907703              DQ722040     1    30    31
browser |    30  100.0%          3     +  14271003  14271032              DQ722040     1    30    31
browser |    28  100.0%          3     -  14481984  14482011              DQ722040     3    30    31
browser |    31  100.0%          3     -  19132701  19132731              DQ722040     1    31    31
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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