DQ725759
 

Information on mRNA DQ725759

Description: Mus musculus piRNA piR-141081, 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: DQ725759
Position: chr12:56885359-56885387

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     +  56885359  56885387              DQ725759     1    29    29
browser |    29  100.0%          1     -   4499095   4499123              DQ725759     1    29    29
browser |    29  100.0%          1     +  21707114  21707142              DQ725759     1    29    29
browser |    29  100.0%          1     +  22178289  22178317              DQ725759     1    29    29
browser |    29  100.0%          1     +  26043924  26043952              DQ725759     1    29    29
browser |    29  100.0%          1     +  28505814  28505842              DQ725759     1    29    29
browser |    29  100.0%          1     +  42226499  42226527              DQ725759     1    29    29
browser |    27  100.0%          1     +  49063940  49063966              DQ725759     3    29    29
browser |    29  100.0%          1     +  54677709  54677737              DQ725759     1    29    29
browser |    29  100.0%          1     -  55359065  55359093              DQ725759     1    29    29
browser |    29  100.0%          1     +  94988934  94988962              DQ725759     1    29    29
browser |    28  100.0%          1     -  96178480  96178507              DQ725759     2    29    29
browser |    29  100.0%          1     +  99412393  99412421              DQ725759     1    29    29
browser |    29  100.0%          1     + 100915808 100915836              DQ725759     1    29    29
browser |    29  100.0%          1     - 101024705 101024733              DQ725759     1    29    29
browser |    26  100.0%          1     - 103818525 103818550              DQ725759     4    29    29
browser |    29  100.0%          1     + 107473133 107473161              DQ725759     1    29    29
browser |    28  100.0%          1     - 107797205 107797232              DQ725759     2    29    29
browser |    29  100.0%          1     + 109023724 109023752              DQ725759     1    29    29
browser |    28  100.0%          1     + 109302884 109302911              DQ725759     2    29    29
browser |    29  100.0%          1     - 111108455 111108483              DQ725759     1    29    29
browser |    29  100.0%          1     - 112438940 112438968              DQ725759     1    29    29
browser |    29  100.0%          1     + 112822681 112822711              DQ725759     1    29    29
browser |    26  100.0%          1     - 114919810 114919835              DQ725759     4    29    29
browser |    29  100.0%          1     + 115275139 115275167              DQ725759     1    29    29
browser |    28  100.0%          1     - 116978105 116978132              DQ725759     2    29    29
browser |    29  100.0%          1     + 123242609 123242637              DQ725759     1    29    29
browser |    26  100.0%          1     - 129500150 129500175              DQ725759     4    29    29
browser |    29  100.0%          1     + 141079543 141079571              DQ725759     1    29    29
browser |    29  100.0%          1     - 142868970 142868998              DQ725759     1    29    29
browser |    29  100.0%          1     + 145338698 145338726              DQ725759     1    29    29
browser |    29  100.0%          1     + 160974259 160974287              DQ725759     1    29    29
browser |    29  100.0%          1     + 165571869 165571897              DQ725759     1    29    29
browser |    29  100.0%          1     - 172776975 172777003              DQ725759     1    29    29
browser |    29  100.0%          1     - 179707550 179707578              DQ725759     1    29    29
browser |    29  100.0%          1     + 179887063 179887091              DQ725759     1    29    29
browser |    29  100.0%          1     + 184257159 184257187              DQ725759     1    29    29
browser |    27  100.0%         10     +   6024590   6024616              DQ725759     2    28    29
browser |    29  100.0%         10     +   6616938   6616966              DQ725759     1    29    29
browser |    27  100.0%         10     +  12893250  12893276              DQ725759     3    29    29
browser |    29  100.0%         10     +  17767538  17767566              DQ725759     1    29    29
browser |    26  100.0%         10     +  47804792  47804817              DQ725759     4    29    29
browser |    29  100.0%         10     +  71372609  71372637              DQ725759     1    29    29
browser |    29  100.0%         10     -  73697435  73697463              DQ725759     1    29    29
browser |    29  100.0%         10     +  74173934  74173962              DQ725759     1    29    29
browser |    27  100.0%         10     +  82447164  82447190              DQ725759     1    27    29
browser |    29  100.0%         10     +  84650148  84650176              DQ725759     1    29    29
browser |    28  100.0%         10     +  94592259  94592286              DQ725759     2    29    29
browser |    29  100.0%         10     - 101511175 101511203              DQ725759     1    29    29
browser |    27  100.0%         10     + 103129785 103129811              DQ725759     3    29    29
browser |    26  100.0%         10     + 119210626 119210651              DQ725759     4    29    29
browser |    27  100.0%         10     - 122302635 122302661              DQ725759     3    29    29
browser |    29  100.0%         10     + 125454024 125454052              DQ725759     1    29    29
browser |    29  100.0%         11     +   7772358   7772386              DQ725759     1    29    29
browser |    29  100.0%         11     +   9119814   9119842              DQ725759     1    29    29
browser |    29  100.0%         11     +  13228319  13228347              DQ725759     1    29    29
browser |    26  100.0%         11     -  14809955  14809980              DQ725759     4    29    29
browser |    28  100.0%         11     +  17794134  17794161              DQ725759     1    28    29
browser |    29  100.0%         11     -  17973245  17973273              DQ725759     1    29    29
browser |    29  100.0%         11     -  18689205  18689233              DQ725759     1    29    29
browser |    29  100.0%         11     +  21845849  21845877              DQ725759     1    29    29
browser |    28  100.0%         11     +  48419534  48419561              DQ725759     1    28    29
browser |    29  100.0%         11     +  73509064  73509092              DQ725759     1    29    29
browser |    29  100.0%         12     +  14430603  14430631              DQ725759     1    29    29
browser |    29  100.0%         12     -  24790750  24790778              DQ725759     1    29    29
browser |    29  100.0%         12     -  32514175  32514203              DQ725759     1    29    29
browser |    29  100.0%         12     +  32564794  32564822              DQ725759     1    29    29
browser |    29  100.0%         12     +  37326004  37326032              DQ725759     1    29    29
browser |    27  100.0%         12     +  37368790  37368816              DQ725759     3    29    29
browser |    29  100.0%         12     -  39044195  39044223              DQ725759     1    29    29
browser |    29  100.0%         12     -  44552855  44552883              DQ725759     1    29    29
browser |    27  100.0%         12     +  49065436  49065462              DQ725759     3    29    29
browser |    29  100.0%         12     +  57604283  57604311              DQ725759     1    29    29
browser |    29  100.0%         12     +  57608413  57608441              DQ725759     1    29    29
browser |    29  100.0%         12     +  61737933  61737961              DQ725759     1    29    29
browser |    29  100.0%         12     -  62897775  62897803              DQ725759     1    29    29
browser |    29  100.0%         12     +  66466698  66466726              DQ725759     1    29    29
browser |    29  100.0%         12     -  83393460  83393488              DQ725759     1    29    29
browser |    29  100.0%         12     +  92389698  92389726              DQ725759     1    29    29
browser |    29  100.0%         12     - 115325860 115325888              DQ725759     1    29    29
browser |    29  100.0%         12     - 115338765 115338793              DQ725759     1    29    29
browser |    29  100.0%         12     - 115427755 115427783              DQ725759     1    29    29
browser |    29  100.0%         13     -  15245585  15245613              DQ725759     1    29    29
browser |    28  100.0%         13     -  17774450  17774477              DQ725759     2    29    29
browser |    29  100.0%         13     +  19045774  19045802              DQ725759     1    29    29
browser |    29  100.0%         13     -  19176740  19176768              DQ725759     1    29    29
browser |    29  100.0%         13     +  24104114  24104142              DQ725759     1    29    29
browser |    29  100.0%         13     +  26190878  26190906              DQ725759     1    29    29
browser |    29  100.0%         13     -  31940055  31940083              DQ725759     1    29    29
browser |    28  100.0%         13     +  35273494  35273521              DQ725759     2    29    29
browser |    29  100.0%         13     +  40245808  40245836              DQ725759     1    29    29
browser |    29  100.0%         13     +  61113283  61113311              DQ725759     1    29    29
browser |    29  100.0%         13     +  61136159  61136187              DQ725759     1    29    29
browser |    29  100.0%         13     +  63973618  63973646              DQ725759     1    29    29
browser |    29  100.0%         13     +  75566399  75566427              DQ725759     1    29    29
browser |    28  100.0%         13     +  86255339  86255366              DQ725759     2    29    29
browser |    29  100.0%         13     +  87346854  87346882              DQ725759     1    29    29
browser |    28  100.0%         13     -  89920626  89920653              DQ725759     1    28    29
browser |    29  100.0%         13     + 106400763 106400791              DQ725759     1    29    29
browser |    28  100.0%         13     + 113565604 113565631              DQ725759     2    29    29
browser |    26  100.0%         13     + 118789791 118789816              DQ725759     4    29    29
browser |    29  100.0%         14     -   4425690   4425718              DQ725759     1    29    29
browser |    26  100.0%         14     +   4530676   4530701              DQ725759     4    29    29
browser |    26  100.0%         14     +   6799531   6799556              DQ725759     4    29    29
browser |    29  100.0%         14     +   7228869   7228897              DQ725759     1    29    29
browser |    29  100.0%         14     +  11541544  11541572              DQ725759     1    29    29
browser |    29  100.0%         14     -  38133945  38133973              DQ725759     1    29    29
browser |    29  100.0%         14     -  45034410  45034438              DQ725759     1    29    29
browser |    26  100.0%         14     +  58983826  58983851              DQ725759     4    29    29
browser |    29  100.0%         14     +  62163778  62163806              DQ725759     1    29    29
browser |    29  100.0%         14     -  66870620  66870648              DQ725759     1    29    29
browser |    29  100.0%         14     +  86340383  86340411              DQ725759     1    29    29
browser |    28  100.0%         14     +  89186049  89186076              DQ725759     1    28    29
browser |    27  100.0%         14     +  89232144  89232170              DQ725759     1    27    29
browser |    29  100.0%         14     +  97376934  97376962              DQ725759     1    29    29
browser |    29  100.0%         14     +  97661408  97661436              DQ725759     1    29    29
browser |    27  100.0%         14     + 108145341 108145367              DQ725759     3    29    29
browser |    29  100.0%         14     - 113486775 113486803              DQ725759     1    29    29
browser |    29  100.0%         14     + 113774583 113774611              DQ725759     1    29    29
browser |    28  100.0%         14     - 114613365 114613392              DQ725759     2    29    29
browser |    29  100.0%         15     -   9358325   9358353              DQ725759     1    29    29
browser |    29  100.0%         15     +  11499334  11499362              DQ725759     1    29    29
browser |    29  100.0%         15     +  22181018  22181046              DQ725759     1    29    29
browser |    29  100.0%         15     +  33930259  33930287              DQ725759     1    29    29
browser |    29  100.0%         15     +  41343419  41343447              DQ725759     1    29    29
browser |    29  100.0%         15     -  43706640  43706668              DQ725759     1    29    29
browser |    29  100.0%         15     +  46883584  46883612              DQ725759     1    29    29
browser |    28  100.0%         15     -  61830460  61830487              DQ725759     2    29    29
browser |    29  100.0%         15     +  70399528  70399556              DQ725759     1    29    29
browser |    29  100.0%         15     +  93843088  93843116              DQ725759     1    29    29
browser |    29  100.0%         16     -   6379010   6379038              DQ725759     1    29    29
browser |    29  100.0%         16     -   9308825   9308853              DQ725759     1    29    29
browser |    29  100.0%         16     +  14355139  14355167              DQ725759     1    29    29
browser |    27  100.0%         16     +  14374314  14374340              DQ725759     1    27    29
browser |    29  100.0%         16     +  16420939  16420967              DQ725759     1    29    29
browser |    29  100.0%         16     -  24957450  24957478              DQ725759     1    29    29
browser |    29  100.0%         16     +  25218383  25218411              DQ725759     1    29    29
browser |    27  100.0%         16     -  26019555  26019581              DQ725759     3    29    29
browser |    28  100.0%         16     +  36901775  36901802              DQ725759     2    29    29
browser |    29  100.0%         16     -  42645720  42645748              DQ725759     1    29    29
browser |    28  100.0%         16     -  43082631  43082658              DQ725759     1    28    29
browser |    29  100.0%         16     +  44675678  44675706              DQ725759     1    29    29
browser |    29  100.0%         16     +  47030663  47030691              DQ725759     1    29    29
browser |    29  100.0%         16     +  63515033  63515061              DQ725759     1    29    29
browser |    29  100.0%         16     +  67116633  67116661              DQ725759     1    29    29
browser |    28  100.0%         16     +  70600979  70601006              DQ725759     1    28    29
browser |    29  100.0%         16     +  72086084  72086112              DQ725759     1    29    29
browser |    29  100.0%         16     -  74162940  74162968              DQ725759     1    29    29
browser |    29  100.0%         16     +  79042979  79043007              DQ725759     1    29    29
browser |    28  100.0%         16     +  86482544  86482571              DQ725759     1    28    29
browser |    27  100.0%         16     +  86896024  86896050              DQ725759     1    27    29
browser |    27  100.0%         17     +   8493706   8493732              DQ725759     3    29    29
browser |    26  100.0%         17     +  16786746  16786771              DQ725759     3    28    29
browser |    28  100.0%         17     +  20729394  20729421              DQ725759     1    28    29
browser |    29  100.0%         17     +  38621538  38621566              DQ725759     1    29    29
browser |    28  100.0%         17     +  41979110  41979137              DQ725759     2    29    29
browser |    29  100.0%         17     +  52506078  52506106              DQ725759     1    29    29
browser |    29  100.0%         17     +  53214338  53214366              DQ725759     1    29    29
browser |    26  100.0%         17     +  53374246  53374271              DQ725759     4    29    29
browser |    29  100.0%         17     -  62287935  62287963              DQ725759     1    29    29
browser |    26  100.0%         17     +  69835886  69835911              DQ725759     4    29    29
browser |    29  100.0%         17     +  76108898  76108926              DQ725759     1    29    29
browser |    29  100.0%         17     -  77738585  77738613              DQ725759     1    29    29
browser |    29  100.0%         18     +   7055573   7055601              DQ725759     1    29    29
browser |    29  100.0%         18     +   7082133   7082161              DQ725759     1    29    29
browser |    27  100.0%         18     +   7137254   7137280              DQ725759     1    27    29
browser |    27  100.0%         18     +  10657221  10657247              DQ725759     3    29    29
browser |    29  100.0%         18     +  14580454  14580482              DQ725759     1    29    29
browser |    29  100.0%         18     +  26457984  26458012              DQ725759     1    29    29
browser |    29  100.0%         18     +  45822579  45822607              DQ725759     1    29    29
browser |    29  100.0%         18     +  54445914  54445942              DQ725759     1    29    29
browser |    28  100.0%         18     +  59556725  59556752              DQ725759     2    29    29
browser |    29  100.0%         18     -  65540985  65541013              DQ725759     1    29    29
browser |    29  100.0%         18     -  71374425  71374453              DQ725759     1    29    29
browser |    29  100.0%         18     +  89581254  89581282              DQ725759     1    29    29
browser |    29  100.0%         18     -  89765435  89765463              DQ725759     1    29    29
browser |    29  100.0%         19     +   7993868   7993896              DQ725759     1    29    29
browser |    29  100.0%         19     +   8287928   8287956              DQ725759     1    29    29
browser |    29  100.0%         19     +  38002079  38002107              DQ725759     1    29    29
browser |    29  100.0%         19     +  53577639  53577667              DQ725759     1    29    29
browser |    29  100.0%         19     +  54991059  54991087              DQ725759     1    29    29
browser |    27  100.0%          2     +   9230189   9230215              DQ725759     1    27    29
browser |    29  100.0%          2     -  12851700  12851728              DQ725759     1    29    29
browser |    28  100.0%          2     +  13037999  13038026              DQ725759     1    28    29
browser |    29  100.0%          2     -  15258690  15258718              DQ725759     1    29    29
browser |    29  100.0%          2     -  16686890  16686918              DQ725759     1    29    29
browser |    29  100.0%          2     +  39172289  39172317              DQ725759     1    29    29
browser |    29  100.0%          2     +  40470933  40470961              DQ725759     1    29    29
browser |    29  100.0%          2     +  41508933  41508961              DQ725759     1    29    29
browser |    28  100.0%          2     +  49126319  49126346              DQ725759     1    28    29
browser |    29  100.0%          2     +  52910513  52910541              DQ725759     1    29    29
browser |    29  100.0%          2     +  53455694  53455722              DQ725759     1    29    29
browser |    29  100.0%          2     +  55856919  55856947              DQ725759     1    29    29
browser |    29  100.0%          2     +  56387804  56387832              DQ725759     1    29    29
browser |    29  100.0%          2     -  74161460  74161488              DQ725759     1    29    29
browser |    29  100.0%          2     -  79440135  79440163              DQ725759     1    29    29
browser |    29  100.0%          2     +  82365479  82365507              DQ725759     1    29    29
browser |    29  100.0%          2     +  86116454  86116482              DQ725759     1    29    29
browser |    29  100.0%          2     -  88996820  88996848              DQ725759     1    29    29
browser |    29  100.0%          2     +  89857549  89857577              DQ725759     1    29    29
browser |    28  100.0%          2     +  94628119  94628146              DQ725759     1    28    29
browser |    29  100.0%          2     +  95770554  95770582              DQ725759     1    29    29
browser |    26  100.0%          2     + 107277687 107277712              DQ725759     4    29    29
browser |    29  100.0%          2     + 111572364 111572392              DQ725759     1    29    29
browser |    29  100.0%          2     + 112615763 112615791              DQ725759     1    29    29
browser |    29  100.0%          2     + 122329048 122329076              DQ725759     1    29    29
browser |    27  100.0%          2     + 122409700 122409726              DQ725759     3    29    29
browser |    29  100.0%          2     - 123475185 123475213              DQ725759     1    29    29
browser |    29  100.0%          2     + 141940573 141940601              DQ725759     1    29    29
browser |    27  100.0%          2     - 159612305 159612331              DQ725759     3    29    29
browser |    27  100.0%          3     +   4868425   4868451              DQ725759     2    28    29
browser |    29  100.0%          3     +   6006173   6006201              DQ725759     1    29    29
browser |    26  100.0%          3     -   6841215   6841240              DQ725759     4    29    29
browser |    29  100.0%          3     +   7033984   7034012              DQ725759     1    29    29
browser |    29  100.0%          3     -   8903880   8903908              DQ725759     1    29    29
browser |    29  100.0%          3     +   9575983   9576011              DQ725759     1    29    29
browser |    28  100.0%          3     -  10916466  10916493              DQ725759     1    28    29
browser |    29  100.0%          3     +  12907674  12907702              DQ725759     1    29    29
browser |    29  100.0%          3     +  14271003  14271031              DQ725759     1    29    29
browser |    27  100.0%          3     -  14481985  14482011              DQ725759     3    29    29
browser |    29  100.0%          3     +  22433394  22433422              DQ725759     1    29    29
browser |    29  100.0%          3     -  25646120  25646148              DQ725759     1    29    29
browser |    29  100.0%          3     +  35659373  35659401              DQ725759     1    29    29
browser |    29  100.0%          3     +  44644513  44644541              DQ725759     1    29    29
browser |    29  100.0%          3     +  48209743  48209771              DQ725759     1    29    29
browser |    29  100.0%          3     -  50248360  50248388              DQ725759     1    29    29
browser |    27  100.0%          3     -  61894950  61894976              DQ725759     3    29    29
browser |    29  100.0%          3     +  74592104  74592132              DQ725759     1    29    29
browser |    29  100.0%          3     +  76166278  76166306              DQ725759     1    29    29
browser |    29  100.0%          3     +  76211574  76211602              DQ725759     1    29    29
browser |    29  100.0%          3     +  77491634  77491662              DQ725759     1    29    29
browser |    27  100.0%          3     +  86427434  86427460              DQ725759     1    27    29
browser |    29  100.0%          3     -  92427680  92427708              DQ725759     1    29    29
browser |    26  100.0%          3     + 106971416 106971441              DQ725759     4    29    29
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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