DQ557163
 

Information on mRNA DQ557163

Description: Mus musculus piRNA piR-24275, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
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: 2008-11-02
Version: 1
mRNA sequence: DQ557163
Position: chr12:56797242-56797271

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     +  56797242  56797271              DQ557163     1    30    31
browser |    30  100.0%          1     +   5879927   5879956              DQ557163     1    30    31
browser |    30  100.0%          1     +   6505956   6505985              DQ557163     1    30    31
browser |    31  100.0%          1     -   8065662   8065692              DQ557163     1    31    31
browser |    30  100.0%          1     -   8228104   8228133              DQ557163     1    30    31
browser |    30  100.0%          1     +   8730967   8730996              DQ557163     1    30    31
browser |    31  100.0%          1     -   8859137   8859167              DQ557163     1    31    31
browser |    31  100.0%          1     +  11439103  11439133              DQ557163     1    31    31
browser |    31  100.0%          1     -  13622527  13622557              DQ557163     1    31    31
browser |    30  100.0%          1     -  16810174  16810203              DQ557163     1    30    31
browser |    31  100.0%          1     +  17596207  17596237              DQ557163     1    31    31
browser |    31  100.0%          1     -  18028767  18028797              DQ557163     1    31    31
browser |    30  100.0%          1     -  18588798  18588827              DQ557163     1    30    31
browser |    30  100.0%          1     -  19694382  19694411              DQ557163     1    30    31
browser |    31  100.0%          1     +  22070820  22070850              DQ557163     1    31    31
browser |    30  100.0%          1     -  26454790  26454819              DQ557163     1    30    31
browser |    30  100.0%          1     +  26513532  26513561              DQ557163     1    30    31
browser |    30  100.0%          1     -  27220938  27220967              DQ557163     1    30    31
browser |    31  100.0%          1     +  28496726  28496756              DQ557163     1    31    31
browser |    31  100.0%          1     +  29986662  29986692              DQ557163     1    31    31
browser |    31  100.0%          1     -  31510392  31510422              DQ557163     1    31    31
browser |    30  100.0%          1     -  34388271  34388300              DQ557163     1    30    31
browser |    30  100.0%          1     -  35829267  35829296              DQ557163     1    30    31
browser |    30  100.0%          1     -  40738947  40738976              DQ557163     1    30    31
browser |    30  100.0%          1     +  47265376  47265405              DQ557163     1    30    31
browser |    31  100.0%          1     +  48400717  48400747              DQ557163     1    31    31
browser |    30  100.0%          1     +  53172207  53172236              DQ557163     1    30    31
browser |    30  100.0%          1     +  58367882  58367911              DQ557163     1    30    31
browser |    31  100.0%          1     +  58791073  58791103              DQ557163     1    31    31
browser |    30  100.0%          1     +  58856190  58856219              DQ557163     1    30    31
browser |    30  100.0%          1     +  60769376  60769405              DQ557163     1    30    31
browser |    31  100.0%          1     -  65855519  65855549              DQ557163     1    31    31
browser |    31  100.0%          1     -  76593232  76593262              DQ557163     1    31    31
browser |    30  100.0%          1     +  81547251  81547280              DQ557163     1    30    31
browser |    30  100.0%          1     -  82480517  82480546              DQ557163     1    30    31
browser |    30  100.0%          1     +  87066733  87066762              DQ557163     1    30    31
browser |    30  100.0%          1     -  87389594  87389623              DQ557163     1    30    31
browser |    30  100.0%          1     -  89128522  89128551              DQ557163     1    30    31
browser |    30  100.0%          1     +  91404306  91404335              DQ557163     1    30    31
browser |    30  100.0%          1     -  93886004  93886033              DQ557163     1    30    31
browser |    30  100.0%          1     -  95624592  95624621              DQ557163     1    30    31
browser |    30  100.0%          1     -  97102203  97102232              DQ557163     1    30    31
browser |    31  100.0%          1     + 100458129 100458159              DQ557163     1    31    31
browser |    31  100.0%          1     + 101911241 101911271              DQ557163     1    31    31
browser |    30  100.0%          1     + 103138270 103138299              DQ557163     1    30    31
browser |    31  100.0%          1     - 103407735 103407765              DQ557163     1    31    31
browser |    31  100.0%          1     - 104293968 104293998              DQ557163     1    31    31
browser |    30  100.0%          1     - 106731815 106731844              DQ557163     2    31    31
browser |    31  100.0%          1     - 108885767 108885797              DQ557163     1    31    31
browser |    30  100.0%          1     - 109542847 109542876              DQ557163     1    30    31
browser |    30  100.0%          1     + 111186727 111186756              DQ557163     1    30    31
browser |    30  100.0%          1     - 111632815 111632844              DQ557163     1    30    31
browser |    31  100.0%          1     + 112197447 112197477              DQ557163     1    31    31
browser |    30  100.0%          1     - 112858924 112858953              DQ557163     1    30    31
browser |    30  100.0%          1     - 112945522 112945551              DQ557163     1    30    31
browser |    30  100.0%          1     + 116581375 116581404              DQ557163     1    30    31
browser |    30  100.0%          1     + 117635033 117635062              DQ557163     1    30    31
browser |    30  100.0%          1     - 125246310 125246339              DQ557163     1    30    31
browser |    30  100.0%          1     + 125276476 125276505              DQ557163     1    30    31
browser |    30  100.0%          1     + 127491369 127491398              DQ557163     1    30    31
browser |    30  100.0%          1     + 127808168 127808197              DQ557163     1    30    31
browser |    31  100.0%          1     + 136737180 136737210              DQ557163     1    31    31
browser |    31  100.0%          1     + 143724366 143724396              DQ557163     1    31    31
browser |    31  100.0%          1     - 144261621 144261651              DQ557163     1    31    31
browser |    31  100.0%          1     + 146163008 146163038              DQ557163     1    31    31
browser |    30  100.0%          1     + 159802701 159802730              DQ557163     1    30    31
browser |    31  100.0%          1     - 161361174 161361204              DQ557163     1    31    31
browser |    30  100.0%          1     - 166181473 166181502              DQ557163     1    30    31
browser |    30  100.0%          1     + 166595574 166595603              DQ557163     1    30    31
browser |    30  100.0%          1     - 169945069 169945098              DQ557163     1    30    31
browser |    31  100.0%          1     - 171658792 171658822              DQ557163     1    31    31
browser |    31  100.0%          1     - 172095032 172095062              DQ557163     1    31    31
browser |    30  100.0%          1     + 174874106 174874135              DQ557163     1    30    31
browser |    30  100.0%          1     + 176376000 176376029              DQ557163     1    30    31
browser |    31  100.0%          1     + 177955825 177955855              DQ557163     1    31    31
browser |    30  100.0%          1     - 178003387 178003416              DQ557163     1    30    31
browser |    31  100.0%          1     - 179723281 179723311              DQ557163     1    31    31
browser |    30  100.0%          1     + 181096457 181096486              DQ557163     1    30    31
browser |    31  100.0%          1     - 181322175 181322205              DQ557163     1    31    31
browser |    31  100.0%          1     - 183297993 183298023              DQ557163     1    31    31
browser |    31  100.0%          1     - 185037270 185037300              DQ557163     1    31    31
browser |    31  100.0%          1     - 195004370 195004400              DQ557163     1    31    31
browser |    30  100.0%         10     +   3556297   3556326              DQ557163     1    30    31
browser |    31  100.0%         10     -   7316275   7316305              DQ557163     1    31    31
browser |    31  100.0%         10     -   8476759   8476789              DQ557163     1    31    31
browser |    31  100.0%         10     -  11571738  11571768              DQ557163     1    31    31
browser |    30  100.0%         10     +  19420010  19420039              DQ557163     1    30    31
browser |    30  100.0%         10     -  19674774  19674803              DQ557163     1    30    31
browser |    30  100.0%         10     +  21523583  21523612              DQ557163     1    30    31
browser |    31  100.0%         10     +  22404475  22404505              DQ557163     1    31    31
browser |    30  100.0%         10     +  22564529  22564558              DQ557163     1    30    31
browser |    31  100.0%         10     +  23752584  23752614              DQ557163     1    31    31
browser |    30  100.0%         10     +  24980656  24980685              DQ557163     1    30    31
browser |    30  100.0%         10     -  25846032  25846061              DQ557163     1    30    31
browser |    30  100.0%         10     -  31360327  31360356              DQ557163     1    30    31
browser |    30  100.0%         10     +  34623187  34623216              DQ557163     1    30    31
browser |    31  100.0%         10     +  37728796  37728826              DQ557163     1    31    31
browser |    31  100.0%         10     -  38467403  38467433              DQ557163     1    31    31
browser |    30  100.0%         10     -  41718254  41718283              DQ557163     1    30    31
browser |    30  100.0%         10     +  43648296  43648325              DQ557163     1    30    31
browser |    31  100.0%         10     -  43754572  43754602              DQ557163     1    31    31
browser |    30  100.0%         10     -  47548404  47548433              DQ557163     1    30    31
browser |    31  100.0%         10     +  47558170  47558200              DQ557163     1    31    31
browser |    30  100.0%         10     -  51760812  51760841              DQ557163     1    30    31
browser |    30  100.0%         10     -  56598560  56598589              DQ557163     1    30    31
browser |    30  100.0%         10     -  57015480  57015509              DQ557163     1    30    31
browser |    30  100.0%         10     -  62941482  62941511              DQ557163     1    30    31
browser |    30  100.0%         10     +  65478990  65479019              DQ557163     1    30    31
browser |    30  100.0%         10     +  66563605  66563634              DQ557163     1    30    31
browser |    30  100.0%         10     -  71528970  71528999              DQ557163     1    30    31
browser |    31  100.0%         10     +  81511738  81511768              DQ557163     1    31    31
browser |    31  100.0%         10     +  81670866  81670896              DQ557163     1    31    31
browser |    30  100.0%         10     -  81805444  81805473              DQ557163     1    30    31
browser |    31  100.0%         10     +  82409686  82409716              DQ557163     1    31    31
browser |    31  100.0%         10     +  83307095  83307125              DQ557163     1    31    31
browser |    30  100.0%         10     +  83512150  83512179              DQ557163     1    30    31
browser |    31  100.0%         10     -  85552777  85552807              DQ557163     1    31    31
browser |    31  100.0%         10     -  88488564  88488594              DQ557163     1    31    31
browser |    31  100.0%         10     -  92356107  92356137              DQ557163     1    31    31
browser |    30  100.0%         10     +  94203298  94203327              DQ557163     1    30    31
browser |    30  100.0%         10     +  96033758  96033787              DQ557163     1    30    31
browser |    30  100.0%         10     -  99176704  99176733              DQ557163     1    30    31
browser |    31  100.0%         10     - 104392930 104392960              DQ557163     1    31    31
browser |    30  100.0%         10     - 104673148 104673177              DQ557163     1    30    31
browser |    30  100.0%         10     - 105014667 105014696              DQ557163     1    30    31
browser |    30  100.0%         10     - 107837077 107837106              DQ557163     1    30    31
browser |    30  100.0%         10     + 109156444 109156473              DQ557163     1    30    31
browser |    30  100.0%         10     - 110533848 110533877              DQ557163     1    30    31
browser |    31  100.0%         10     + 113563970 113564000              DQ557163     1    31    31
browser |    30  100.0%         10     + 116447531 116447560              DQ557163     1    30    31
browser |    30  100.0%         10     - 117908271 117908300              DQ557163     1    30    31
browser |    30  100.0%         10     - 121002356 121002385              DQ557163     1    30    31
browser |    31  100.0%         10     - 121978064 121978094              DQ557163     1    31    31
browser |    30  100.0%         10     + 122205140 122205169              DQ557163     1    30    31
browser |    31  100.0%         10     - 122343401 122343431              DQ557163     1    31    31
browser |    31  100.0%         10     + 122674017 122674047              DQ557163     1    31    31
browser |    30  100.0%         10     - 124413943 124413972              DQ557163     1    30    31
browser |    30  100.0%         10     + 124520211 124520240              DQ557163     1    30    31
browser |    30  100.0%         10     + 129230056 129230085              DQ557163     1    30    31
browser |    30  100.0%         10     - 129762891 129762920              DQ557163     1    30    31
browser |    31  100.0%         10     + 130400265 130400295              DQ557163     1    31    31
browser |    31  100.0%         11     +   7531050   7531080              DQ557163     1    31    31
browser |    31  100.0%         11     +   9036210   9036240              DQ557163     1    31    31
browser |    30  100.0%         11     +   9663349   9663378              DQ557163     1    30    31
browser |    30  100.0%         11     -  10712044  10712073              DQ557163     1    30    31
browser |    30  100.0%         11     -  12513654  12513683              DQ557163     1    30    31
browser |    31  100.0%         11     +  14848068  14848098              DQ557163     1    31    31
browser |    30  100.0%         11     -  15179424  15179453              DQ557163     1    30    31
browser |    30  100.0%         11     +  18761822  18761851              DQ557163     1    30    31
browser |    30  100.0%         11     +  19518791  19518820              DQ557163     1    30    31
browser |    31  100.0%         11     +  20460482  20460512              DQ557163     1    31    31
browser |    30  100.0%         11     -  20468110  20468139              DQ557163     1    30    31
browser |    30  100.0%         11     +  23173949  23173978              DQ557163     1    30    31
browser |    30  100.0%         11     +  23195562  23195591              DQ557163     1    30    31
browser |    31  100.0%         11     -  27085493  27085523              DQ557163     1    31    31
browser |    30  100.0%         11     +  27905335  27905364              DQ557163     1    30    31
browser |    31  100.0%         11     -  28049026  28049056              DQ557163     1    31    31
browser |    30  100.0%         11     +  31402929  31402958              DQ557163     1    30    31
browser |    30  100.0%         11     +  39959918  39959947              DQ557163     1    30    31
browser |    30  100.0%         11     -  51330242  51330271              DQ557163     1    30    31
browser |    30  100.0%         11     +  55137129  55137158              DQ557163     1    30    31
browser |    30  100.0%         11     -  61312995  61313024              DQ557163     1    30    31
browser |    30  100.0%         11     -  63360284  63360313              DQ557163     1    30    31
browser |    30  100.0%         11     +  65347976  65348005              DQ557163     1    30    31
browser |    30  100.0%         11     +  66843435  66843464              DQ557163     1    30    31
browser |    31  100.0%         11     +  70959016  70959046              DQ557163     1    31    31
browser |    31  100.0%         11     -  74021491  74021521              DQ557163     1    31    31
browser |    31  100.0%         11     -  79765267  79765297              DQ557163     1    31    31
browser |    30  100.0%         11     -  81438098  81438127              DQ557163     1    30    31
browser |    30  100.0%         11     +  82227439  82227468              DQ557163     1    30    31
browser |    31  100.0%         11     -  84953259  84953289              DQ557163     1    31    31
browser |    30  100.0%         11     +  85181762  85181791              DQ557163     1    30    31
browser |    30  100.0%         11     -  86738170  86738199              DQ557163     1    30    31
browser |    30  100.0%         11     +  88807149  88807178              DQ557163     1    30    31
browser |    31  100.0%         11     -  90399786  90399816              DQ557163     1    31    31
browser |    30  100.0%         11     -  90794247  90794276              DQ557163     1    30    31
browser |    30  100.0%         11     +  90856366  90856395              DQ557163     1    30    31
browser |    30  100.0%         11     -  91991617  91991646              DQ557163     1    30    31
browser |    30  100.0%         11     -  98505821  98505850              DQ557163     1    30    31
browser |    30  100.0%         11     +  99606312  99606341              DQ557163     1    30    31
browser |    31  100.0%         11     - 100555476 100555506              DQ557163     1    31    31
browser |    30  100.0%         11     + 106186693 106186722              DQ557163     1    30    31
browser |    30  100.0%         11     - 111075063 111075092              DQ557163     1    30    31
browser |    30  100.0%         11     + 111111838 111111867              DQ557163     1    30    31
browser |    30  100.0%         11     + 115651092 115651121              DQ557163     1    30    31
browser |    30  100.0%         11     - 116678120 116678149              DQ557163     1    30    31
browser |    30  100.0%         11     - 117392415 117392444              DQ557163     1    30    31
browser |    31  100.0%         11     - 120213713 120213743              DQ557163     1    31    31
browser |    30  100.0%         11     - 120962466 120962495              DQ557163     1    30    31
browser |    30  100.0%         12     -   3054101   3054130              DQ557163     1    30    31
browser |    30  100.0%         12     +   3086368   3086397              DQ557163     1    30    31
browser |    30  100.0%         12     +   3386175   3386204              DQ557163     1    30    31
browser |    30  100.0%         12     -   6568269   6568298              DQ557163     1    30    31
browser |    30  100.0%         12     +  11159023  11159052              DQ557163     1    30    31
browser |    30  100.0%         12     -  17173948  17173977              DQ557163     1    30    31
browser |    31  100.0%         12     +  18330455  18330485              DQ557163     1    31    31
browser |    31  100.0%         12     -  19826237  19826267              DQ557163     1    31    31
browser |    31  100.0%         12     +  19850841  19850871              DQ557163     1    31    31
browser |    31  100.0%         12     -  21655495  21655525              DQ557163     1    31    31
browser |    31  100.0%         12     -  22093701  22093731              DQ557163     1    31    31
browser |    31  100.0%         12     -  23252569  23252599              DQ557163     1    31    31
browser |    30  100.0%         12     -  24447204  24447233              DQ557163     1    30    31
browser |    31  100.0%         12     -  24743823  24743853              DQ557163     1    31    31
browser |    31  100.0%         12     +  26157887  26157917              DQ557163     1    31    31
browser |    30  100.0%         12     +  31413514  31413543              DQ557163     1    30    31
browser |    30  100.0%         12     -  32079728  32079757              DQ557163     1    30    31
browser |    31  100.0%         12     -  39483553  39483583              DQ557163     1    31    31
browser |    30  100.0%         12     -  40453818  40453847              DQ557163     1    30    31
browser |    30  100.0%         12     -  41415235  41415264              DQ557163     1    30    31
browser |    31  100.0%         12     +  44817293  44817323              DQ557163     1    31    31
browser |    30  100.0%         12     -  48580690  48580719              DQ557163     1    30    31
browser |    30  100.0%         12     -  49043300  49043329              DQ557163     1    30    31
browser |    31  100.0%         12     +  60759048  60759078              DQ557163     1    31    31
browser |    30  100.0%         12     +  61338708  61338737              DQ557163     1    30    31
browser |    30  100.0%         12     +  65079310  65079339              DQ557163     1    30    31
browser |    30  100.0%         12     +  65853368  65853397              DQ557163     1    30    31
browser |    31  100.0%         12     +  66459168  66459198              DQ557163     1    31    31
browser |    30  100.0%         12     +  68673921  68673950              DQ557163     1    30    31
browser |    31  100.0%         12     -  72686788  72686818              DQ557163     1    31    31
browser |    30  100.0%         12     -  80465797  80465826              DQ557163     1    30    31
browser |    30  100.0%         12     +  85453162  85453191              DQ557163     1    30    31
browser |    30  100.0%         12     -  93478059  93478088              DQ557163     1    30    31
browser |    30  100.0%         12     +  94008649  94008678              DQ557163     1    30    31
browser |    31  100.0%         12     +  94240171  94240201              DQ557163     1    31    31
browser |    30  100.0%         12     +  96199572  96199601              DQ557163     1    30    31
browser |    31  100.0%         12     -  98323219  98323249              DQ557163     1    31    31
browser |    31  100.0%         12     + 105271848 105271878              DQ557163     1    31    31
browser |    30  100.0%         12     - 109870081 109870110              DQ557163     1    30    31
browser |    31  100.0%         12     - 114489411 114489441              DQ557163     1    31    31
browser |    31  100.0%         12     - 114598770 114598800              DQ557163     1    31    31
browser |    30  100.0%         12     - 119556253 119556282              DQ557163     1    30    31
browser |    30  100.0%         13     -   4390178   4390207              DQ557163     1    30    31
browser |    31  100.0%         13     +   4878986   4879016              DQ557163     1    31    31
browser |    30  100.0%         13     -   5329757   5329786              DQ557163     1    30    31
browser |    30  100.0%         13     +   7325340   7325369              DQ557163     1    30    31
browser |    30  100.0%         13     +   7327828   7327857              DQ557163     1    30    31
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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