DQ540698
 

Information on mRNA DQ540698

Description: Mus musculus piRNA piR-810, 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: DQ540698
Position: chr12:56885361-56885388

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 |    28  100.0%         12     +  56885361  56885388              DQ540698     1    28    30
browser |    28  100.0%          1     -   4499094   4499121              DQ540698     1    28    30
browser |    30  100.0%          1     +   5789313   5789342              DQ540698     1    30    30
browser |    30  100.0%          1     -   9076956   9076985              DQ540698     1    30    30
browser |    30  100.0%          1     -  12973921  12973950              DQ540698     1    30    30
browser |    27  100.0%          1     +  16593396  16593422              DQ540698     2    28    30
browser |    30  100.0%          1     -  21619050  21619079              DQ540698     1    30    30
browser |    28  100.0%          1     +  21707116  21707143              DQ540698     1    28    30
browser |    28  100.0%          1     +  22178291  22178318              DQ540698     1    28    30
browser |    30  100.0%          1     -  23858785  23858814              DQ540698     1    30    30
browser |    29  100.0%          1     +  26043926  26043954              DQ540698     1    29    30
browser |    28  100.0%          1     +  28505816  28505843              DQ540698     1    28    30
browser |    28  100.0%          1     +  42226501  42226528              DQ540698     1    28    30
browser |    28  100.0%          1     +  49063940  49063967              DQ540698     1    28    30
browser |    28  100.0%          1     +  54677711  54677738              DQ540698     1    28    30
browser |    28  100.0%          1     -  55359064  55359091              DQ540698     1    28    30
browser |    30  100.0%          1     -  66528151  66528180              DQ540698     1    30    30
browser |    30  100.0%          1     -  71397536  71397565              DQ540698     1    30    30
browser |    28  100.0%          1     +  94988936  94988963              DQ540698     1    28    30
browser |    28  100.0%          1     -  96178479  96178506              DQ540698     1    28    30
browser |    29  100.0%          1     -  97196030  97196058              DQ540698     2    30    30
browser |    28  100.0%          1     +  99412395  99412422              DQ540698     1    28    30
browser |    30  100.0%          1     + 100915810 100915839              DQ540698     1    30    30
browser |    30  100.0%          1     - 101024702 101024731              DQ540698     1    30    30
browser |    27  100.0%          1     - 103818524 103818550              DQ540698     2    28    30
browser |    29  100.0%          1     + 107473135 107473163              DQ540698     1    29    30
browser |    28  100.0%          1     - 107797204 107797231              DQ540698     1    28    30
browser |    28  100.0%          1     + 109023726 109023753              DQ540698     1    28    30
browser |    28  100.0%          1     + 109302885 109302912              DQ540698     1    28    30
browser |    28  100.0%          1     - 111108454 111108481              DQ540698     1    28    30
browser |    28  100.0%          1     - 112438939 112438966              DQ540698     1    28    30
browser |    27  100.0%          1     - 114919809 114919835              DQ540698     2    28    30
browser |    28  100.0%          1     + 115275141 115275168              DQ540698     1    28    30
browser |    28  100.0%          1     - 116978104 116978131              DQ540698     1    28    30
browser |    28  100.0%          1     + 123242611 123242638              DQ540698     1    28    30
browser |    28  100.0%          1     - 123527287 123527314              DQ540698     3    30    30
browser |    30  100.0%          1     - 124756596 124756625              DQ540698     1    30    30
browser |    27  100.0%          1     - 129500149 129500175              DQ540698     2    28    30
browser |    28  100.0%          1     + 141079545 141079572              DQ540698     1    28    30
browser |    28  100.0%          1     - 142868969 142868996              DQ540698     1    28    30
browser |    28  100.0%          1     + 145338700 145338727              DQ540698     1    28    30
browser |    28  100.0%          1     + 160974261 160974288              DQ540698     1    28    30
browser |    30  100.0%          1     + 165571871 165571900              DQ540698     1    30    30
browser |    28  100.0%          1     - 172776974 172777001              DQ540698     1    28    30
browser |    30  100.0%          1     - 179707547 179707576              DQ540698     1    30    30
browser |    28  100.0%          1     + 179887065 179887092              DQ540698     1    28    30
browser |    28  100.0%          1     + 184257161 184257188              DQ540698     1    28    30
browser |    28  100.0%         10     +   6616940   6616967              DQ540698     1    28    30
browser |    30  100.0%         10     +  12893250  12893279              DQ540698     1    30    30
browser |    29  100.0%         10     +  17767540  17767568              DQ540698     1    29    30
browser |    27  100.0%         10     +  47804792  47804818              DQ540698     2    28    30
browser |    29  100.0%         10     -  50005156  50005184              DQ540698     1    29    30
browser |    28  100.0%         10     +  71372611  71372638              DQ540698     1    28    30
browser |    28  100.0%         10     -  73697434  73697461              DQ540698     1    28    30
browser |    28  100.0%         10     +  74173936  74173963              DQ540698     1    28    30
browser |    30  100.0%         10     +  84650150  84650179              DQ540698     1    30    30
browser |    30  100.0%         10     +  94592260  94592289              DQ540698     1    30    30
browser |    28  100.0%         10     - 101511174 101511201              DQ540698     1    28    30
browser |    28  100.0%         10     + 103129785 103129812              DQ540698     1    28    30
browser |    27  100.0%         10     + 117098518 117098544              DQ540698     3    29    30
browser |    29  100.0%         10     + 119210626 119210654              DQ540698     2    30    30
browser |    28  100.0%         10     - 122302634 122302661              DQ540698     1    28    30
browser |    28  100.0%         10     + 125454026 125454053              DQ540698     1    28    30
browser |    28  100.0%         11     +   7772360   7772387              DQ540698     1    28    30
browser |    28  100.0%         11     +   9119816   9119843              DQ540698     1    28    30
browser |    28  100.0%         11     +  13228321  13228348              DQ540698     1    28    30
browser |    29  100.0%         11     -  14809952  14809980              DQ540698     2    30    30
browser |    28  100.0%         11     -  17973244  17973271              DQ540698     1    28    30
browser |    28  100.0%         11     -  18689204  18689231              DQ540698     1    28    30
browser |    28  100.0%         11     +  21845851  21845878              DQ540698     1    28    30
browser |    27  100.0%         11     +  41458804  41458830              DQ540698     4    30    30
browser |    30  100.0%         11     -  56507075  56507104              DQ540698     1    30    30
browser |    28  100.0%         11     +  73509066  73509093              DQ540698     1    28    30
browser |    28  100.0%         12     +  14430605  14430632              DQ540698     1    28    30
browser |    27  100.0%         12     +  21641181  21641207              DQ540698     2    28    30
browser |    28  100.0%         12     -  24790749  24790776              DQ540698     1    28    30
browser |    29  100.0%         12     -  28142495  28142523              DQ540698     2    30    30
browser |    28  100.0%         12     -  32514174  32514201              DQ540698     1    28    30
browser |    28  100.0%         12     +  32564796  32564823              DQ540698     1    28    30
browser |    28  100.0%         12     +  37326006  37326033              DQ540698     1    28    30
browser |    28  100.0%         12     +  37368790  37368817              DQ540698     1    28    30
browser |    30  100.0%         12     -  39044192  39044221              DQ540698     1    30    30
browser |    28  100.0%         12     -  44552854  44552881              DQ540698     1    28    30
browser |    28  100.0%         12     +  49065436  49065463              DQ540698     1    28    30
browser |    28  100.0%         12     +  57604285  57604312              DQ540698     1    28    30
browser |    28  100.0%         12     +  57608415  57608442              DQ540698     1    28    30
browser |    28  100.0%         12     +  61737935  61737962              DQ540698     1    28    30
browser |    28  100.0%         12     -  62897774  62897801              DQ540698     1    28    30
browser |    28  100.0%         12     +  66466700  66466727              DQ540698     1    28    30
browser |    28  100.0%         12     -  83393459  83393486              DQ540698     1    28    30
browser |    28  100.0%         12     +  92389700  92389727              DQ540698     1    28    30
browser |    29  100.0%         12     - 115125161 115125189              DQ540698     1    29    30
browser |    29  100.0%         12     - 115325858 115325886              DQ540698     1    29    30
browser |    28  100.0%         12     - 115338764 115338791              DQ540698     1    28    30
browser |    29  100.0%         12     - 115427753 115427781              DQ540698     1    29    30
browser |    27  100.0%         13     +  11585746  11585772              DQ540698     2    28    30
browser |    28  100.0%         13     -  15245584  15245611              DQ540698     1    28    30
browser |    28  100.0%         13     -  17774449  17774476              DQ540698     1    28    30
browser |    28  100.0%         13     +  19045776  19045803              DQ540698     1    28    30
browser |    28  100.0%         13     -  19176739  19176766              DQ540698     1    28    30
browser |    28  100.0%         13     +  24104116  24104143              DQ540698     1    28    30
browser |    28  100.0%         13     +  26190880  26190907              DQ540698     1    28    30
browser |    28  100.0%         13     -  31940054  31940081              DQ540698     1    28    30
browser |    28  100.0%         13     +  35273495  35273522              DQ540698     1    28    30
browser |    28  100.0%         13     +  40245810  40245837              DQ540698     1    28    30
browser |    30  100.0%         13     +  49989683  49989712              DQ540698     1    30    30
browser |    28  100.0%         13     +  61113285  61113312              DQ540698     1    28    30
browser |    28  100.0%         13     +  61136161  61136188              DQ540698     1    28    30
browser |    28  100.0%         13     +  63973620  63973647              DQ540698     1    28    30
browser |    27  100.0%         13     +  75469236  75469262              DQ540698     2    28    30
browser |    28  100.0%         13     +  75566401  75566428              DQ540698     1    28    30
browser |    30  100.0%         13     +  84611468  84611497              DQ540698     1    30    30
browser |    28  100.0%         13     +  86255340  86255367              DQ540698     1    28    30
browser |    28  100.0%         13     +  87346856  87346883              DQ540698     1    28    30
browser |    28  100.0%         13     + 106400765 106400792              DQ540698     1    28    30
browser |    28  100.0%         13     + 113565605 113565632              DQ540698     1    28    30
browser |    30  100.0%         13     + 115703663 115703692              DQ540698     1    30    30
browser |    28  100.0%         14     -   4425689   4425716              DQ540698     1    28    30
browser |    27  100.0%         14     +   4530676   4530702              DQ540698     2    28    30
browser |    27  100.0%         14     +   6799531   6799557              DQ540698     2    28    30
browser |    28  100.0%         14     +   7228871   7228898              DQ540698     1    28    30
browser |    28  100.0%         14     -   8245745   8245772              DQ540698     3    30    30
browser |    27  100.0%         14     -  10420494  10420520              DQ540698     2    28    30
browser |    30  100.0%         14     +  11471563  11471592              DQ540698     1    30    30
browser |    28  100.0%         14     +  11541546  11541573              DQ540698     1    28    30
browser |    28  100.0%         14     -  38133944  38133971              DQ540698     1    28    30
browser |    28  100.0%         14     -  45034409  45034436              DQ540698     1    28    30
browser |    29  100.0%         14     -  53044871  53044899              DQ540698     1    29    30
browser |    28  100.0%         14     -  54535774  54535966              DQ540698     1    28    30
browser |    27  100.0%         14     +  58983826  58983852              DQ540698     2    28    30
browser |    28  100.0%         14     +  62163780  62163807              DQ540698     1    28    30
browser |    30  100.0%         14     -  66304550  66304579              DQ540698     1    30    30
browser |    28  100.0%         14     -  66870619  66870646              DQ540698     1    28    30
browser |    30  100.0%         14     -  81463750  81463779              DQ540698     1    30    30
browser |    28  100.0%         14     +  86340385  86340412              DQ540698     1    28    30
browser |    28  100.0%         14     +  97376936  97376963              DQ540698     1    28    30
browser |    28  100.0%         14     +  97661410  97661437              DQ540698     1    28    30
browser |    28  100.0%         14     + 108145341 108145368              DQ540698     1    28    30
browser |    28  100.0%         14     - 113486774 113486801              DQ540698     1    28    30
browser |    28  100.0%         14     + 113774585 113774612              DQ540698     1    28    30
browser |    28  100.0%         14     - 114613364 114613391              DQ540698     1    28    30
browser |    28  100.0%         15     -   9358324   9358351              DQ540698     1    28    30
browser |    28  100.0%         15     +  11499336  11499363              DQ540698     1    28    30
browser |    30  100.0%         15     +  19416653  19416682              DQ540698     1    30    30
browser |    28  100.0%         15     +  22181020  22181047              DQ540698     1    28    30
browser |    29  100.0%         15     +  33930261  33930289              DQ540698     1    29    30
browser |    30  100.0%         15     -  35050090  35050119              DQ540698     1    30    30
browser |    28  100.0%         15     +  41343421  41343448              DQ540698     1    28    30
browser |    28  100.0%         15     -  43706639  43706666              DQ540698     1    28    30
browser |    28  100.0%         15     +  46883586  46883613              DQ540698     1    28    30
browser |    28  100.0%         15     -  61830459  61830486              DQ540698     1    28    30
browser |    28  100.0%         15     +  70399530  70399557              DQ540698     1    28    30
browser |    27  100.0%         15     +  93843090  93843116              DQ540698     1    27    30
browser |    27  100.0%         16     -   6379010   6379036              DQ540698     1    27    30
browser |    28  100.0%         16     -   9308824   9308851              DQ540698     1    28    30
browser |    28  100.0%         16     +  14355141  14355168              DQ540698     1    28    30
browser |    28  100.0%         16     +  16420941  16420968              DQ540698     1    28    30
browser |    27  100.0%         16     -  24957450  24957476              DQ540698     1    27    30
browser |    28  100.0%         16     +  25218385  25218412              DQ540698     1    28    30
browser |    28  100.0%         16     -  26019554  26019581              DQ540698     1    28    30
browser |    28  100.0%         16     +  36901776  36901803              DQ540698     1    28    30
browser |    30  100.0%         16     -  42645717  42645746              DQ540698     1    30    30
browser |    28  100.0%         16     +  44675680  44675707              DQ540698     1    28    30
browser |    28  100.0%         16     +  47030665  47030692              DQ540698     1    28    30
browser |    28  100.0%         16     +  63515035  63515062              DQ540698     1    28    30
browser |    30  100.0%         16     +  65786003  65786032              DQ540698     1    30    30
browser |    28  100.0%         16     +  67116635  67116662              DQ540698     1    28    30
browser |    29  100.0%         16     -  68602816  68602844              DQ540698     1    29    30
browser |    29  100.0%         16     +  72086086  72086114              DQ540698     1    29    30
browser |    28  100.0%         16     -  74162939  74162966              DQ540698     1    28    30
browser |    28  100.0%         16     +  79042981  79043008              DQ540698     1    28    30
browser |    29  100.0%         16     -  96458711  96458739              DQ540698     1    29    30
browser |    30  100.0%         17     +   8493706   8493735              DQ540698     1    30    30
browser |    28  100.0%         17     +  38621540  38621567              DQ540698     1    28    30
browser |    28  100.0%         17     +  41979111  41979138              DQ540698     1    28    30
browser |    28  100.0%         17     +  52506080  52506107              DQ540698     1    28    30
browser |    30  100.0%         17     +  53214340  53214369              DQ540698     1    30    30
browser |    27  100.0%         17     +  53374246  53374272              DQ540698     2    28    30
browser |    28  100.0%         17     -  62287934  62287961              DQ540698     1    28    30
browser |    27  100.0%         17     +  69835886  69835912              DQ540698     2    28    30
browser |    28  100.0%         17     +  76108900  76108927              DQ540698     1    28    30
browser |    28  100.0%         17     -  77738584  77738611              DQ540698     1    28    30
browser |    28  100.0%         18     +   7055575   7055602              DQ540698     1    28    30
browser |    28  100.0%         18     +   7082135   7082162              DQ540698     1    28    30
browser |    28  100.0%         18     +  10657221  10657248              DQ540698     1    28    30
browser |    28  100.0%         18     +  14580456  14580483              DQ540698     1    28    30
browser |    28  100.0%         18     +  26457986  26458013              DQ540698     1    28    30
browser |    28  100.0%         18     +  31494140  31494167              DQ540698     3    30    30
browser |    29  100.0%         18     +  32433314  32433342              DQ540698     2    30    30
browser |    29  100.0%         18     +  45822581  45822609              DQ540698     1    29    30
browser |    27  100.0%         18     +  50435612  50435638              DQ540698     2    28    30
browser |    28  100.0%         18     +  54445916  54445943              DQ540698     1    28    30
browser |    27  100.0%         18     +  59556726  59556752              DQ540698     1    27    30
browser |    30  100.0%         18     -  65540982  65541011              DQ540698     1    30    30
browser |    28  100.0%         18     -  71374424  71374451              DQ540698     1    28    30
browser |    30  100.0%         18     +  83807063  83807092              DQ540698     1    30    30
browser |    28  100.0%         18     +  89581256  89581283              DQ540698     1    28    30
browser |    30  100.0%         18     -  89613881  89613910              DQ540698     1    30    30
browser |    30  100.0%         18     -  89665371  89665400              DQ540698     1    30    30
browser |    28  100.0%         18     -  89765434  89765461              DQ540698     1    28    30
browser |    28  100.0%         19     +   7993870   7993897              DQ540698     1    28    30
browser |    28  100.0%         19     +   8287930   8287957              DQ540698     1    28    30
browser |    28  100.0%         19     +  38002081  38002108              DQ540698     1    28    30
browser |    28  100.0%         19     +  53577641  53577668              DQ540698     1    28    30
browser |    28  100.0%         19     +  54991061  54991088              DQ540698     1    28    30
browser |    27  100.0%          2     +  11891117  11891143              DQ540698     2    28    30
browser |    28  100.0%          2     -  12851699  12851726              DQ540698     1    28    30
browser |    28  100.0%          2     -  15258689  15258716              DQ540698     1    28    30
browser |    28  100.0%          2     -  16686889  16686916              DQ540698     1    28    30
browser |    30  100.0%          2     +  18508123  18508152              DQ540698     1    30    30
browser |    28  100.0%          2     +  39172291  39172318              DQ540698     1    28    30
browser |    27  100.0%          2     +  40470935  40470961              DQ540698     1    27    30
browser |    28  100.0%          2     +  41508935  41508962              DQ540698     1    28    30
browser |    27  100.0%          2     +  52910515  52910541              DQ540698     1    27    30
browser |    28  100.0%          2     +  53455696  53455723              DQ540698     1    28    30
browser |    30  100.0%          2     +  55856921  55856950              DQ540698     1    30    30
browser |    28  100.0%          2     +  56387806  56387833              DQ540698     1    28    30
browser |    29  100.0%          2     +  60866383  60866411              DQ540698     1    29    30
browser |    29  100.0%          2     +  61670008  61670036              DQ540698     1    29    30
browser |    29  100.0%          2     -  61690141  61690169              DQ540698     1    29    30
browser |    28  100.0%          2     +  66600491  66600518              DQ540698     1    28    30
browser |    28  100.0%          2     -  74161459  74161486              DQ540698     1    28    30
browser |    30  100.0%          2     -  79440132  79440161              DQ540698     1    30    30
browser |    28  100.0%          2     +  82365481  82365508              DQ540698     1    28    30
browser |    27  100.0%          2     +  86116456  86116482              DQ540698     1    27    30
browser |    30  100.0%          2     -  88714931  88714960              DQ540698     1    30    30
browser |    28  100.0%          2     -  88996819  88996846              DQ540698     1    28    30
browser |    27  100.0%          2     +  89036811  89036837              DQ540698     2    28    30
browser |    28  100.0%          2     +  89857551  89857578              DQ540698     1    28    30
browser |    29  100.0%          2     +  94622919  94622947              DQ540698     2    30    30
browser |    28  100.0%          2     +  95770556  95770583              DQ540698     1    28    30
browser |    27  100.0%          2     -  96319314  96319340              DQ540698     2    28    30
browser |    29  100.0%          2     - 105460266 105460294              DQ540698     1    29    30
browser |    27  100.0%          2     + 107277687 107277713              DQ540698     2    28    30
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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