AB351862
 

Information on mRNA AB351862

Description: Mus musculus non-coding RNA, oocyte_piRNA2678, complete sequence.
Gene: n/a
Product: n/a
Author: Watanabe,T., Totoki,Y., Toyoda,A., Kaneda,M., Kuramochi-Miyagawa,S., Obata,Y., Chiba,H., Kohara,Y., Kono,T., Nakano,T., Surani,M.A., Sakaki,Y. and Sasaki,H.
Organism: Mus musculus
Tissue: ovary
Development stage: p8
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB351862
Position: chrX:15628627-15628652

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 |    26  100.0%          X     +  15628627  15628652              AB351862     1    26    27
browser |    27  100.0%          1     +   3986289   3986315              AB351862     1    27    27
browser |    26  100.0%          1     +   6131421   6131446              AB351862     1    26    27
browser |    27  100.0%          1     +  14011526  14011552              AB351862     1    27    27
browser |    27  100.0%          1     +  52921930  52921956              AB351862     1    27    27
browser |    27  100.0%          1     -  60504212  60504238              AB351862     1    27    27
browser |    25  100.0%          1     +  61719413  61719437              AB351862     3    27    27
browser |    27  100.0%          1     -  69971580  69971606              AB351862     1    27    27
browser |    26  100.0%          1     +  76122110  76122135              AB351862     1    26    27
browser |    27  100.0%          1     -  78556232  78556258              AB351862     1    27    27
browser |    27  100.0%          1     -  92504417  92504443              AB351862     1    27    27
browser |    26  100.0%          1     - 101958856 101958881              AB351862     1    26    27
browser |    25  100.0%          1     - 111309592 111309616              AB351862     1    25    27
browser |    27  100.0%          1     + 127496425 127496451              AB351862     1    27    27
browser |    27  100.0%          1     - 133386710 133386736              AB351862     1    27    27
browser |    26  100.0%          1     + 165751090 165751117              AB351862     1    26    27
browser |    26  100.0%          1     - 170679358 170679383              AB351862     1    26    27
browser |    27  100.0%          1     + 183891261 183891287              AB351862     1    27    27
browser |    27  100.0%          1     + 185509209 185509235              AB351862     1    27    27
browser |    26  100.0%          1     + 194237542 194237567              AB351862     1    26    27
browser |    27  100.0%         10     -  38343195  38343221              AB351862     1    27    27
browser |    27  100.0%         10     -  49374122  49374148              AB351862     1    27    27
browser |    27  100.0%         10     -  59009838  59009864              AB351862     1    27    27
browser |    26  100.0%         10     +  59233359  59233384              AB351862     1    26    27
browser |    27  100.0%         10     +  59981605  59981631              AB351862     1    27    27
browser |    26  100.0%         10     +  83234134  83234159              AB351862     1    26    27
browser |    27  100.0%         10     -  91876101  91876127              AB351862     1    27    27
browser |    26  100.0%         10     -  94819431  94819457              AB351862     1    26    27
browser |    27  100.0%         10     +  95466105  95466131              AB351862     1    27    27
browser |    27  100.0%         10     + 121348040 121348066              AB351862     1    27    27
browser |    27  100.0%         10     + 126578871 126578897              AB351862     1    27    27
browser |    27  100.0%         11     -   4081242   4081268              AB351862     1    27    27
browser |    27  100.0%         11     +  12126718  12126744              AB351862     1    27    27
browser |    27  100.0%         11     -  26487626  26487652              AB351862     1    27    27
browser |    27  100.0%         11     -  26989130  26989156              AB351862     1    27    27
browser |    27  100.0%         11     -  42394035  42394061              AB351862     1    27    27
browser |    26  100.0%         11     -  50928172  50928197              AB351862     1    26    27
browser |    27  100.0%         11     -  52007923  52007949              AB351862     1    27    27
browser |    27  100.0%         11     +  57245282  57245308              AB351862     1    27    27
browser |    27  100.0%         11     -  59911208  59911234              AB351862     1    27    27
browser |    27  100.0%         11     +  72705843  72705869              AB351862     1    27    27
browser |    27  100.0%         11     -  86033368  86033394              AB351862     1    27    27
browser |    26  100.0%         11     +  95332676  95332701              AB351862     1    26    27
browser |    25  100.0%         11     + 103333222 103333246              AB351862     1    25    27
browser |    25  100.0%         12     -   7915592   7915616              AB351862     1    25    27
browser |    27  100.0%         12     -  13671457  13671483              AB351862     1    27    27
browser |    27  100.0%         12     +  36793724  36793750              AB351862     1    27    27
browser |    27  100.0%         12     +  39863579  39863606              AB351862     1    27    27
browser |    27  100.0%         12     +  41866703  41866729              AB351862     1    27    27
browser |    25  100.0%         12     +  60521121  60521145              AB351862     3    27    27
browser |    27  100.0%         12     -  64947402  64947428              AB351862     1    27    27
browser |    27  100.0%         12     -  65620942  65620968              AB351862     1    27    27
browser |    26  100.0%         12     -  65707240  65707265              AB351862     1    26    27
browser |    27  100.0%         12     +  65818637  65818663              AB351862     1    27    27
browser |    26  100.0%         12     - 101622024 101622049              AB351862     1    26    27
browser |    27  100.0%         12     - 104671890 104671916              AB351862     1    27    27
browser |    27  100.0%         13     +  11455254  11455280              AB351862     1    27    27
browser |    27  100.0%         13     +  69581182  69581208              AB351862     1    27    27
browser |    27  100.0%         13     +  96234332  96234358              AB351862     1    27    27
browser |    27  100.0%         13     + 105528075 105528101              AB351862     1    27    27
browser |    27  100.0%         13     - 105764925 105764951              AB351862     1    27    27
browser |    27  100.0%         13     - 109412686 109412712              AB351862     1    27    27
browser |    27  100.0%         13     - 113744812 113744838              AB351862     1    27    27
browser |    27  100.0%         13     - 120210594 120210620              AB351862     1    27    27
browser |    27  100.0%         14     -   3557777   3557803              AB351862     1    27    27
browser |    27  100.0%         14     +   5105874   5105900              AB351862     1    27    27
browser |    27  100.0%         14     +   7295375   7295401              AB351862     1    27    27
browser |    27  100.0%         14     +  22940807  22940833              AB351862     1    27    27
browser |    27  100.0%         14     -  35839627  35839653              AB351862     1    27    27
browser |    25  100.0%         14     -  38207985  38208009              AB351862     1    25    27
browser |    25  100.0%         14     -  39729973  39729997              AB351862     1    25    27
browser |    26  100.0%         14     +  50576450  50576475              AB351862     1    26    27
browser |    27  100.0%         14     -  70451333  70451359              AB351862     1    27    27
browser |    26  100.0%         14     -  87213366  87213391              AB351862     2    27    27
browser |    27  100.0%         14     -  96900761  96900787              AB351862     1    27    27
browser |    25  100.0%         14     + 104371093 104371117              AB351862     1    25    27
browser |    27  100.0%         14     + 109258254 109258280              AB351862     1    27    27
browser |    27  100.0%         14     + 115808188 115808214              AB351862     1    27    27
browser |    25  100.0%         14     + 116155665 116155689              AB351862     1    25    27
browser |    27  100.0%         14     - 120323351 120323377              AB351862     1    27    27
browser |    27  100.0%         15     -  23021013  23021039              AB351862     1    27    27
browser |    27  100.0%         15     +  25544465  25544491              AB351862     1    27    27
browser |    27  100.0%         15     +  36634920  36634946              AB351862     1    27    27
browser |    27  100.0%         15     +  45015784  45015810              AB351862     1    27    27
browser |    27  100.0%         15     -  61064055  61064081              AB351862     1    27    27
browser |    27  100.0%         15     -  61257335  61257361              AB351862     1    27    27
browser |    27  100.0%         15     -  82589262  82589288              AB351862     1    27    27
browser |    27  100.0%         15     +  89771264  89771290              AB351862     1    27    27
browser |    27  100.0%         15     +  94013859  94013885              AB351862     1    27    27
browser |    27  100.0%         15     -  96982869  96982895              AB351862     1    27    27
browser |    27  100.0%         16     +  14233480  14233506              AB351862     1    27    27
browser |    26  100.0%         16     +  14643493  14643518              AB351862     1    26    27
browser |    27  100.0%         16     +  22174276  22174302              AB351862     1    27    27
browser |    27  100.0%         16     -  27221538  27221564              AB351862     1    27    27
browser |    27  100.0%         16     -  30815450  30815476              AB351862     1    27    27
browser |    26  100.0%         16     +  31289668  31289693              AB351862     1    26    27
browser |    26  100.0%         16     -  53376971  53376996              AB351862     1    26    27
browser |    27  100.0%         16     +  65911181  65911207              AB351862     1    27    27
browser |    27  100.0%         16     +  95899031  95899057              AB351862     1    27    27
browser |    27  100.0%         17     -  18216814  18216840              AB351862     1    27    27
browser |    27  100.0%         17     +  22947841  22947867              AB351862     1    27    27
browser |    27  100.0%         17     +  76094232  76094258              AB351862     1    27    27
browser |    27  100.0%         17     +  76677493  76677519              AB351862     1    27    27
browser |    27  100.0%         17     +  83936061  83936087              AB351862     1    27    27
browser |    27  100.0%         17     -  92886156  92886182              AB351862     1    27    27
browser |    27  100.0%         17     -  94642930  94642956              AB351862     1    27    27
browser |    27  100.0%         18     +  10906631  10906657              AB351862     1    27    27
browser |    27  100.0%         18     -  22933349  22933375              AB351862     1    27    27
browser |    27  100.0%         18     +  25362078  25362104              AB351862     1    27    27
browser |    27  100.0%         18     +  33404635  33404661              AB351862     1    27    27
browser |    27  100.0%         18     +  42759922  42759948              AB351862     1    27    27
browser |    27  100.0%         18     -  50255775  50255801              AB351862     1    27    27
browser |    25  100.0%         18     +  60138587  60138611              AB351862     1    25    27
browser |    27  100.0%         18     +  82397604  82397630              AB351862     1    27    27
browser |    27  100.0%         19     -   3686354   3686380              AB351862     1    27    27
browser |    26  100.0%         19     -   4275844   4275869              AB351862     1    26    27
browser |    26  100.0%         19     +   8079533   8079559              AB351862     1    26    27
browser |    27  100.0%         19     -   9753377   9753403              AB351862     1    27    27
browser |    27  100.0%         19     +  14665826  14665852              AB351862     1    27    27
browser |    25  100.0%         19     +  55308501  55308525              AB351862     3    27    27
browser |    26  100.0%          2     +  15492100  15492125              AB351862     2    27    27
browser |    26  100.0%          2     +  16522905  16522930              AB351862     1    26    27
browser |    26  100.0%          2     -  16595774  16595799              AB351862     1    26    27
browser |    25  100.0%          2     +  17160757  17160781              AB351862     1    25    27
browser |    27  100.0%          2     -  19320324  19320350              AB351862     1    27    27
browser |    27  100.0%          2     +  25578841  25578867              AB351862     1    27    27
browser |    26  100.0%          2     -  36288133  36288158              AB351862     1    26    27
browser |    26  100.0%          2     -  36470170  36470195              AB351862     1    26    27
browser |    25  100.0%          2     -  53285221  53285245              AB351862     1    25    27
browser |    26  100.0%          2     +  59309580  59309605              AB351862     1    26    27
browser |    25  100.0%          2     -  95188657  95188681              AB351862     3    27    27
browser |    27  100.0%          2     +  98582312  98582338              AB351862     1    27    27
browser |    27  100.0%          2     + 108745975 108746001              AB351862     1    27    27
browser |    27  100.0%          2     + 146787137 146787163              AB351862     1    27    27
browser |    26  100.0%          2     + 155180841 155180866              AB351862     1    26    27
browser |    27  100.0%          2     - 159069736 159069762              AB351862     1    27    27
browser |    27  100.0%          3     -   5738783   5738809              AB351862     1    27    27
browser |    27  100.0%          3     -   6116479   6116505              AB351862     1    27    27
browser |    27  100.0%          3     +  13111319  13111345              AB351862     1    27    27
browser |    27  100.0%          3     -  23708221  23708247              AB351862     1    27    27
browser |    26  100.0%          3     +  25179576  25179601              AB351862     1    26    27
browser |    27  100.0%          3     +  26086174  26086200              AB351862     1    27    27
browser |    27  100.0%          3     +  31279805  31279831              AB351862     1    27    27
browser |    27  100.0%          3     -  31841457  31841483              AB351862     1    27    27
browser |    27  100.0%          3     -  77226381  77226407              AB351862     1    27    27
browser |    25  100.0%          3     +  90747308  90747332              AB351862     1    25    27
browser |    27  100.0%          3     - 104762999 104763025              AB351862     1    27    27
browser |    27  100.0%          3     + 107789486 107789512              AB351862     1    27    27
browser |    27  100.0%          3     + 124094250 124094276              AB351862     1    27    27
browser |    27  100.0%          3     - 142781026 142781052              AB351862     1    27    27
browser |    25  100.0%          3     + 152818747 152818771              AB351862     3    27    27
browser |    27  100.0%          3     + 154779246 154779272              AB351862     1    27    27
browser |    27  100.0%          3     + 155178614 155178640              AB351862     1    27    27
browser |    27  100.0%          3     + 156517270 156517296              AB351862     1    27    27
browser |    26  100.0%          4     +   3468868   3468893              AB351862     1    26    27
browser |    26  100.0%          4     -   3801637   3801662              AB351862     1    26    27
browser |    27  100.0%          4     -  23771034  23771060              AB351862     1    27    27
browser |    27  100.0%          4     -  41851468  41851494              AB351862     1    27    27
browser |    27  100.0%          4     -  41945381  41945407              AB351862     1    27    27
browser |    27  100.0%          4     -  42009709  42009735              AB351862     1    27    27
browser |    27  100.0%          4     +  42051352  42051378              AB351862     1    27    27
browser |    27  100.0%          4     -  42200350  42200376              AB351862     1    27    27
browser |    27  100.0%          4     -  42297611  42297637              AB351862     1    27    27
browser |    27  100.0%          4     -  42361924  42361950              AB351862     1    27    27
browser |    27  100.0%          4     -  42442722  42442748              AB351862     1    27    27
browser |    27  100.0%          4     +  42484560  42484586              AB351862     1    27    27
browser |    27  100.0%          4     +  42548678  42548704              AB351862     1    27    27
browser |    27  100.0%          4     -  42697497  42697523              AB351862     1    27    27
browser |    27  100.0%          4     +  42731704  42731730              AB351862     1    27    27
browser |    27  100.0%          4     +  42809743  42809769              AB351862     1    27    27
browser |    27  100.0%          4     -  48570823  48570849              AB351862     1    27    27
browser |    26  100.0%          4     -  79209177  79209202              AB351862     2    27    27
browser |    27  100.0%          4     +  95344167  95344193              AB351862     1    27    27
browser |    26  100.0%          4     + 112099232 112099257              AB351862     2    27    27
browser |    26  100.0%          4     + 126718408 126718433              AB351862     1    26    27
browser |    25  100.0%          4     + 146540330 146540354              AB351862     1    25    27
browser |    27  100.0%          4     - 146999387 146999413              AB351862     1    27    27
browser |    27  100.0%          4     + 147568656 147568682              AB351862     1    27    27
browser |    27  100.0%          5     +  14131339  14131365              AB351862     1    27    27
browser |    27  100.0%          5     -  14531917  14531943              AB351862     1    27    27
browser |    25  100.0%          5     +  18210214  18210238              AB351862     1    25    27
browser |    27  100.0%          5     -  22356706  22356732              AB351862     1    27    27
browser |    25  100.0%          5     -  22749630  22749654              AB351862     1    25    27
browser |    26  100.0%          5     -  30289793  30289818              AB351862     1    26    27
browser |    27  100.0%          5     +  38199156  38199182              AB351862     1    27    27
browser |    27  100.0%          5     -  42017908  42017934              AB351862     1    27    27
browser |    27  100.0%          5     -  52895252  52895278              AB351862     1    27    27
browser |    27  100.0%          5     +  85120369  85120395              AB351862     1    27    27
browser |    26  100.0%          5     +  89542042  89542067              AB351862     1    26    27
browser |    27  100.0%          5     -  98560795  98560821              AB351862     1    27    27
browser |    27  100.0%          5     + 101854990 101855016              AB351862     1    27    27
browser |    27  100.0%          5     - 112637028 112637054              AB351862     1    27    27
browser |    27  100.0%          5     - 120378972 120378998              AB351862     1    27    27
browser |    27  100.0%          5     + 120380453 120380479              AB351862     1    27    27
browser |    27  100.0%          5     - 126840220 126840246              AB351862     1    27    27
browser |    27  100.0%          5     - 145762638 145762664              AB351862     1    27    27
browser |    26  100.0%          5     - 151367232 151367257              AB351862     1    26    27
browser |    27  100.0%          6     -   7715362   7715388              AB351862     1    27    27
browser |    26  100.0%          6     -  13125361  13125386              AB351862     1    26    27
browser |    25  100.0%          6     +  24925706  24925730              AB351862     1    25    27
browser |    27  100.0%          6     +  43867022  43867048              AB351862     1    27    27
browser |    27  100.0%          6     +  49217761  49217787              AB351862     1    27    27
browser |    27  100.0%          6     +  49630210  49630236              AB351862     1    27    27
browser |    27  100.0%          6     -  90121101  90121127              AB351862     1    27    27
browser |    27  100.0%          6     - 106169953 106169979              AB351862     1    27    27
browser |    27  100.0%          6     - 112965273 112965299              AB351862     1    27    27
browser |    27  100.0%          6     - 137023255 137023281              AB351862     1    27    27
browser |    25  100.0%          6     - 147824595 147824619              AB351862     1    25    27
browser |    27  100.0%          6     + 148989922 148989948              AB351862     1    27    27
browser |    27  100.0%          6     + 149347931 149347957              AB351862     1    27    27
browser |    27  100.0%          7     -   6630539   6630565              AB351862     1    27    27
browser |    26  100.0%          7     -  15958661  15958686              AB351862     1    26    27
browser |    27  100.0%          7     +  25923853  25923879              AB351862     1    27    27
browser |    27  100.0%          7     +  27485696  27485722              AB351862     1    27    27
browser |    27  100.0%          7     +  60738208  60738234              AB351862     1    27    27
browser |    26  100.0%          7     -  61311889  61311915              AB351862     1    26    27
browser |    27  100.0%          7     +  63964425  63964451              AB351862     1    27    27
browser |    27  100.0%          7     -  65291667  65291693              AB351862     1    27    27
browser |    27  100.0%          7     +  67634108  67634134              AB351862     1    27    27
browser |    27  100.0%          7     +  92869302  92869328              AB351862     1    27    27
browser |    27  100.0%          7     + 110292720 110292746              AB351862     1    27    27
browser |    27  100.0%          8     -   9804481   9804507              AB351862     1    27    27
browser |    27  100.0%          8     +  17462035  17462061              AB351862     1    27    27
browser |    27  100.0%          8     +  31097249  31097275              AB351862     1    27    27
browser |    25  100.0%          8     +  46680888  46680912              AB351862     3    27    27
browser |    27  100.0%          8     -  61949603  61949629              AB351862     1    27    27
browser |    25  100.0%          8     +  74985945  74985969              AB351862     3    27    27
browser |    27  100.0%          8     -  75187789  75187815              AB351862     1    27    27
browser |    26  100.0%          8     +  75830532  75830557              AB351862     1    26    27
browser |    26  100.0%          8     -  77095988  77096013              AB351862     1    26    27
browser |    27  100.0%          9     +   8520207   8520233              AB351862     1    27    27
browser |    27  100.0%          9     -  11236586  11236612              AB351862     1    27    27
browser |    27  100.0%          9     -  11479548  11479574              AB351862     1    27    27
browser |    27  100.0%          9     -  16581837  16581863              AB351862     1    27    27
browser |    27  100.0%          9     +  28385561  28385587              AB351862     1    27    27
browser |    27  100.0%          9     -  93833380  93833406              AB351862     1    27    27
browser |    27  100.0%          X     +  13123213  13123239              AB351862     1    27    27
browser |    27  100.0%          X     +  18449726  18449752              AB351862     1    27    27
browser |    26  100.0%          X     -  45731444  45731469              AB351862     1    26    27
browser |    27  100.0%          X     +  49429117  49429143              AB351862     1    27    27
browser |    25  100.0%          X     -  61964065  61964089              AB351862     1    25    27
browser |    27  100.0%          X     -  63206621  63206647              AB351862     1    27    27
browser |    27  100.0%          X     - 116488415 116488441              AB351862     1    27    27
browser |    27  100.0%          X     + 117060412 117060438              AB351862     1    27    27
browser |    27  100.0%          X     - 119054678 119054704              AB351862     1    27    27
browser |    27  100.0%          X     + 120157440 120157466              AB351862     1    27    27
browser |    27  100.0%          X     + 161963936 161963962              AB351862     1    27    27
browser |    27  100.0%          X     + 164347612 164347638              AB351862     1    27    27

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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