AB350421
 

Information on mRNA AB350421

Description: Mus musculus non-coding RNA, oocyte_piRNA1237, 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: AB350421
Position: chr12:56797715-56797743

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     -  56797715  56797743              AB350421     1    29    29
browser |    29  100.0%          1     -   5880400   5880428              AB350421     1    29    29
browser |    29  100.0%          1     +   8065191   8065219              AB350421     1    29    29
browser |    29  100.0%          1     +  18028296  18028324              AB350421     1    29    29
browser |    29  100.0%          1     +  18588326  18588354              AB350421     1    29    29
browser |    29  100.0%          1     +  23341467  23341495              AB350421     1    29    29
browser |    29  100.0%          1     -  26392189  26392217              AB350421     1    29    29
browser |    29  100.0%          1     +  26454318  26454346              AB350421     1    29    29
browser |    29  100.0%          1     +  29695190  29695218              AB350421     1    29    29
browser |    29  100.0%          1     +  34387799  34387827              AB350421     1    29    29
browser |    29  100.0%          1     +  45774548  45774576              AB350421     1    29    29
browser |    29  100.0%          1     +  48129506  48129534              AB350421     1    29    29
browser |    29  100.0%          1     -  48401190  48401218              AB350421     1    29    29
browser |    29  100.0%          1     -  58856663  58856691              AB350421     1    29    29
browser |    29  100.0%          1     -  60769849  60769877              AB350421     1    29    29
browser |    29  100.0%          1     +  64423502  64423530              AB350421     1    29    29
browser |    29  100.0%          1     -  65005311  65005339              AB350421     1    29    29
browser |    29  100.0%          1     -  66062618  66062646              AB350421     1    29    29
browser |    27  100.0%          1     -  69741169  69741195              AB350421     3    29    29
browser |    29  100.0%          1     -  76753264  76753292              AB350421     1    29    29
browser |    29  100.0%          1     -  81547724  81547752              AB350421     1    29    29
browser |    29  100.0%          1     -  87067206  87067234              AB350421     1    29    29
browser |    27  100.0%          1     + 103517797 103517823              AB350421     3    29    29
browser |    27  100.0%          1     - 104221239 104221265              AB350421     3    29    29
browser |    29  100.0%          1     - 108342431 108342459              AB350421     1    29    29
browser |    27  100.0%          1     + 110258042 110258068              AB350421     3    29    29
browser |    29  100.0%          1     + 112858452 112858480              AB350421     1    29    29
browser |    29  100.0%          1     + 114114281 114114309              AB350421     1    29    29
browser |    28  100.0%          1     - 118079958 118079985              AB350421     2    29    29
browser |    29  100.0%          1     - 120502500 120502528              AB350421     1    29    29
browser |    29  100.0%          1     - 127491842 127491870              AB350421     1    29    29
browser |    29  100.0%          1     + 130463297 130463325              AB350421     1    29    29
browser |    29  100.0%          1     + 139653845 139653873              AB350421     1    29    29
browser |    29  100.0%          1     + 140964391 140964419              AB350421     1    29    29
browser |    29  100.0%          1     - 141300529 141300557              AB350421     1    29    29
browser |    29  100.0%          1     - 142516543 142516571              AB350421     1    29    29
browser |    29  100.0%          1     - 148338320 148338348              AB350421     1    29    29
browser |    29  100.0%          1     - 149387880 149387908              AB350421     1    29    29
browser |    27  100.0%          1     + 152539897 152539923              AB350421     3    29    29
browser |    29  100.0%          1     - 160647367 160647395              AB350421     1    29    29
browser |    29  100.0%          1     + 162669363 162669391              AB350421     1    29    29
browser |    29  100.0%          1     + 169944597 169944625              AB350421     1    29    29
browser |    29  100.0%          1     + 177886862 177886890              AB350421     1    29    29
browser |    29  100.0%          1     + 191840944 191840972              AB350421     1    29    29
browser |    29  100.0%          1     + 195003899 195003927              AB350421     1    29    29
browser |    29  100.0%         10     +  11571267  11571295              AB350421     1    29    29
browser |    29  100.0%         10     -  23753057  23753085              AB350421     1    29    29
browser |    29  100.0%         10     +  25845560  25845588              AB350421     1    29    29
browser |    27  100.0%         10     +  30965915  30965941              AB350421     3    29    29
browser |    29  100.0%         10     +  33764206  33764234              AB350421     1    29    29
browser |    29  100.0%         10     -  55595568  55595596              AB350421     1    29    29
browser |    27  100.0%         10     +  59218904  59218930              AB350421     3    29    29
browser |    27  100.0%         10     -  65790537  65790563              AB350421     3    29    29
browser |    29  100.0%         10     -  66564078  66564106              AB350421     1    29    29
browser |    29  100.0%         10     +  70628501  70628529              AB350421     1    29    29
browser |    29  100.0%         10     +  71528498  71528526              AB350421     1    29    29
browser |    29  100.0%         10     +  77787852  77787880              AB350421     1    29    29
browser |    29  100.0%         10     +  77857463  77857491              AB350421     1    29    29
browser |    29  100.0%         10     -  78657627  78657655              AB350421     1    29    29
browser |    29  100.0%         10     +  84581811  84581839              AB350421     1    29    29
browser |    29  100.0%         10     +  85552306  85552334              AB350421     1    29    29
browser |    29  100.0%         10     +  88488093  88488121              AB350421     1    29    29
browser |    29  100.0%         10     -  90164334  90164362              AB350421     1    29    29
browser |    29  100.0%         10     -  96034231  96034259              AB350421     1    29    29
browser |    29  100.0%         10     -  97164150  97164178              AB350421     1    29    29
browser |    29  100.0%         10     -  99385923  99385951              AB350421     1    29    29
browser |    29  100.0%         10     + 104392459 104392487              AB350421     1    29    29
browser |    29  100.0%         10     - 104659270 104659298              AB350421     1    29    29
browser |    29  100.0%         10     + 117907799 117907827              AB350421     1    29    29
browser |    29  100.0%         10     - 122674490 122674518              AB350421     1    29    29
browser |    29  100.0%         10     + 124442916 124442944              AB350421     1    29    29
browser |    29  100.0%         10     - 129230529 129230557              AB350421     1    29    29
browser |    29  100.0%         10     - 130400738 130400766              AB350421     1    29    29
browser |    29  100.0%         11     -   6097331   6097359              AB350421     1    29    29
browser |    29  100.0%         11     -  12461208  12461236              AB350421     1    29    29
browser |    29  100.0%         11     +  12513182  12513210              AB350421     1    29    29
browser |    29  100.0%         11     -  12907935  12907963              AB350421     1    29    29
browser |    29  100.0%         11     -  19519264  19519292              AB350421     1    29    29
browser |    29  100.0%         11     -  23174422  23174450              AB350421     1    29    29
browser |    29  100.0%         11     +  28048555  28048583              AB350421     1    29    29
browser |    27  100.0%         11     -  51559796  51559822              AB350421     3    29    29
browser |    29  100.0%         11     -  54473239  54473267              AB350421     1    29    29
browser |    27  100.0%         11     +  61312525  61312551              AB350421     3    29    29
browser |    29  100.0%         11     +  64684238  64684266              AB350421     1    29    29
browser |    29  100.0%         11     -  65348449  65348477              AB350421     1    29    29
browser |    29  100.0%         11     +  74432239  74432267              AB350421     1    29    29
browser |    29  100.0%         11     +  74776482  74776510              AB350421     1    29    29
browser |    29  100.0%         11     -  88807622  88807650              AB350421     1    29    29
browser |    29  100.0%         11     -  90724366  90724394              AB350421     1    29    29
browser |    29  100.0%         11     + 100555005 100555033              AB350421     1    29    29
browser |    27  100.0%         11     - 105923024 105923050              AB350421     3    29    29
browser |    29  100.0%         11     - 108293876 108293904              AB350421     1    29    29
browser |    29  100.0%         11     + 113804281 113804309              AB350421     1    29    29
browser |    27  100.0%         11     + 116281534 116281560              AB350421     3    29    29
browser |    29  100.0%         11     + 116677648 116677676              AB350421     1    29    29
browser |    29  100.0%         12     +   3053637   3053665              AB350421     1    29    29
browser |    29  100.0%         12     -   3386648   3386676              AB350421     1    29    29
browser |    29  100.0%         12     +   8454582   8454610              AB350421     1    29    29
browser |    28  100.0%         12     +  19759737  19759764              AB350421     2    29    29
browser |    29  100.0%         12     -  44817766  44817794              AB350421     1    29    29
browser |    29  100.0%         12     -  61339181  61339209              AB350421     1    29    29
browser |    29  100.0%         12     +  62582875  62582903              AB350421     1    29    29
browser |    29  100.0%         12     -  65079783  65079811              AB350421     1    29    29
browser |    29  100.0%         12     +  65681309  65681337              AB350421     1    29    29
browser |    29  100.0%         12     +  68793306  68793334              AB350421     1    29    29
browser |    29  100.0%         12     -  70713774  70713802              AB350421     1    29    29
browser |    29  100.0%         12     -  79614453  79614481              AB350421     1    29    29
browser |    29  100.0%         12     -  82511780  82511808              AB350421     1    29    29
browser |    29  100.0%         12     -  85453635  85453663              AB350421     1    29    29
browser |    29  100.0%         12     +  93477587  93477615              AB350421     1    29    29
browser |    27  100.0%         12     -  94009122  94009148              AB350421     3    29    29
browser |    29  100.0%         12     - 108049477 108049505              AB350421     1    29    29
browser |    29  100.0%         12     + 114598299 114598327              AB350421     1    29    29
browser |    29  100.0%         13     -   4953575   4953603              AB350421     1    29    29
browser |    29  100.0%         13     -   8523593   8523621              AB350421     1    29    29
browser |    29  100.0%         13     +  15607403  15607431              AB350421     1    29    29
browser |    29  100.0%         13     +  26552391  26552419              AB350421     1    29    29
browser |    27  100.0%         13     -  28314224  28314250              AB350421     3    29    29
browser |    29  100.0%         13     +  30555368  30555396              AB350421     1    29    29
browser |    29  100.0%         13     -  31423172  31423200              AB350421     1    29    29
browser |    27  100.0%         13     +  38294981  38295007              AB350421     3    29    29
browser |    29  100.0%         13     +  43432291  43432319              AB350421     1    29    29
browser |    29  100.0%         13     +  44419085  44419113              AB350421     1    29    29
browser |    27  100.0%         13     +  52140786  52140812              AB350421     3    29    29
browser |    29  100.0%         13     -  63310236  63310264              AB350421     1    29    29
browser |    29  100.0%         13     +  79712890  79712918              AB350421     1    29    29
browser |    27  100.0%         13     +  86922159  86922185              AB350421     3    29    29
browser |    29  100.0%         13     -  87500959  87500987              AB350421     1    29    29
browser |    29  100.0%         13     +  87705658  87705686              AB350421     1    29    29
browser |    29  100.0%         13     +  94873301  94873329              AB350421     1    29    29
browser |    27  100.0%         13     +  97985840  97985866              AB350421     3    29    29
browser |    29  100.0%         13     +  98220724  98220752              AB350421     1    29    29
browser |    27  100.0%         13     - 100729407 100729433              AB350421     3    29    29
browser |    29  100.0%         13     + 111205705 111205733              AB350421     1    29    29
browser |    29  100.0%         13     + 111637612 111637640              AB350421     1    29    29
browser |    29  100.0%         13     + 113410748 113410776              AB350421     1    29    29
browser |    29  100.0%         13     - 114762699 114762727              AB350421     1    29    29
browser |    27  100.0%         13     + 116027065 116027091              AB350421     3    29    29
browser |    29  100.0%         13     - 116720405 116720433              AB350421     1    29    29
browser |    29  100.0%         13     - 119270681 119270709              AB350421     1    29    29
browser |    29  100.0%         14     +   3457966   3457994              AB350421     1    29    29
browser |    29  100.0%         14     -   6650983   6651011              AB350421     1    29    29
browser |    29  100.0%         14     +  35921941  35921969              AB350421     1    29    29
browser |    29  100.0%         14     -  42141866  42141894              AB350421     1    29    29
browser |    29  100.0%         14     -  53001184  53001212              AB350421     1    29    29
browser |    29  100.0%         14     -  63885643  63885671              AB350421     1    29    29
browser |    29  100.0%         14     -  64704724  64704752              AB350421     1    29    29
browser |    29  100.0%         14     +  66852498  66852526              AB350421     1    29    29
browser |    29  100.0%         14     +  75663993  75664021              AB350421     1    29    29
browser |    29  100.0%         14     +  78573519  78573547              AB350421     1    29    29
browser |    29  100.0%         14     -  79025934  79025962              AB350421     1    29    29
browser |    29  100.0%         14     -  80035996  80036024              AB350421     1    29    29
browser |    29  100.0%         14     -  80863924  80863952              AB350421     1    29    29
browser |    29  100.0%         14     -  85098415  85098443              AB350421     1    29    29
browser |    29  100.0%         14     +  86829189  86829217              AB350421     1    29    29
browser |    29  100.0%         14     -  88276986  88277014              AB350421     1    29    29
browser |    29  100.0%         14     +  90533420  90533448              AB350421     1    29    29
browser |    28  100.0%         14     -  92065176  92065203              AB350421     2    29    29
browser |    29  100.0%         14     +  96522582  96522610              AB350421     1    29    29
browser |    29  100.0%         14     + 100487292 100487320              AB350421     1    29    29
browser |    29  100.0%         14     - 104348101 104348129              AB350421     1    29    29
browser |    29  100.0%         14     + 108408266 108408294              AB350421     1    29    29
browser |    29  100.0%         14     - 112576071 112576099              AB350421     1    29    29
browser |    29  100.0%         14     - 112871014 112871042              AB350421     1    29    29
browser |    29  100.0%         14     + 113257243 113257271              AB350421     1    29    29
browser |    29  100.0%         14     + 113526820 113526848              AB350421     1    29    29
browser |    29  100.0%         14     + 114744551 114744579              AB350421     1    29    29
browser |    29  100.0%         14     + 117417642 117417670              AB350421     1    29    29
browser |    29  100.0%         14     - 118099436 118099464              AB350421     1    29    29
browser |    29  100.0%         14     - 120199415 120199443              AB350421     1    29    29
browser |    27  100.0%         15     -  12061925  12061951              AB350421     3    29    29
browser |    28  100.0%         15     +  17573907  17573934              AB350421     2    29    29
browser |    29  100.0%         15     -  20976856  20976884              AB350421     1    29    29
browser |    29  100.0%         15     -  27292077  27292105              AB350421     1    29    29
browser |    29  100.0%         15     -  27388930  27388958              AB350421     1    29    29
browser |    29  100.0%         15     +  38480307  38480335              AB350421     1    29    29
browser |    27  100.0%         15     +  39037715  39037741              AB350421     3    29    29
browser |    29  100.0%         15     +  43195347  43195375              AB350421     1    29    29
browser |    29  100.0%         15     +  47221254  47221282              AB350421     1    29    29
browser |    29  100.0%         15     +  56040549  56040577              AB350421     1    29    29
browser |    29  100.0%         15     -  74238444  74238472              AB350421     1    29    29
browser |    29  100.0%         15     -  75083335  75083363              AB350421     1    29    29
browser |    29  100.0%         15     -  77785243  77785271              AB350421     1    29    29
browser |    29  100.0%         15     -  82480814  82480842              AB350421     1    29    29
browser |    29  100.0%         15     -  86200407  86200435              AB350421     1    29    29
browser |    29  100.0%         15     -  90526509  90526537              AB350421     1    29    29
browser |    29  100.0%         15     -  92626536  92626564              AB350421     1    29    29
browser |    29  100.0%         15     +  96877239  96877267              AB350421     1    29    29
browser |    29  100.0%         15     -  97453943  97453971              AB350421     1    29    29
browser |    29  100.0%         16     -   4567090   4567118              AB350421     1    29    29
browser |    29  100.0%         16     -   7857715   7857743              AB350421     1    29    29
browser |    29  100.0%         16     +  11499284  11499312              AB350421     1    29    29
browser |    29  100.0%         16     +  12795479  12795507              AB350421     1    29    29
browser |    29  100.0%         16     -  12923447  12923475              AB350421     1    29    29
browser |    29  100.0%         16     -  19861160  19861188              AB350421     1    29    29
browser |    29  100.0%         16     -  20397453  20397481              AB350421     1    29    29
browser |    27  100.0%         16     +  31968178  31968204              AB350421     3    29    29
browser |    29  100.0%         16     +  32399337  32399365              AB350421     1    29    29
browser |    29  100.0%         16     -  33671583  33671611              AB350421     1    29    29
browser |    27  100.0%         16     +  34403995  34404021              AB350421     3    29    29
browser |    29  100.0%         16     -  36119240  36119268              AB350421     1    29    29
browser |    29  100.0%         16     -  38540553  38540581              AB350421     1    29    29
browser |    29  100.0%         16     +  50731456  50731484              AB350421     1    29    29
browser |    29  100.0%         16     -  52837051  52837079              AB350421     1    29    29
browser |    29  100.0%         16     +  53393080  53393108              AB350421     1    29    29
browser |    29  100.0%         16     -  55500604  55500632              AB350421     1    29    29
browser |    29  100.0%         16     -  58474580  58474608              AB350421     1    29    29
browser |    29  100.0%         16     -  58948106  58948134              AB350421     1    29    29
browser |    29  100.0%         16     -  60751943  60751971              AB350421     1    29    29
browser |    29  100.0%         16     +  66040177  66040205              AB350421     1    29    29
browser |    29  100.0%         16     +  71485128  71485156              AB350421     1    29    29
browser |    29  100.0%         16     -  74574586  74574614              AB350421     1    29    29
browser |    29  100.0%         16     -  78244725  78244753              AB350421     1    29    29
browser |    29  100.0%         16     -  79171431  79171459              AB350421     1    29    29
browser |    27  100.0%         16     +  79741351  79741377              AB350421     3    29    29
browser |    29  100.0%         16     -  80562599  80562627              AB350421     1    29    29
browser |    29  100.0%         16     +  80870011  80870039              AB350421     1    29    29
browser |    29  100.0%         16     -  82038702  82038730              AB350421     1    29    29
browser |    29  100.0%         16     +  82381643  82381671              AB350421     1    29    29
browser |    27  100.0%         16     +  83158912  83158938              AB350421     3    29    29
browser |    29  100.0%         16     -  88593370  88593398              AB350421     1    29    29
browser |    27  100.0%         16     +  89241114  89241140              AB350421     3    29    29
browser |    29  100.0%         16     -  89859066  89859094              AB350421     1    29    29
browser |    27  100.0%         16     -  97577578  97577604              AB350421     3    29    29
browser |    29  100.0%         17     -   6399056   6399084              AB350421     1    29    29
browser |    29  100.0%         17     +  13462495  13462523              AB350421     1    29    29
browser |    29  100.0%         17     +  13635069  13635097              AB350421     1    29    29
browser |    29  100.0%         17     +  15086434  15086462              AB350421     1    29    29
browser |    29  100.0%         17     +  35587557  35587585              AB350421     1    29    29
browser |    29  100.0%         17     +  36319291  36319319              AB350421     1    29    29
browser |    29  100.0%         17     -  38852555  38852583              AB350421     1    29    29
browser |    29  100.0%         17     +  45956883  45956911              AB350421     1    29    29
browser |    29  100.0%         17     -  54128527  54128555              AB350421     1    29    29
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browser |    29  100.0%          8     + 116009920 116009948              AB350421     1    29    29
browser |    29  100.0%          8     + 117624321 117624349              AB350421     1    29    29
browser |    29  100.0%          8     - 117733181 117733209              AB350421     1    29    29
browser |    29  100.0%          8     + 119773224 119773252              AB350421     1    29    29
browser |    27  100.0%          8     + 122133387 122133413              AB350421     3    29    29
browser |    29  100.0%          8     + 127141615 127141643              AB350421     1    29    29
browser |    29  100.0%          8     - 129283158 129283186              AB350421     1    29    29
browser |    29  100.0%          9     -   3465216   3465244              AB350421     1    29    29
browser |    27  100.0%          9     -   6784290   6784316              AB350421     3    29    29
browser |    27  100.0%          9     -  10197309  10197335              AB350421     3    29    29
browser |    29  100.0%          9     +  11633934  11633962              AB350421     1    29    29
browser |    29  100.0%          9     -  33070914  33070942              AB350421     1    29    29
browser |    29  100.0%          9     -  39808882  39808910              AB350421     1    29    29
browser |    29  100.0%          9     -  60639314  60639342              AB350421     1    29    29
browser |    27  100.0%          9     -  73207592  73207618              AB350421     3    29    29
browser |    29  100.0%          9     -  84104404  84104432              AB350421     1    29    29
browser |    29  100.0%          9     -  85950636  85950664              AB350421     1    29    29
browser |    29  100.0%          9     +  87470985  87471013              AB350421     1    29    29
browser |    29  100.0%          9     +  88704669  88704697              AB350421     1    29    29
browser |    29  100.0%          9     -  92535239  92535267              AB350421     1    29    29
browser |    29  100.0%          9     +  98649815  98649843              AB350421     1    29    29
browser |    29  100.0%          9     +  99619106  99619134              AB350421     1    29    29
browser |    29  100.0%          9     - 101174226 101174254              AB350421     1    29    29
browser |    27  100.0%          9     - 110803526 110803552              AB350421     3    29    29
browser |    29  100.0%          9     - 114912955 114912983              AB350421     1    29    29
browser |    29  100.0%          9     - 119697262 119697290              AB350421     1    29    29
browser |    29  100.0%          9     - 120468891 120468919              AB350421     1    29    29
browser |    27  100.0%          9     - 121156216 121156242              AB350421     3    29    29
browser |    29  100.0%          9     - 121241300 121241328              AB350421     1    29    29
browser |    27  100.0%          9     - 122236568 122236594              AB350421     3    29    29
browser |    29  100.0%          9     - 123025737 123025765              AB350421     1    29    29
browser |    29  100.0%          X     -   3613132   3613160              AB350421     1    29    29
browser |    29  100.0%          X     -   4365752   4365780              AB350421     1    29    29
browser |    29  100.0%          X     +   8385374   8385402              AB350421     1    29    29
browser |    29  100.0%          X     +  18202741  18202769              AB350421     1    29    29
browser |    29  100.0%          X     -  22436032  22436060              AB350421     1    29    29
browser |    29  100.0%          X     +  29380407  29380435              AB350421     1    29    29
browser |    29  100.0%          X     -  29427951  29427979              AB350421     1    29    29
browser |    29  100.0%          X     -  32650782  32650810              AB350421     1    29    29
browser |    29  100.0%          X     -  40815825  40815853              AB350421     1    29    29
browser |    29  100.0%          X     -  53233169  53233197              AB350421     1    29    29
browser |    29  100.0%          X     -  71921428  71921456              AB350421     1    29    29
browser |    29  100.0%          X     +  80691642  80691670              AB350421     1    29    29
browser |    29  100.0%          X     +  88345137  88345165              AB350421     1    29    29
browser |    29  100.0%          X     +  90861854  90861882              AB350421     1    29    29
browser |    29  100.0%          X     +  95392695  95392723              AB350421     1    29    29
browser |    27  100.0%          X     +  97150817  97150843              AB350421     3    29    29
browser |    29  100.0%          X     + 112821313 112821341              AB350421     1    29    29
browser |    29  100.0%          X     - 113209954 113209982              AB350421     1    29    29
browser |    27  100.0%          X     + 114460882 114460908              AB350421     3    29    29
browser |    27  100.0%          X     + 119887736 119887762              AB350421     3    29    29
browser |    29  100.0%          X     - 120354619 120354647              AB350421     1    29    29
browser |    29  100.0%          X     - 120465644 120465672              AB350421     1    29    29
browser |    29  100.0%          X     - 122476542 122476570              AB350421     1    29    29
browser |    29  100.0%          X     + 124960886 124960914              AB350421     1    29    29
browser |    29  100.0%          X     - 126842654 126842682              AB350421     1    29    29
browser |    29  100.0%          X     + 126859341 126859369              AB350421     1    29    29
browser |    29  100.0%          X     + 127628091 127628119              AB350421     1    29    29
browser |    29  100.0%          X     + 144714543 144714571              AB350421     1    29    29
browser |    29  100.0%          X     + 154562991 154563019              AB350421     1    29    29
browser |    29  100.0%          X     - 156407522 156407550              AB350421     1    29    29
browser |    29  100.0%          X     + 159069910 159069938              AB350421     1    29    29
browser |    29  100.0%          Y     -  31294862  31294890              AB350421     1    29    29
browser |    29  100.0%          Y     -  33168057  33168085              AB350421     1    29    29
browser |    29  100.0%          Y     +  40106021  40106049              AB350421     1    29    29
browser |    29  100.0%          Y     -  42194289  42194317              AB350421     1    29    29
browser |    27  100.0%          Y     -  42467938  42467964              AB350421     3    29    29

View details of parts of alignment within browser window
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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