AB350137
 

Information on mRNA AB350137

Description: Mus musculus non-coding RNA, oocyte_piRNA953, 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: AB350137
Position: chr12:56795877-56795901

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 |    25  100.0%         12     -  56795877  56795901              AB350137     1    25    25
browser |    25  100.0%          1     -   4628571   4628595              AB350137     1    25    25
browser |    25  100.0%          1     -   5875812   5875836              AB350137     1    25    25
browser |    25  100.0%          1     +   6241760   6241784              AB350137     1    25    25
browser |    25  100.0%          1     -   6501841   6501865              AB350137     1    25    25
browser |    25  100.0%          1     +   8069780   8069804              AB350137     1    25    25
browser |    25  100.0%          1     +   8232225   8232249              AB350137     1    25    25
browser |    25  100.0%          1     -  10801331  10801355              AB350137     1    25    25
browser |    25  100.0%          1     -  11958589  11958613              AB350137     1    25    25
browser |    25  100.0%          1     -  12018089  12018113              AB350137     1    25    25
browser |    25  100.0%          1     +  13626645  13626669              AB350137     1    25    25
browser |    25  100.0%          1     +  16814294  16814318              AB350137     1    25    25
browser |    25  100.0%          1     +  18032882  18032906              AB350137     1    25    25
browser |    25  100.0%          1     +  18590168  18590192              AB350137     1    25    25
browser |    25  100.0%          1     +  19698502  19698526              AB350137     1    25    25
browser |    25  100.0%          1     +  21653873  21653897              AB350137     1    25    25
browser |    25  100.0%          1     -  22066720  22066744              AB350137     1    25    25
browser |    25  100.0%          1     +  23344162  23344186              AB350137     1    25    25
browser |    25  100.0%          1     -  26389498  26389522              AB350137     1    25    25
browser |    25  100.0%          1     +  26458909  26458933              AB350137     1    25    25
browser |    25  100.0%          1     +  27225058  27225082              AB350137     1    25    25
browser |    25  100.0%          1     -  29983050  29983074              AB350137     1    25    25
browser |    25  100.0%          1     +  34957007  34957031              AB350137     1    25    25
browser |    25  100.0%          1     +  35833387  35833411              AB350137     1    25    25
browser |    25  100.0%          1     -  37319120  37319144              AB350137     1    25    25
browser |    25  100.0%          1     +  37816430  37816454              AB350137     1    25    25
browser |    25  100.0%          1     +  38746769  38746793              AB350137     1    25    25
browser |    25  100.0%          1     -  48394738  48394762              AB350137     1    25    25
browser |    25  100.0%          1     -  53170029  53170053              AB350137     1    25    25
browser |    25  100.0%          1     -  58363767  58363791              AB350137     1    25    25
browser |    25  100.0%          1     -  58789892  58789916              AB350137     1    25    25
browser |    25  100.0%          1     -  58852078  58852102              AB350137     1    25    25
browser |    25  100.0%          1     -  59385632  59385656              AB350137     1    25    25
browser |    25  100.0%          1     -  81543136  81543160              AB350137     1    25    25
browser |    25  100.0%          1     +  82482449  82482473              AB350137     1    25    25
browser |    25  100.0%          1     -  84974854  84974878              AB350137     1    25    25
browser |    25  100.0%          1     -  87062618  87062642              AB350137     1    25    25
browser |    25  100.0%          1     +  87393714  87393738              AB350137     1    25    25
browser |    25  100.0%          1     +  89129671  89129695              AB350137     1    25    25
browser |    25  100.0%          1     -  91400194  91400218              AB350137     1    25    25
browser |    25  100.0%          1     +  93887757  93887781              AB350137     1    25    25
browser |    25  100.0%          1     +  97105823  97105847              AB350137     1    25    25
browser |    25  100.0%          1     - 101907123 101907147              AB350137     1    25    25
browser |    25  100.0%          1     + 102965225 102965249              AB350137     1    25    25
browser |    25  100.0%          1     - 103134155 103134179              AB350137     1    25    25
browser |    25  100.0%          1     + 103520484 103520508              AB350137     1    25    25
browser |    25  100.0%          1     - 104218548 104218572              AB350137     1    25    25
browser |    25  100.0%          1     - 107967784 107967808              AB350137     1    25    25
browser |    25  100.0%          1     - 108337843 108337867              AB350137     1    25    25
browser |    25  100.0%          1     - 109057659 109057683              AB350137     1    25    25
browser |    25  100.0%          1     + 109546964 109546988              AB350137     1    25    25
browser |    25  100.0%          1     + 110260735 110260759              AB350137     1    25    25
browser |    25  100.0%          1     - 110866590 110866614              AB350137     1    25    25
browser |    25  100.0%          1     - 111182615 111182639              AB350137     1    25    25
browser |    25  100.0%          1     + 111636934 111636958              AB350137     1    25    25
browser |    25  100.0%          1     - 112193328 112193352              AB350137     1    25    25
browser |    25  100.0%          1     - 112493280 112493304              AB350137     1    25    25
browser |    25  100.0%          1     + 112861927 112861951              AB350137     1    25    25
browser |    25  100.0%          1     + 112949642 112949666              AB350137     1    25    25
browser |    25  100.0%          1     + 114116952 114116976              AB350137     1    25    25
browser |    25  100.0%          1     - 115814350 115814374              AB350137     1    25    25
browser |    25  100.0%          1     - 116577260 116577284              AB350137     1    25    25
browser |    25  100.0%          1     + 125250427 125250451              AB350137     1    25    25
browser |    25  100.0%          1     + 126356121 126356145              AB350137     1    25    25
browser |    25  100.0%          1     + 126870853 126870877              AB350137     1    25    25
browser |    25  100.0%          1     - 159798586 159798610              AB350137     1    25    25
browser |    25  100.0%          1     - 160644700 160644724              AB350137     1    25    25
browser |    25  100.0%          1     + 162673955 162673979              AB350137     1    25    25
browser |    25  100.0%          1     - 163297316 163297340              AB350137     1    25    25
browser |    25  100.0%          1     - 166591958 166591982              AB350137     1    25    25
browser |    25  100.0%          1     + 169375199 169375223              AB350137     1    25    25
browser |    25  100.0%          1     + 169949190 169949214              AB350137     1    25    25
browser |    25  100.0%          1     - 174870803 174870827              AB350137     1    25    25
browser |    25  100.0%          1     - 176371885 176371909              AB350137     1    25    25
browser |    25  100.0%          1     + 177891454 177891478              AB350137     1    25    25
browser |    25  100.0%          1     + 178007507 178007531              AB350137     1    25    25
browser |    25  100.0%          1     + 179727400 179727424              AB350137     1    25    25
browser |    24  100.0%          1     + 180442694 180442717              AB350137     1    24    25
browser |    25  100.0%          1     - 181092341 181092365              AB350137     1    25    25
browser |    25  100.0%          1     + 181325793 181325817              AB350137     1    25    25
browser |    25  100.0%          1     + 183302112 183302136              AB350137     1    25    25
browser |    25  100.0%          1     + 191843615 191843639              AB350137     1    25    25
browser |    25  100.0%          1     + 195008488 195008512              AB350137     1    25    25
browser |    25  100.0%         10     -   3267588   3267612              AB350137     1    25    25
browser |    25  100.0%         10     -   3552181   3552205              AB350137     1    25    25
browser |    25  100.0%         10     -   6518012   6518036              AB350137     1    25    25
browser |    25  100.0%         10     +   7365200   7365224              AB350137     1    25    25
browser |    25  100.0%         10     +   8480880   8480904              AB350137     1    25    25
browser |    25  100.0%         10     +   9726263   9726287              AB350137     1    25    25
browser |    25  100.0%         10     +  11575858  11575882              AB350137     1    25    25
browser |    25  100.0%         10     -  15056998  15057022              AB350137     1    25    25
browser |    25  100.0%         10     -  19415895  19415919              AB350137     1    25    25
browser |    25  100.0%         10     +  19675981  19676005              AB350137     1    25    25
browser |    25  100.0%         10     -  19887625  19887649              AB350137     1    25    25
browser |    25  100.0%         10     +  21091182  21091206              AB350137     1    25    25
browser |    25  100.0%         10     -  21519468  21519492              AB350137     1    25    25
browser |    25  100.0%         10     -  22400368  22400392              AB350137     1    25    25
browser |    25  100.0%         10     -  22560414  22560438              AB350137     1    25    25
browser |    25  100.0%         10     -  23748469  23748493              AB350137     1    25    25
browser |    25  100.0%         10     +  24566210  24566234              AB350137     1    25    25
browser |    25  100.0%         10     -  24978693  24978717              AB350137     1    25    25
browser |    25  100.0%         10     +  30360289  30360313              AB350137     1    25    25
browser |    25  100.0%         10     +  30695820  30695844              AB350137     1    25    25
browser |    25  100.0%         10     +  30970505  30970529              AB350137     1    25    25
browser |    25  100.0%         10     +  31364450  31364474              AB350137     1    25    25
browser |    25  100.0%         10     +  31629594  31629618              AB350137     1    25    25
browser |    25  100.0%         10     +  33765766  33765790              AB350137     1    25    25
browser |    25  100.0%         10     +  41722372  41722396              AB350137     1    25    25
browser |    25  100.0%         10     +  50370299  50370323              AB350137     1    25    25
browser |    25  100.0%         10     +  51762743  51762767              AB350137     1    25    25
browser |    25  100.0%         10     -  55592877  55592901              AB350137     1    25    25
browser |    25  100.0%         10     -  65787849  65787873              AB350137     1    25    25
browser |    25  100.0%         10     -  78653542  78653566              AB350137     1    25    25
browser |    25  100.0%         10     +  80815411  80815435              AB350137     1    25    25
browser |    25  100.0%         10     -  81507630  81507654              AB350137     1    25    25
browser |    25  100.0%         10     -  81666758  81666782              AB350137     1    25    25
browser |    24  100.0%         10     +  81809560  81809583              AB350137     1    24    25
browser |    25  100.0%         10     -  83302985  83303009              AB350137     1    25    25
browser |    25  100.0%         10     -  83508035  83508059              AB350137     1    25    25
browser |    25  100.0%         10     +  84584482  84584506              AB350137     1    25    25
browser |    25  100.0%         10     +  85555285  85555309              AB350137     1    25    25
browser |    25  100.0%         10     -  85605541  85605565              AB350137     1    25    25
browser |    25  100.0%         10     +  88492666  88492690              AB350137     1    25    25
browser |    25  100.0%         10     +  88802787  88802811              AB350137     1    25    25
browser |    25  100.0%         10     -  90161721  90161745              AB350137     1    25    25
browser |    25  100.0%         10     -  92587613  92587637              AB350137     1    25    25
browser |    25  100.0%         10     -  94199687  94199711              AB350137     1    25    25
browser |    25  100.0%         10     -  95994359  95994383              AB350137     1    25    25
browser |    25  100.0%         10     -  96029643  96029667              AB350137     1    25    25
browser |    25  100.0%         10     -  97157671  97157695              AB350137     1    25    25
browser |    25  100.0%         10     -  98935308  98935332              AB350137     1    25    25
browser |    25  100.0%         10     +  99180821  99180845              AB350137     1    25    25
browser |    25  100.0%         10     -  99383018  99383042              AB350137     1    25    25
browser |    25  100.0%         10     + 100418357 100418381              AB350137     1    25    25
browser |    25  100.0%         10     - 104656603 104656627              AB350137     1    25    25
browser |    25  100.0%         10     + 104677268 104677292              AB350137     1    25    25
browser |    25  100.0%         10     + 105016394 105016418              AB350137     1    25    25
browser |    25  100.0%         10     - 105509762 105509786              AB350137     1    25    25
browser |    25  100.0%         10     + 107841197 107841221              AB350137     1    25    25
browser |    25  100.0%         10     + 111892993 111893017              AB350137     1    25    25
browser |    25  100.0%         10     + 124418064 124418088              AB350137     1    25    25
browser |    25  100.0%         10     + 124445569 124445593              AB350137     1    25    25
browser |    25  100.0%         10     - 129225941 129225965              AB350137     1    25    25
browser |    24  100.0%         10     + 129764261 129764284              AB350137     1    24    25
browser |    25  100.0%         11     -   6092742   6092766              AB350137     1    25    25
browser |    25  100.0%         11     +   6484517   6484541              AB350137     1    25    25
browser |    25  100.0%         11     -   7526938   7526962              AB350137     1    25    25
browser |    25  100.0%         11     -   7985105   7985129              AB350137     1    25    25
browser |    25  100.0%         11     -   9659237   9659261              AB350137     1    25    25
browser |    25  100.0%         11     +  10716163  10716187              AB350137     1    25    25
browser |    25  100.0%         11     -  12458541  12458565              AB350137     1    25    25
browser |    25  100.0%         11     +  12517774  12517798              AB350137     1    25    25
browser |    25  100.0%         11     -  12905268  12905292              AB350137     1    25    25
browser |    25  100.0%         11     +  15183544  15183568              AB350137     1    25    25
browser |    25  100.0%         11     -  15233793  15233817              AB350137     1    25    25
browser |    25  100.0%         11     +  15836546  15836570              AB350137     1    25    25
browser |    25  100.0%         11     +  16181399  16181423              AB350137     1    25    25
browser |    25  100.0%         11     -  18757707  18757731              AB350137     1    25    25
browser |    25  100.0%         11     -  19517426  19517450              AB350137     1    25    25
browser |    25  100.0%         11     -  19739976  19740000              AB350137     1    25    25
browser |    25  100.0%         11     -  22286505  22286529              AB350137     1    25    25
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browser |    25  100.0%         11     -  23169834  23169858              AB350137     1    25    25
browser |    25  100.0%         11     +  26509477  26509501              AB350137     1    25    25
browser |    25  100.0%         11     -  27902330  27902354              AB350137     1    25    25
browser |    25  100.0%         11     +  28053144  28053168              AB350137     1    25    25
browser |    25  100.0%         11     +  29078515  29078539              AB350137     1    25    25
browser |    25  100.0%         11     -  31398817  31398841              AB350137     1    25    25
browser |    25  100.0%         11     -  39955806  39955830              AB350137     1    25    25
browser |    25  100.0%         11     -  51557105  51557129              AB350137     1    25    25
browser |    25  100.0%         11     +  63364404  63364428              AB350137     1    25    25
browser |    25  100.0%         11     +  64686933  64686957              AB350137     1    25    25
browser |    25  100.0%         11     +  74025609  74025633              AB350137     1    25    25
browser |    25  100.0%         11     +  74434910  74434934              AB350137     1    25    25
browser |    25  100.0%         11     +  74781074  74781098              AB350137     1    25    25
browser |    25  100.0%         11     +  81442218  81442242              AB350137     1    25    25
browser |    25  100.0%         11     -  82226074  82226098              AB350137     1    25    25
browser |    25  100.0%         11     +  84957374  84957398              AB350137     1    25    25
browser |    25  100.0%         11     -  85177647  85177671              AB350137     1    25    25
browser |    25  100.0%         11     -  88803039  88803063              AB350137     1    25    25
browser |    25  100.0%         11     -  90721698  90721722              AB350137     1    25    25
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browser |    25  100.0%         11     + 100559094 100559118              AB350137     1    25    25
browser |    25  100.0%         11     - 105920333 105920357              AB350137     1    25    25
browser |    25  100.0%         11     - 106184767 106184791              AB350137     1    25    25
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browser |    25  100.0%         11     - 111107723 111107747              AB350137     1    25    25
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browser |    25  100.0%         11     + 116682240 116682264              AB350137     1    25    25
browser |    23  100.0%         11     + 117394527 117394549              AB350137     2    24    25
browser |    25  100.0%         11     + 120217834 120217858              AB350137     1    25    25
browser |    25  100.0%         11     + 120964397 120964421              AB350137     1    25    25
browser |    25  100.0%         12     +   3058218   3058242              AB350137     1    25    25
browser |    25  100.0%         12     +   3111992   3112016              AB350137     1    25    25
browser |    25  100.0%         12     +   6572390   6572414              AB350137     1    25    25
browser |    25  100.0%         12     +   6858875   6858899              AB350137     1    25    25
browser |    25  100.0%         12     -  11154907  11154931              AB350137     1    25    25
browser |    25  100.0%         12     -  14645417  14645441              AB350137     1    25    25
browser |    25  100.0%         12     +  17178068  17178092              AB350137     1    25    25
browser |    25  100.0%         12     +  17297138  17297162              AB350137     1    25    25
browser |    25  100.0%         12     -  19309491  19309515              AB350137     1    25    25
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browser |    25  100.0%         12     +  24451321  24451345              AB350137     1    25    25
browser |    25  100.0%         12     -  31409402  31409426              AB350137     1    25    25
browser |    25  100.0%         12     +  32081098  32081122              AB350137     1    25    25
browser |    25  100.0%         12     +  32649299  32649323              AB350137     1    25    25
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browser |    25  100.0%         12     +  39484972  39484996              AB350137     1    25    25
browser |    25  100.0%         12     +  40457939  40457963              AB350137     1    25    25
browser |    25  100.0%         12     +  41419356  41419380              AB350137     1    25    25
browser |    25  100.0%         12     -  44199765  44199789              AB350137     1    25    25
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browser |    25  100.0%         12     +  48584811  48584835              AB350137     1    25    25
browser |    25  100.0%         12     -  49268376  49268400              AB350137     1    25    25
browser |    25  100.0%         12     -  52220797  52220821              AB350137     1    25    25
browser |    25  100.0%         12     -  52778136  52778160              AB350137     1    25    25
browser |    25  100.0%         12     -  60754938  60754962              AB350137     1    25    25
browser |    25  100.0%         12     -  64200824  64200848              AB350137     1    25    25
browser |    25  100.0%         12     -  65075197  65075221              AB350137     1    25    25
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browser |    25  100.0%          Y     -  11211024  11211048              AB350137     1    25    25
browser |    25  100.0%          Y     +  12544081  12544105              AB350137     1    25    25
browser |    25  100.0%          Y     -  15106252  15106276              AB350137     1    25    25
browser |    25  100.0%          Y     +  15358617  15358641              AB350137     1    25    25
browser |    25  100.0%          Y     -  15896423  15896447              AB350137     1    25    25
browser |    25  100.0%          Y     +  17255955  17255979              AB350137     1    25    25
browser |    25  100.0%          Y     -  19818855  19818879              AB350137     1    25    25
browser |    25  100.0%          Y     +  20071138  20071162              AB350137     1    25    25
browser |    25  100.0%          Y     -  21874569  21874593              AB350137     1    25    25
browser |    25  100.0%          Y     -  23482061  23482085              AB350137     1    25    25
browser |    25  100.0%          Y     -  31290277  31290301              AB350137     1    25    25
browser |    25  100.0%          Y     -  33163472  33163496              AB350137     1    25    25
browser |    25  100.0%          Y     +  35056208  35056232              AB350137     1    25    25
browser |    25  100.0%          Y     -  35704646  35704670              AB350137     1    25    25
browser |    25  100.0%          Y     -  39960581  39960605              AB350137     1    25    25
browser |    25  100.0%          Y     +  40110610  40110634              AB350137     1    25    25
browser |    25  100.0%          Y     -  42189704  42189728              AB350137     1    25    25
browser |    25  100.0%          Y     -  42327178  42327202              AB350137     1    25    25
browser |    25  100.0%          Y     +  43177590  43177614              AB350137     1    25    25
browser |    25  100.0%          Y     +  46190224  46190248              AB350137     1    25    25
browser |    25  100.0%          Y     +  68894780  68894804              AB350137     1    25    25
browser |    25  100.0%          Y     +  81110003  81110027              AB350137     1    25    25
browser |    25  100.0%          Y     -  82267489  82267513              AB350137     1    25    25
browser |    25  100.0%          Y     +  84726114  84726138              AB350137     1    25    25
browser |    25  100.0%          Y     -  85101215  85101239              AB350137     1    25    25
browser |    25  100.0%          Y     +  87790957  87790981              AB350137     1    25    25
browser |    25  100.0%          Y     +  88475648  88475672              AB350137     1    25    25

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