AB352882
 

Information on mRNA AB352882

Description: Mus musculus non-coding RNA, oocyte_piRNA3698, 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: AB352882
Position: chr12:56795873-56795903

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 |    31  100.0%         12     -  56795873  56795903              AB352882     1    31    31
browser |    31  100.0%          1     -   4628567   4628597              AB352882     1    31    31
browser |    31  100.0%          1     -   5875808   5875838              AB352882     1    31    31
browser |    31  100.0%          1     +   6241758   6241788              AB352882     1    31    31
browser |    31  100.0%          1     -   6501837   6501867              AB352882     1    31    31
browser |    31  100.0%          1     +   8069778   8069808              AB352882     1    31    31
browser |    31  100.0%          1     +   8232223   8232253              AB352882     1    31    31
browser |    31  100.0%          1     -  10801327  10801357              AB352882     1    31    31
browser |    31  100.0%          1     -  11958585  11958615              AB352882     1    31    31
browser |    31  100.0%          1     -  12018085  12018115              AB352882     1    31    31
browser |    31  100.0%          1     +  13626643  13626673              AB352882     1    31    31
browser |    31  100.0%          1     +  16814292  16814322              AB352882     1    31    31
browser |    31  100.0%          1     +  18032880  18032910              AB352882     1    31    31
browser |    31  100.0%          1     +  18590166  18590196              AB352882     1    31    31
browser |    31  100.0%          1     +  19698500  19698530              AB352882     1    31    31
browser |    31  100.0%          1     +  21653871  21653901              AB352882     1    31    31
browser |    31  100.0%          1     -  22066716  22066746              AB352882     1    31    31
browser |    31  100.0%          1     +  23344160  23344190              AB352882     1    31    31
browser |    31  100.0%          1     -  26389494  26389524              AB352882     1    31    31
browser |    31  100.0%          1     +  26458907  26458937              AB352882     1    31    31
browser |    31  100.0%          1     +  27225056  27225086              AB352882     1    31    31
browser |    31  100.0%          1     -  29983046  29983076              AB352882     1    31    31
browser |    31  100.0%          1     +  34957005  34957035              AB352882     1    31    31
browser |    31  100.0%          1     +  35833385  35833415              AB352882     1    31    31
browser |    31  100.0%          1     -  37319116  37319146              AB352882     1    31    31
browser |    31  100.0%          1     +  37816428  37816458              AB352882     1    31    31
browser |    31  100.0%          1     +  38746767  38746797              AB352882     1    31    31
browser |    31  100.0%          1     -  48394734  48394764              AB352882     1    31    31
browser |    31  100.0%          1     -  53170025  53170055              AB352882     1    31    31
browser |    31  100.0%          1     -  58363763  58363793              AB352882     1    31    31
browser |    31  100.0%          1     -  58789888  58789918              AB352882     1    31    31
browser |    31  100.0%          1     -  58852074  58852104              AB352882     1    31    31
browser |    31  100.0%          1     -  59385628  59385658              AB352882     1    31    31
browser |    31  100.0%          1     -  81543132  81543162              AB352882     1    31    31
browser |    31  100.0%          1     +  82482447  82482477              AB352882     1    31    31
browser |    31  100.0%          1     -  84974850  84974880              AB352882     1    31    31
browser |    31  100.0%          1     -  87062614  87062644              AB352882     1    31    31
browser |    31  100.0%          1     +  87393712  87393742              AB352882     1    31    31
browser |    31  100.0%          1     +  89129669  89129699              AB352882     1    31    31
browser |    31  100.0%          1     -  91400190  91400220              AB352882     1    31    31
browser |    31  100.0%          1     +  93887755  93887785              AB352882     1    31    31
browser |    31  100.0%          1     +  97105821  97105851              AB352882     1    31    31
browser |    31  100.0%          1     - 101907119 101907149              AB352882     1    31    31
browser |    31  100.0%          1     + 102965223 102965253              AB352882     1    31    31
browser |    31  100.0%          1     - 103134151 103134181              AB352882     1    31    31
browser |    31  100.0%          1     + 103520482 103520512              AB352882     1    31    31
browser |    31  100.0%          1     - 104218544 104218574              AB352882     1    31    31
browser |    31  100.0%          1     - 107967780 107967810              AB352882     1    31    31
browser |    31  100.0%          1     - 108337839 108337869              AB352882     1    31    31
browser |    31  100.0%          1     - 109057655 109057685              AB352882     1    31    31
browser |    31  100.0%          1     + 109546962 109546992              AB352882     1    31    31
browser |    31  100.0%          1     + 110260733 110260763              AB352882     1    31    31
browser |    31  100.0%          1     - 110866586 110866616              AB352882     1    31    31
browser |    31  100.0%          1     - 111182611 111182641              AB352882     1    31    31
browser |    31  100.0%          1     + 111636932 111636962              AB352882     1    31    31
browser |    31  100.0%          1     - 112193324 112193354              AB352882     1    31    31
browser |    31  100.0%          1     - 112493276 112493306              AB352882     1    31    31
browser |    31  100.0%          1     + 112861925 112861955              AB352882     1    31    31
browser |    31  100.0%          1     + 112949640 112949670              AB352882     1    31    31
browser |    31  100.0%          1     + 114116950 114116980              AB352882     1    31    31
browser |    31  100.0%          1     - 115814346 115814376              AB352882     1    31    31
browser |    31  100.0%          1     - 116577256 116577286              AB352882     1    31    31
browser |    31  100.0%          1     + 125250425 125250455              AB352882     1    31    31
browser |    31  100.0%          1     + 126356119 126356149              AB352882     1    31    31
browser |    31  100.0%          1     + 126870851 126870881              AB352882     1    31    31
browser |    31  100.0%          1     - 159798582 159798612              AB352882     1    31    31
browser |    29  100.0%          1     - 160644696 160644724              AB352882     3    31    31
browser |    31  100.0%          1     + 162673953 162673983              AB352882     1    31    31
browser |    31  100.0%          1     - 163297312 163297342              AB352882     1    31    31
browser |    31  100.0%          1     - 166591954 166591984              AB352882     1    31    31
browser |    31  100.0%          1     + 169375197 169375227              AB352882     1    31    31
browser |    31  100.0%          1     + 169949188 169949218              AB352882     1    31    31
browser |    31  100.0%          1     - 174870799 174870829              AB352882     1    31    31
browser |    31  100.0%          1     - 176371881 176371911              AB352882     1    31    31
browser |    31  100.0%          1     + 177891452 177891482              AB352882     1    31    31
browser |    31  100.0%          1     + 178007505 178007535              AB352882     1    31    31
browser |    31  100.0%          1     + 179727398 179727428              AB352882     1    31    31
browser |    31  100.0%          1     - 181092337 181092367              AB352882     1    31    31
browser |    31  100.0%          1     + 181325791 181325821              AB352882     1    31    31
browser |    31  100.0%          1     + 183302110 183302140              AB352882     1    31    31
browser |    31  100.0%          1     + 191843613 191843643              AB352882     1    31    31
browser |    31  100.0%          1     + 195008486 195008516              AB352882     1    31    31
browser |    31  100.0%         10     -   3267584   3267614              AB352882     1    31    31
browser |    31  100.0%         10     -   3552177   3552207              AB352882     1    31    31
browser |    31  100.0%         10     -   6518008   6518038              AB352882     1    31    31
browser |    31  100.0%         10     +   7365198   7365228              AB352882     1    31    31
browser |    31  100.0%         10     +   8480878   8480908              AB352882     1    31    31
browser |    31  100.0%         10     +   9726261   9726291              AB352882     1    31    31
browser |    31  100.0%         10     +  11575856  11575886              AB352882     1    31    31
browser |    31  100.0%         10     -  15056994  15057024              AB352882     1    31    31
browser |    31  100.0%         10     -  19415891  19415921              AB352882     1    31    31
browser |    31  100.0%         10     +  19675979  19676009              AB352882     1    31    31
browser |    31  100.0%         10     -  19887621  19887651              AB352882     1    31    31
browser |    31  100.0%         10     +  21091180  21091210              AB352882     1    31    31
browser |    31  100.0%         10     -  21519464  21519494              AB352882     1    31    31
browser |    31  100.0%         10     -  22400364  22400394              AB352882     1    31    31
browser |    31  100.0%         10     -  22560410  22560440              AB352882     1    31    31
browser |    31  100.0%         10     -  23748465  23748495              AB352882     1    31    31
browser |    31  100.0%         10     +  24566208  24566238              AB352882     1    31    31
browser |    31  100.0%         10     -  24978689  24978719              AB352882     1    31    31
browser |    31  100.0%         10     +  30360287  30360317              AB352882     1    31    31
browser |    31  100.0%         10     +  30695818  30695848              AB352882     1    31    31
browser |    31  100.0%         10     +  30970503  30970533              AB352882     1    31    31
browser |    31  100.0%         10     +  31364448  31364478              AB352882     1    31    31
browser |    31  100.0%         10     +  31629592  31629622              AB352882     1    31    31
browser |    31  100.0%         10     +  33765764  33765794              AB352882     1    31    31
browser |    31  100.0%         10     -  34619068  34619098              AB352882     1    31    31
browser |    31  100.0%         10     -  39638155  39638185              AB352882     1    31    31
browser |    31  100.0%         10     +  41722370  41722400              AB352882     1    31    31
browser |    31  100.0%         10     +  50370297  50370327              AB352882     1    31    31
browser |    31  100.0%         10     +  51762741  51762771              AB352882     1    31    31
browser |    31  100.0%         10     -  78653538  78653568              AB352882     1    31    31
browser |    31  100.0%         10     +  80815409  80815439              AB352882     1    31    31
browser |    31  100.0%         10     -  81507626  81507656              AB352882     1    31    31
browser |    31  100.0%         10     -  81666754  81666784              AB352882     1    31    31
browser |    31  100.0%         10     -  83302981  83303011              AB352882     1    31    31
browser |    31  100.0%         10     -  83508031  83508061              AB352882     1    31    31
browser |    31  100.0%         10     +  84584480  84584510              AB352882     1    31    31
browser |    31  100.0%         10     +  85555283  85555313              AB352882     1    31    31
browser |    31  100.0%         10     -  85605537  85605567              AB352882     1    31    31
browser |    31  100.0%         10     +  88492664  88492694              AB352882     1    31    31
browser |    31  100.0%         10     +  88802785  88802815              AB352882     1    31    31
browser |    31  100.0%         10     -  90161717  90161747              AB352882     1    31    31
browser |    31  100.0%         10     -  92587609  92587639              AB352882     1    31    31
browser |    31  100.0%         10     -  94199683  94199713              AB352882     1    31    31
browser |    31  100.0%         10     -  95994355  95994385              AB352882     1    31    31
browser |    31  100.0%         10     -  96029639  96029669              AB352882     1    31    31
browser |    31  100.0%         10     -  97157667  97157697              AB352882     1    31    31
browser |    31  100.0%         10     -  98935304  98935334              AB352882     1    31    31
browser |    31  100.0%         10     +  99180819  99180849              AB352882     1    31    31
browser |    31  100.0%         10     -  99383014  99383044              AB352882     1    31    31
browser |    31  100.0%         10     + 100418355 100418385              AB352882     1    31    31
browser |    31  100.0%         10     - 104656599 104656629              AB352882     1    31    31
browser |    31  100.0%         10     + 104677266 104677296              AB352882     1    31    31
browser |    31  100.0%         10     + 105016392 105016422              AB352882     1    31    31
browser |    31  100.0%         10     - 105509758 105509788              AB352882     1    31    31
browser |    31  100.0%         10     + 107841195 107841225              AB352882     1    31    31
browser |    31  100.0%         10     + 111892991 111893021              AB352882     1    31    31
browser |    31  100.0%         10     + 124418062 124418092              AB352882     1    31    31
browser |    31  100.0%         10     + 124445567 124445597              AB352882     1    31    31
browser |    31  100.0%         10     - 129225937 129225967              AB352882     1    31    31
browser |    31  100.0%         11     -   6092738   6092768              AB352882     1    31    31
browser |    31  100.0%         11     +   6484515   6484545              AB352882     1    31    31
browser |    31  100.0%         11     -   7526934   7526964              AB352882     1    31    31
browser |    31  100.0%         11     -   7985101   7985131              AB352882     1    31    31
browser |    31  100.0%         11     -   9659233   9659263              AB352882     1    31    31
browser |    31  100.0%         11     +  10716161  10716191              AB352882     1    31    31
browser |    31  100.0%         11     -  12458537  12458567              AB352882     1    31    31
browser |    31  100.0%         11     +  12517772  12517802              AB352882     1    31    31
browser |    31  100.0%         11     -  12905264  12905294              AB352882     1    31    31
browser |    31  100.0%         11     +  15183542  15183572              AB352882     1    31    31
browser |    31  100.0%         11     -  15233789  15233819              AB352882     1    31    31
browser |    31  100.0%         11     +  15836544  15836574              AB352882     1    31    31
browser |    31  100.0%         11     +  16181397  16181427              AB352882     1    31    31
browser |    31  100.0%         11     -  18757703  18757733              AB352882     1    31    31
browser |    31  100.0%         11     -  19517422  19517452              AB352882     1    31    31
browser |    31  100.0%         11     -  19739972  19740002              AB352882     1    31    31
browser |    31  100.0%         11     -  22286501  22286531              AB352882     1    31    31
browser |    31  100.0%         11     +  22531733  22531763              AB352882     1    31    31
browser |    31  100.0%         11     -  23169830  23169860              AB352882     1    31    31
browser |    31  100.0%         11     +  26509475  26509505              AB352882     1    31    31
browser |    31  100.0%         11     -  27902326  27902356              AB352882     1    31    31
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browser |    31  100.0%         11     +  29078513  29078543              AB352882     1    31    31
browser |    31  100.0%         11     -  31398813  31398843              AB352882     1    31    31
browser |    31  100.0%         11     -  39955802  39955832              AB352882     1    31    31
browser |    31  100.0%         11     +  43553390  43553420              AB352882     1    31    31
browser |    31  100.0%         11     -  51557101  51557131              AB352882     1    31    31
browser |    31  100.0%         11     +  64686931  64686961              AB352882     1    31    31
browser |    31  100.0%         11     +  74025607  74025637              AB352882     1    31    31
browser |    31  100.0%         11     +  74434908  74434938              AB352882     1    31    31
browser |    31  100.0%         11     +  74781072  74781102              AB352882     1    31    31
browser |    31  100.0%         11     +  81442216  81442246              AB352882     1    31    31
browser |    31  100.0%         11     -  82226070  82226100              AB352882     1    31    31
browser |    31  100.0%         11     +  84957372  84957402              AB352882     1    31    31
browser |    31  100.0%         11     -  85177643  85177673              AB352882     1    31    31
browser |    31  100.0%         11     -  88803035  88803065              AB352882     1    31    31
browser |    31  100.0%         11     -  90721694  90721724              AB352882     1    31    31
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browser |    30  100.0%         11     -  90852247  90852276              AB352882     2    31    31
browser |    31  100.0%         11     +  91995735  91995765              AB352882     1    31    31
browser |    31  100.0%         11     +  98509939  98509969              AB352882     1    31    31
browser |    31  100.0%         11     + 100559092 100559122              AB352882     1    31    31
browser |    31  100.0%         11     - 105920329 105920359              AB352882     1    31    31
browser |    31  100.0%         11     - 106184763 106184793              AB352882     1    31    31
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browser |    31  100.0%         11     - 111107719 111107749              AB352882     1    31    31
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browser |    31  100.0%         11     + 116284225 116284255              AB352882     1    31    31
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browser |    31  100.0%         11     + 120217832 120217862              AB352882     1    31    31
browser |    31  100.0%         11     + 120964395 120964425              AB352882     1    31    31
browser |    31  100.0%         12     +   3058216   3058246              AB352882     1    31    31
browser |    31  100.0%         12     +   3111990   3112020              AB352882     1    31    31
browser |    31  100.0%         12     +   6572388   6572418              AB352882     1    31    31
browser |    31  100.0%         12     +   6858873   6858903              AB352882     1    31    31
browser |    31  100.0%         12     -  11154903  11154933              AB352882     1    31    31
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browser |    31  100.0%         12     +  17178066  17178096              AB352882     1    31    31
browser |    31  100.0%         12     +  17297136  17297166              AB352882     1    31    31
browser |    31  100.0%         12     -  19309487  19309517              AB352882     1    31    31
browser |    31  100.0%         12     +  24451319  24451349              AB352882     1    31    31
browser |    31  100.0%         12     -  31409398  31409428              AB352882     1    31    31
browser |    31  100.0%         12     +  32081096  32081126              AB352882     1    31    31
browser |    31  100.0%         12     +  32649297  32649327              AB352882     1    31    31
browser |    31  100.0%         12     +  32955174  32955204              AB352882     1    31    31
browser |    31  100.0%         12     +  39484970  39485000              AB352882     1    31    31
browser |    31  100.0%         12     +  40457937  40457967              AB352882     1    31    31
browser |    31  100.0%         12     +  41419354  41419384              AB352882     1    31    31
browser |    31  100.0%         12     -  44199761  44199791              AB352882     1    31    31
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browser |    31  100.0%         12     +  48584809  48584839              AB352882     1    31    31
browser |    31  100.0%         12     +  49047418  49047448              AB352882     1    31    31
browser |    31  100.0%         12     -  49268372  49268402              AB352882     1    31    31
browser |    31  100.0%         12     -  52220793  52220823              AB352882     1    31    31
browser |    31  100.0%         12     -  52778132  52778162              AB352882     1    31    31
browser |    31  100.0%         12     -  60754934  60754964              AB352882     1    31    31
browser |    31  100.0%         12     -  64200820  64200850              AB352882     1    31    31
browser |    31  100.0%         12     -  65075193  65075223              AB352882     1    31    31
browser |    31  100.0%         12     -  65849249  65849279              AB352882     1    31    31
browser |    31  100.0%         12     -  66455049  66455079              AB352882     1    31    31
browser |    31  100.0%         12     -  79609861  79609891              AB352882     1    31    31
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browser |    31  100.0%          Y     -  21874565  21874595              AB352882     1    31    31
browser |    31  100.0%          Y     -  23482057  23482087              AB352882     1    31    31
browser |    31  100.0%          Y     -  31290273  31290303              AB352882     1    31    31
browser |    31  100.0%          Y     -  33163468  33163498              AB352882     1    31    31
browser |    31  100.0%          Y     +  35056206  35056236              AB352882     1    31    31
browser |    31  100.0%          Y     -  35704642  35704672              AB352882     1    31    31
browser |    31  100.0%          Y     -  39960577  39960607              AB352882     1    31    31
browser |    31  100.0%          Y     +  40110608  40110638              AB352882     1    31    31
browser |    31  100.0%          Y     -  42189700  42189730              AB352882     1    31    31
browser |    31  100.0%          Y     -  42327174  42327204              AB352882     1    31    31
browser |    31  100.0%          Y     +  43177588  43177618              AB352882     1    31    31
browser |    31  100.0%          Y     +  46190222  46190252              AB352882     1    31    31
browser |    31  100.0%          Y     +  68894778  68894808              AB352882     1    31    31
browser |    31  100.0%          Y     +  81110001  81110031              AB352882     1    31    31
browser |    31  100.0%          Y     -  82267485  82267515              AB352882     1    31    31
browser |    31  100.0%          Y     +  84726112  84726142              AB352882     1    31    31
browser |    31  100.0%          Y     -  85101211  85101241              AB352882     1    31    31
browser |    31  100.0%          Y     +  87790955  87790985              AB352882     1    31    31
browser |    31  100.0%          Y     +  88475646  88475676              AB352882     1    31    31

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