AB350523
 

Information on mRNA AB350523

Description: Mus musculus non-coding RNA, oocyte_piRNA1339, 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: AB350523
Position: chr12:56795390-56795410

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 |    21  100.0%         12     -  56795390  56795410              AB350523     1    21    21
browser |    21  100.0%          1     +   6242251   6242271              AB350523     1    21    21
browser |    21  100.0%          1     +   8070272   8070292              AB350523     1    21    21
browser |    21  100.0%          1     +   8232707   8232727              AB350523     1    21    21
browser |    21  100.0%          1     -  10800844  10800864              AB350523     1    21    21
browser |    21  100.0%          1     -  11958102  11958122              AB350523     1    21    21
browser |    21  100.0%          1     -  12017602  12017622              AB350523     1    21    21
browser |    21  100.0%          1     +  16814785  16814805              AB350523     1    21    21
browser |    21  100.0%          1     +  18590659  18590679              AB350523     1    21    21
browser |    21  100.0%          1     +  21654364  21654384              AB350523     1    21    21
browser |    21  100.0%          1     +  23344655  23344675              AB350523     1    21    21
browser |    21  100.0%          1     -  26389009  26389029              AB350523     1    21    21
browser |    21  100.0%          1     +  26459400  26459420              AB350523     1    21    21
browser |    21  100.0%          1     -  26510209  26510229              AB350523     1    21    21
browser |    21  100.0%          1     +  27225549  27225569              AB350523     1    21    21
browser |    21  100.0%          1     -  29982563  29982583              AB350523     1    21    21
browser |    21  100.0%          1     +  34389665  34389685              AB350523     1    21    21
browser |    21  100.0%          1     +  34957498  34957518              AB350523     1    21    21
browser |    21  100.0%          1     +  35833879  35833899              AB350523     1    21    21
browser |    21  100.0%          1     -  37318644  37318664              AB350523     1    21    21
browser |    21  100.0%          1     +  38747260  38747280              AB350523     1    21    21
browser |    21  100.0%          1     +  40740838  40740858              AB350523     1    21    21
browser |    21  100.0%          1     +  45777735  45777755              AB350523     1    21    21
browser |    21  100.0%          1     -  47263352  47263372              AB350523     1    21    21
browser |    21  100.0%          1     +  48132670  48132690              AB350523     1    21    21
browser |    21  100.0%          1     -  48394251  48394271              AB350523     1    21    21
browser |    21  100.0%          1     -  53169541  53169561              AB350523     1    21    21
browser |    21  100.0%          1     -  58363280  58363300              AB350523     1    21    21
browser |    21  100.0%          1     -  58851590  58851610              AB350523     1    21    21
browser |    21  100.0%          1     -  60764774  60764794              AB350523     1    21    21
browser |    21  100.0%          1     -  62574036  62574056              AB350523     1    21    21
browser |    21  100.0%          1     -  64218103  64218123              AB350523     1    21    21
browser |    21  100.0%          1     -  67791353  67791373              AB350523     1    21    21
browser |    21  100.0%          1     -  81542649  81542669              AB350523     1    21    21
browser |    21  100.0%          1     +  82482940  82482960              AB350523     1    21    21
browser |    21  100.0%          1     -  84974367  84974387              AB350523     1    21    21
browser |    21  100.0%          1     -  87062130  87062150              AB350523     1    21    21
browser |    21  100.0%          1     +  87394206  87394226              AB350523     1    21    21
browser |    21  100.0%          1     +  89130162  89130182              AB350523     1    21    21
browser |    21  100.0%          1     -  91399706  91399726              AB350523     1    21    21
browser |    21  100.0%          1     +  97108174  97108194              AB350523     1    21    21
browser |    21  100.0%          1     - 101906636 101906656              AB350523     1    21    21
browser |    21  100.0%          1     + 102965717 102965737              AB350523     1    21    21
browser |    21  100.0%          1     - 103133668 103133688              AB350523     1    21    21
browser |    21  100.0%          1     + 103520975 103520995              AB350523     1    21    21
browser |    21  100.0%          1     - 107967297 107967317              AB350523     1    21    21
browser |    21  100.0%          1     - 108337355 108337375              AB350523     1    21    21
browser |    21  100.0%          1     - 109057170 109057190              AB350523     1    21    21
browser |    21  100.0%          1     + 109547455 109547475              AB350523     1    21    21
browser |    21  100.0%          1     + 110261227 110261247              AB350523     1    21    21
browser |    21  100.0%          1     - 110866103 110866123              AB350523     1    21    21
browser |    21  100.0%          1     - 111182128 111182148              AB350523     1    21    21
browser |    21  100.0%          1     + 111637425 111637445              AB350523     1    21    21
browser |    21  100.0%          1     - 112192841 112192861              AB350523     1    21    21
browser |    21  100.0%          1     - 112492793 112492813              AB350523     1    21    21
browser |    21  100.0%          1     + 112862418 112862438              AB350523     1    21    21
browser |    21  100.0%          1     + 112950134 112950154              AB350523     1    21    21
browser |    21  100.0%          1     + 114117443 114117463              AB350523     1    21    21
browser |    21  100.0%          1     - 115813863 115813883              AB350523     1    21    21
browser |    21  100.0%          1     - 116576773 116576793              AB350523     1    21    21
browser |    21  100.0%          1     - 120499344 120499364              AB350523     1    21    21
browser |    21  100.0%          1     + 125250918 125250938              AB350523     1    21    21
browser |    21  100.0%          1     + 126356612 126356632              AB350523     1    21    21
browser |    21  100.0%          1     + 126871339 126871359              AB350523     1    21    21
browser |    21  100.0%          1     + 130466192 130466212              AB350523     1    21    21
browser |    21  100.0%          1     - 159798098 159798118              AB350523     1    21    21
browser |    21  100.0%          1     - 160644211 160644231              AB350523     1    21    21
browser |    21  100.0%          1     + 162674447 162674467              AB350523     1    21    21
browser |    21  100.0%          1     - 163296828 163296848              AB350523     1    21    21
browser |    21  100.0%          1     - 166591471 166591491              AB350523     1    21    21
browser |    21  100.0%          1     + 169375690 169375710              AB350523     1    21    21
browser |    21  100.0%          1     + 172096520 172096540              AB350523     1    21    21
browser |    21  100.0%          1     - 174870316 174870336              AB350523     1    21    21
browser |    21  100.0%          1     - 176371398 176371418              AB350523     1    21    21
browser |    21  100.0%          1     + 177891916 177891936              AB350523     1    21    21
browser |    21  100.0%          1     + 181326284 181326304              AB350523     1    21    21
browser |    21  100.0%          1     + 191844108 191844128              AB350523     1    21    21
browser |    21  100.0%          1     + 195008979 195008999              AB350523     1    21    21
browser |    21  100.0%         10     -   3267101   3267121              AB350523     1    21    21
browser |    21  100.0%         10     -   3551693   3551713              AB350523     1    21    21
browser |    21  100.0%         10     +   8481371   8481391              AB350523     1    21    21
browser |    21  100.0%         10     +   9726754   9726774              AB350523     1    21    21
browser |    21  100.0%         10     +  11576349  11576369              AB350523     1    21    21
browser |    21  100.0%         10     -  19415408  19415428              AB350523     1    21    21
browser |    21  100.0%         10     +  19676481  19676501              AB350523     1    21    21
browser |    21  100.0%         10     +  21091673  21091693              AB350523     1    21    21
browser |    21  100.0%         10     -  21518981  21519001              AB350523     1    21    21
browser |    21  100.0%         10     -  22399884  22399904              AB350523     1    21    21
browser |    21  100.0%         10     -  22559927  22559947              AB350523     1    21    21
browser |    21  100.0%         10     -  23747982  23748002              AB350523     1    21    21
browser |    21  100.0%         10     +  24566703  24566723              AB350523     1    21    21
browser |    21  100.0%         10     -  24978206  24978226              AB350523     1    21    21
browser |    21  100.0%         10     +  25848414  25848434              AB350523     1    21    21
browser |    21  100.0%         10     +  30696312  30696332              AB350523     1    21    21
browser |    21  100.0%         10     +  30970998  30971018              AB350523     1    21    21
browser |    21  100.0%         10     +  31630085  31630105              AB350523     1    21    21
browser |    21  100.0%         10     +  32814386  32814406              AB350523     1    21    21
browser |    21  100.0%         10     -  34618585  34618605              AB350523     1    21    21
browser |    21  100.0%         10     +  41722863  41722883              AB350523     1    21    21
browser |    21  100.0%         10     +  50370790  50370810              AB350523     1    21    21
browser |    21  100.0%         10     +  51763234  51763254              AB350523     1    21    21
browser |    21  100.0%         10     +  54468820  54468840              AB350523     1    21    21
browser |    21  100.0%         10     -  55592389  55592409              AB350523     1    21    21
browser |    21  100.0%         10     +  56603171  56603191              AB350523     1    21    21
browser |    21  100.0%         10     -  65475456  65475476              AB350523     1    21    21
browser |    21  100.0%         10     -  65787360  65787380              AB350523     1    21    21
browser |    21  100.0%         10     -  66559006  66559026              AB350523     1    21    21
browser |    21  100.0%         10     -  78653055  78653075              AB350523     1    21    21
browser |    21  100.0%         10     +  80815902  80815922              AB350523     1    21    21
browser |    21  100.0%         10     -  83302498  83302518              AB350523     1    21    21
browser |    21  100.0%         10     +  83627684  83627704              AB350523     1    21    21
browser |    21  100.0%         10     +  84584975  84584995              AB350523     1    21    21
browser |    21  100.0%         10     +  85555776  85555796              AB350523     1    21    21
browser |    21  100.0%         10     -  85605054  85605074              AB350523     1    21    21
browser |    21  100.0%         10     +  88493157  88493177              AB350523     1    21    21
browser |    21  100.0%         10     +  88803278  88803298              AB350523     1    21    21
browser |    21  100.0%         10     -  90161232  90161252              AB350523     1    21    21
browser |    21  100.0%         10     -  94199199  94199219              AB350523     1    21    21
browser |    21  100.0%         10     -  95993870  95993890              AB350523     1    21    21
browser |    21  100.0%         10     -  96029156  96029176              AB350523     1    21    21
browser |    21  100.0%         10     -  97157184  97157204              AB350523     1    21    21
browser |    21  100.0%         10     +  99181312  99181332              AB350523     1    21    21
browser |    21  100.0%         10     + 100418848 100418868              AB350523     1    21    21
browser |    21  100.0%         10     + 104397539 104397559              AB350523     1    21    21
browser |    21  100.0%         10     - 104656114 104656134              AB350523     1    21    21
browser |    21  100.0%         10     + 104677760 104677780              AB350523     1    21    21
browser |    21  100.0%         10     - 105509273 105509293              AB350523     1    21    21
browser |    21  100.0%         10     - 109151840 109151860              AB350523     1    21    21
browser |    21  100.0%         10     + 111893484 111893504              AB350523     1    21    21
browser |    21  100.0%         10     - 113559371 113559391              AB350523     1    21    21
browser |    21  100.0%         10     + 117911604 117911624              AB350523     1    21    21
browser |    21  100.0%         10     + 121004401 121004421              AB350523     1    21    21
browser |    21  100.0%         10     - 122202726 122202746              AB350523     1    21    21
browser |    21  100.0%         10     - 122669526 122669546              AB350523     1    21    21
browser |    21  100.0%         10     + 124418556 124418576              AB350523     1    21    21
browser |    21  100.0%         10     + 124446062 124446082              AB350523     1    21    21
browser |    21  100.0%         10     - 124517116 124517136              AB350523     1    21    21
browser |    21  100.0%         10     - 129225454 129225474              AB350523     1    21    21
browser |    21  100.0%         10     + 129764752 129764772              AB350523     1    21    21
browser |    21  100.0%         10     - 130396773 130396793              AB350523     1    21    21
browser |    21  100.0%         11     -   6092254   6092274              AB350523     1    21    21
browser |    21  100.0%         11     +   6485009   6485029              AB350523     1    21    21
browser |    21  100.0%         11     -   7526451   7526471              AB350523     1    21    21
browser |    21  100.0%         11     -   9658749   9658769              AB350523     1    21    21
browser |    21  100.0%         11     +  10716654  10716674              AB350523     1    21    21
browser |    21  100.0%         11     -  12458052  12458072              AB350523     1    21    21
browser |    21  100.0%         11     +  12518266  12518286              AB350523     1    21    21
browser |    21  100.0%         11     -  12904779  12904799              AB350523     1    21    21
browser |    21  100.0%         11     +  15184035  15184055              AB350523     1    21    21
browser |    21  100.0%         11     +  15837038  15837058              AB350523     1    21    21
browser |    21  100.0%         11     -  18757220  18757240              AB350523     1    21    21
browser |    21  100.0%         11     -  19516939  19516959              AB350523     1    21    21
browser |    21  100.0%         11     -  19739489  19739509              AB350523     1    21    21
browser |    21  100.0%         11     -  22286016  22286036              AB350523     1    21    21
browser |    21  100.0%         11     +  22532226  22532246              AB350523     1    21    21
browser |    21  100.0%         11     -  23169346  23169366              AB350523     1    21    21
browser |    21  100.0%         11     -  27901842  27901862              AB350523     1    21    21
browser |    21  100.0%         11     +  28053635  28053655              AB350523     1    21    21
browser |    21  100.0%         11     +  29079008  29079028              AB350523     1    21    21
browser |    21  100.0%         11     +  38377390  38377410              AB350523     1    21    21
browser |    21  100.0%         11     +  43553884  43553904              AB350523     1    21    21
browser |    21  100.0%         11     +  51332104  51332124              AB350523     1    21    21
browser |    21  100.0%         11     -  51556616  51556636              AB350523     1    21    21
browser |    21  100.0%         11     -  54468164  54468184              AB350523     1    21    21
browser |    21  100.0%         11     -  55132526  55132546              AB350523     1    21    21
browser |    21  100.0%         11     +  63364895  63364915              AB350523     1    21    21
browser |    21  100.0%         11     +  64687424  64687444              AB350523     1    21    21
browser |    21  100.0%         11     -  65343377  65343397              AB350523     1    21    21
browser |    21  100.0%         11     +  74026100  74026120              AB350523     1    21    21
browser |    21  100.0%         11     +  74781566  74781586              AB350523     1    21    21
browser |    21  100.0%         11     +  81442710  81442730              AB350523     1    21    21
browser |    21  100.0%         11     -  82225587  82225607              AB350523     1    21    21
browser |    21  100.0%         11     -  85177160  85177180              AB350523     1    21    21
browser |    21  100.0%         11     +  86740215  86740235              AB350523     1    21    21
browser |    21  100.0%         11     -  88802552  88802572              AB350523     1    21    21
browser |    21  100.0%         11     -  90721211  90721231              AB350523     1    21    21
browser |    21  100.0%         11     +  90798301  90798321              AB350523     1    21    21
browser |    21  100.0%         11     -  90851764  90851784              AB350523     1    21    21
browser |    21  100.0%         11     +  91996228  91996248              AB350523     1    21    21
browser |    21  100.0%         11     +  98510433  98510453              AB350523     1    21    21
browser |    21  100.0%         11     -  99604294  99604314              AB350523     1    21    21
browser |    21  100.0%         11     + 100559585 100559605              AB350523     1    21    21
browser |    21  100.0%         11     - 105919845 105919865              AB350523     1    21    21
browser |    21  100.0%         11     - 106184280 106184300              AB350523     1    21    21
browser |    21  100.0%         11     - 108290843 108290863              AB350523     1    21    21
browser |    21  100.0%         11     + 108545229 108545249              AB350523     1    21    21
browser |    21  100.0%         11     + 109914437 109914457              AB350523     1    21    21
browser |    21  100.0%         11     + 111079675 111079695              AB350523     1    21    21
browser |    21  100.0%         11     - 111107236 111107256              AB350523     1    21    21
browser |    21  100.0%         11     + 113809365 113809385              AB350523     1    21    21
browser |    21  100.0%         11     - 115646489 115646509              AB350523     1    21    21
browser |    21  100.0%         11     + 116284721 116284741              AB350523     1    21    21
browser |    21  100.0%         11     + 116682731 116682751              AB350523     1    21    21
browser |    21  100.0%         11     + 117395017 117395037              AB350523     1    21    21
browser |    21  100.0%         11     + 120218325 120218345              AB350523     1    21    21
browser |    21  100.0%         11     + 120964888 120964908              AB350523     1    21    21
browser |    21  100.0%         12     +   3058710   3058730              AB350523     1    21    21
browser |    21  100.0%         12     -   3084486   3084506              AB350523     1    21    21
browser |    21  100.0%         12     +   3112483   3112503              AB350523     1    21    21
browser |    21  100.0%         12     -   3381571   3381591              AB350523     1    21    21
browser |    21  100.0%         12     +   6572881   6572901              AB350523     1    21    21
browser |    21  100.0%         12     +   6859366   6859386              AB350523     1    21    21
browser |    21  100.0%         12     +   8457645   8457665              AB350523     1    21    21
browser |    21  100.0%         12     -  11154419  11154439              AB350523     1    21    21
browser |    21  100.0%         12     -  14644930  14644950              AB350523     1    21    21
browser |    21  100.0%         12     +  17178559  17178579              AB350523     1    21    21
browser |    21  100.0%         12     -  19309004  19309024              AB350523     1    21    21
browser |    21  100.0%         12     +  19830843  19830863              AB350523     1    21    21
browser |    21  100.0%         12     +  24451812  24451832              AB350523     1    21    21
browser |    21  100.0%         12     +  24745320  24745340              AB350523     1    21    21
browser |    21  100.0%         12     +  25644319  25644339              AB350523     1    21    21
browser |    21  100.0%         12     -  31408914  31408934              AB350523     1    21    21
browser |    21  100.0%         12     +  32081590  32081610              AB350523     1    21    21
browser |    21  100.0%         12     +  32649790  32649810              AB350523     1    21    21
browser |    21  100.0%         12     +  32955668  32955688              AB350523     1    21    21
browser |    21  100.0%         12     +  39485463  39485483              AB350523     1    21    21
browser |    21  100.0%         12     +  40458431  40458451              AB350523     1    21    21
browser |    21  100.0%         12     +  41419847  41419867              AB350523     1    21    21
browser |    21  100.0%         12     -  49267889  49267909              AB350523     1    21    21
browser |    21  100.0%         12     -  52777648  52777668              AB350523     1    21    21
browser |    21  100.0%         12     -  60754451  60754471              AB350523     1    21    21
browser |    21  100.0%         12     -  61336670  61336690              AB350523     1    21    21
browser |    21  100.0%         12     -  64200337  64200357              AB350523     1    21    21
browser |    21  100.0%         12     -  65074709  65074729              AB350523     1    21    21
browser |    21  100.0%         12     -  65848766  65848786              AB350523     1    21    21
browser |    21  100.0%         12     -  73358555  73358575              AB350523     1    21    21
browser |    21  100.0%         12     -  79609377  79609397              AB350523     1    21    21
browser |    21  100.0%         12     +  80470408  80470428              AB350523     1    21    21
browser |    21  100.0%         12     +  81633838  81633858              AB350523     1    21    21
browser |    21  100.0%         12     -  85448563  85448583              AB350523     1    21    21
browser |    21  100.0%         12     +  88482620  88482640              AB350523     1    21    21
browser |    21  100.0%         12     +  90737708  90737728              AB350523     1    21    21
browser |    21  100.0%         12     +  93482668  93482688              AB350523     1    21    21
browser |    21  100.0%         12     -  94236072  94236092              AB350523     1    21    21
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View details of parts of alignment within browser window
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View table schema

Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518