AB351024
 

Information on mRNA AB351024

Description: Mus musculus non-coding RNA, oocyte_piRNA1840, 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: AB351024
Position: chrX:15589725-15589749

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%          X     -  15589725  15589749              AB351024     1    25    25
browser |    25  100.0%          1     -   3683928   3683952              AB351024     1    25    25
browser |    25  100.0%          1     +   7149115   7149139              AB351024     1    25    25
browser |    25  100.0%          1     -   7676491   7676515              AB351024     1    25    25
browser |    25  100.0%          1     -  14347836  14347860              AB351024     1    25    25
browser |    25  100.0%          1     +  15233118  15233142              AB351024     1    25    25
browser |    25  100.0%          1     -  15282417  15282441              AB351024     1    25    25
browser |    25  100.0%          1     -  15776323  15776347              AB351024     1    25    25
browser |    25  100.0%          1     +  16087967  16087991              AB351024     1    25    25
browser |    25  100.0%          1     -  16452434  16452458              AB351024     1    25    25
browser |    25  100.0%          1     +  18850839  18850863              AB351024     1    25    25
browser |    25  100.0%          1     +  20773382  20773406              AB351024     1    25    25
browser |    25  100.0%          1     -  22225361  22225385              AB351024     1    25    25
browser |    25  100.0%          1     -  33104804  33104828              AB351024     1    25    25
browser |    25  100.0%          1     -  35907546  35907570              AB351024     1    25    25
browser |    25  100.0%          1     +  36789891  36789915              AB351024     1    25    25
browser |    24  100.0%          1     +  40598880  40598903              AB351024     1    24    25
browser |    24  100.0%          1     +  41881724  41881747              AB351024     1    24    25
browser |    25  100.0%          1     -  42686321  42686345              AB351024     1    25    25
browser |    25  100.0%          1     -  44796752  44796776              AB351024     1    25    25
browser |    24  100.0%          1     +  46340795  46340818              AB351024     1    24    25
browser |    24  100.0%          1     +  47240287  47240310              AB351024     1    24    25
browser |    25  100.0%          1     -  47605045  47605069              AB351024     1    25    25
browser |    25  100.0%          1     -  49809323  49809347              AB351024     1    25    25
browser |    25  100.0%          1     +  51392490  51392514              AB351024     1    25    25
browser |    24  100.0%          1     +  51772256  51772279              AB351024     1    24    25
browser |    25  100.0%          1     -  64191517  64191541              AB351024     1    25    25
browser |    24  100.0%          1     +  65191543  65191566              AB351024     1    24    25
browser |    25  100.0%          1     +  70491160  70491184              AB351024     1    25    25
browser |    25  100.0%          1     +  71474396  71474420              AB351024     1    25    25
browser |    25  100.0%          1     +  75287339  75287363              AB351024     1    25    25
browser |    25  100.0%          1     -  79319039  79319063              AB351024     1    25    25
browser |    25  100.0%          1     -  79487332  79487356              AB351024     1    25    25
browser |    25  100.0%          1     +  85137272  85137296              AB351024     1    25    25
browser |    25  100.0%          1     +  85414705  85414729              AB351024     1    25    25
browser |    25  100.0%          1     -  91397047  91397071              AB351024     1    25    25
browser |    25  100.0%          1     +  92633322  92633346              AB351024     1    25    25
browser |    24  100.0%          1     +  92883556  92883579              AB351024     1    24    25
browser |    25  100.0%          1     -  93710237  93710261              AB351024     1    25    25
browser |    25  100.0%          1     -  97107286  97107310              AB351024     1    25    25
browser |    25  100.0%          1     - 102123256 102123280              AB351024     1    25    25
browser |    25  100.0%          1     + 105317308 105317332              AB351024     1    25    25
browser |    25  100.0%          1     - 105802411 105802435              AB351024     1    25    25
browser |    25  100.0%          1     - 110599328 110599352              AB351024     1    25    25
browser |    25  100.0%          1     + 113667527 113667551              AB351024     1    25    25
browser |    25  100.0%          1     - 113877103 113877127              AB351024     1    25    25
browser |    25  100.0%          1     + 115438281 115438305              AB351024     1    25    25
browser |    25  100.0%          1     + 119490362 119490386              AB351024     1    25    25
browser |    25  100.0%          1     + 120110555 120110579              AB351024     1    25    25
browser |    25  100.0%          1     - 127210277 127210301              AB351024     1    25    25
browser |    24  100.0%          1     - 131720530 131720553              AB351024     1    24    25
browser |    25  100.0%          1     - 132573231 132573255              AB351024     1    25    25
browser |    25  100.0%          1     + 133910870 133910894              AB351024     1    25    25
browser |    24  100.0%          1     + 139411797 139411820              AB351024     1    24    25
browser |    25  100.0%          1     - 140986649 140986673              AB351024     1    25    25
browser |    25  100.0%          1     - 141680214 141680238              AB351024     1    25    25
browser |    25  100.0%          1     - 148636943 148636967              AB351024     1    25    25
browser |    25  100.0%          1     - 149513928 149513952              AB351024     1    25    25
browser |    25  100.0%          1     - 149866997 149867021              AB351024     1    25    25
browser |    25  100.0%          1     + 150146756 150146780              AB351024     1    25    25
browser |    25  100.0%          1     + 158634092 158634116              AB351024     1    25    25
browser |    24  100.0%          1     + 159055609 159055632              AB351024     1    24    25
browser |    25  100.0%          1     + 167385609 167385633              AB351024     1    25    25
browser |    24  100.0%          1     - 167746067 167746090              AB351024     1    24    25
browser |    24  100.0%          1     + 175718074 175718097              AB351024     1    24    25
browser |    25  100.0%          1     + 177414900 177414924              AB351024     1    25    25
browser |    24  100.0%          1     + 177903229 177903252              AB351024     1    24    25
browser |    25  100.0%          1     - 178300122 178300146              AB351024     1    25    25
browser |    24  100.0%          1     - 179909836 179909859              AB351024     1    24    25
browser |    24  100.0%          1     + 190656435 190656458              AB351024     1    24    25
browser |    25  100.0%          1     + 190879722 190879746              AB351024     1    25    25
browser |    25  100.0%         10     +   5525534   5525558              AB351024     1    25    25
browser |    25  100.0%         10     -   6916581   6916605              AB351024     1    25    25
browser |    25  100.0%         10     -   7059881   7059905              AB351024     1    25    25
browser |    25  100.0%         10     -  10440740  10440764              AB351024     1    25    25
browser |    25  100.0%         10     +  13353628  13353652              AB351024     1    25    25
browser |    25  100.0%         10     +  14081470  14081494              AB351024     1    25    25
browser |    25  100.0%         10     +  17376234  17376258              AB351024     1    25    25
browser |    24  100.0%         10     -  23857494  23857517              AB351024     1    24    25
browser |    24  100.0%         10     +  27216374  27216397              AB351024     1    24    25
browser |    25  100.0%         10     +  29673915  29673939              AB351024     1    25    25
browser |    25  100.0%         10     -  37306686  37306710              AB351024     1    25    25
browser |    25  100.0%         10     +  37806931  37806955              AB351024     1    25    25
browser |    24  100.0%         10     -  38693604  38693627              AB351024     1    24    25
browser |    24  100.0%         10     +  42311015  42311038              AB351024     1    24    25
browser |    25  100.0%         10     -  44467601  44467625              AB351024     1    25    25
browser |    25  100.0%         10     +  45444233  45444257              AB351024     1    25    25
browser |    25  100.0%         10     -  46861339  46861363              AB351024     1    25    25
browser |    24  100.0%         10     -  47637490  47637513              AB351024     1    24    25
browser |    25  100.0%         10     -  52513392  52513416              AB351024     1    25    25
browser |    25  100.0%         10     +  55138536  55138560              AB351024     1    25    25
browser |    24  100.0%         10     +  60744650  60744673              AB351024     1    24    25
browser |    25  100.0%         10     -  61350499  61350523              AB351024     1    25    25
browser |    25  100.0%         10     -  62473366  62473390              AB351024     1    25    25
browser |    25  100.0%         10     -  64376349  64376373              AB351024     1    25    25
browser |    25  100.0%         10     +  65312474  65312498              AB351024     1    25    25
browser |    25  100.0%         10     -  65861151  65861175              AB351024     1    25    25
browser |    25  100.0%         10     -  66396372  66396396              AB351024     1    25    25
browser |    24  100.0%         10     +  67097785  67097808              AB351024     1    24    25
browser |    25  100.0%         10     -  67762409  67762433              AB351024     1    25    25
browser |    23  100.0%         10     +  72562572  72562594              AB351024     1    23    25
browser |    25  100.0%         10     +  82293858  82293882              AB351024     1    25    25
browser |    25  100.0%         10     +  87886459  87886483              AB351024     1    25    25
browser |    23  100.0%         10     -  88498721  88498743              AB351024     2    24    25
browser |    25  100.0%         10     +  95577829  95577853              AB351024     1    25    25
browser |    25  100.0%         10     -  97159936  97159960              AB351024     1    25    25
browser |    25  100.0%         10     -  97956878  97956902              AB351024     1    25    25
browser |    25  100.0%         10     -  98789332  98789356              AB351024     1    25    25
browser |    25  100.0%         10     + 103317147 103317171              AB351024     1    25    25
browser |    24  100.0%         10     + 103434447 103434470              AB351024     1    24    25
browser |    25  100.0%         10     + 106438617 106438641              AB351024     1    25    25
browser |    25  100.0%         10     + 108832766 108832790              AB351024     1    25    25
browser |    24  100.0%         10     + 112339685 112339708              AB351024     1    24    25
browser |    24  100.0%         10     + 112950295 112950318              AB351024     1    24    25
browser |    25  100.0%         10     - 116173254 116173278              AB351024     1    25    25
browser |    25  100.0%         10     - 116864684 116864708              AB351024     1    25    25
browser |    25  100.0%         10     + 118060925 118060949              AB351024     1    25    25
browser |    25  100.0%         10     - 118110330 118110354              AB351024     1    25    25
browser |    24  100.0%         10     + 119150018 119150041              AB351024     1    24    25
browser |    25  100.0%         10     + 119239250 119239274              AB351024     1    25    25
browser |    25  100.0%         10     + 121402819 121402843              AB351024     1    25    25
browser |    25  100.0%         10     - 126296274 126296298              AB351024     1    25    25
browser |    24  100.0%         10     + 126622270 126622293              AB351024     1    24    25
browser |    25  100.0%         10     + 128647397 128647421              AB351024     1    25    25
browser |    25  100.0%         10     - 128691083 128691107              AB351024     1    25    25
browser |    24  100.0%         10     + 129826878 129826901              AB351024     1    24    25
browser |    24  100.0%         11     +   4039933   4039956              AB351024     1    24    25
browser |    24  100.0%         11     -   4109523   4109546              AB351024     1    24    25
browser |    23  100.0%         11     +   7534961   7534983              AB351024     3    25    25
browser |    24  100.0%         11     +  11350620  11350643              AB351024     1    24    25
browser |    25  100.0%         11     +  13785721  13785745              AB351024     1    25    25
browser |    25  100.0%         11     -  17106817  17106841              AB351024     1    25    25
browser |    24  100.0%         11     +  19831668  19831691              AB351024     1    24    25
browser |    24  100.0%         11     -  20206871  20206894              AB351024     1    24    25
browser |    24  100.0%         11     +  21093943  21093966              AB351024     1    24    25
browser |    25  100.0%         11     -  22519318  22519342              AB351024     1    25    25
browser |    25  100.0%         11     -  22651275  22651299              AB351024     1    25    25
browser |    24  100.0%         11     -  22752228  22752251              AB351024     1    24    25
browser |    25  100.0%         11     +  25192137  25192161              AB351024     1    25    25
browser |    25  100.0%         11     -  27592242  27592266              AB351024     1    25    25
browser |    25  100.0%         11     -  28914866  28914890              AB351024     1    25    25
browser |    25  100.0%         11     +  31372489  31372513              AB351024     1    25    25
browser |    25  100.0%         11     +  40011175  40011199              AB351024     1    25    25
browser |    25  100.0%         11     -  43129221  43129245              AB351024     1    25    25
browser |    25  100.0%         11     -  47525666  47525690              AB351024     1    25    25
browser |    25  100.0%         11     +  50240898  50240922              AB351024     1    25    25
browser |    25  100.0%         11     -  52445390  52445414              AB351024     1    25    25
browser |    25  100.0%         11     -  57278174  57278198              AB351024     1    25    25
browser |    25  100.0%         11     -  59507137  59507161              AB351024     1    25    25
browser |    24  100.0%         11     -  59681220  59681243              AB351024     1    24    25
browser |    25  100.0%         11     +  60705944  60705968              AB351024     1    25    25
browser |    24  100.0%         11     +  62305020  62305043              AB351024     1    24    25
browser |    25  100.0%         11     -  64348713  64348737              AB351024     1    25    25
browser |    24  100.0%         11     -  65197019  65197042              AB351024     1    24    25
browser |    24  100.0%         11     +  68943891  68943914              AB351024     1    24    25
browser |    25  100.0%         11     +  71157544  71157568              AB351024     1    25    25
browser |    24  100.0%         11     +  73328790  73328813              AB351024     1    24    25
browser |    25  100.0%         11     +  77146778  77146802              AB351024     1    25    25
browser |    25  100.0%         11     +  90938957  90938981              AB351024     1    25    25
browser |    24  100.0%         11     -  92039603  92039626              AB351024     1    24    25
browser |    24  100.0%         11     +  96135090  96135113              AB351024     1    24    25
browser |    23  100.0%         11     + 100379740 100379762              AB351024     2    24    25
browser |    24  100.0%         11     + 102637578 102637601              AB351024     1    24    25
browser |    24  100.0%         11     + 103366891 103366914              AB351024     1    24    25
browser |    24  100.0%         11     - 115623413 115623436              AB351024     1    24    25
browser |    24  100.0%         11     + 117080666 117080689              AB351024     1    24    25
browser |    25  100.0%         11     + 119182286 119182310              AB351024     1    25    25
browser |    24  100.0%         11     + 119551582 119551605              AB351024     1    24    25
browser |    25  100.0%         11     - 121503820 121503844              AB351024     1    25    25
browser |    25  100.0%         12     +   8960102   8960126              AB351024     1    25    25
browser |    25  100.0%         12     +  11815567  11815591              AB351024     1    25    25
browser |    25  100.0%         12     +  12360015  12360039              AB351024     1    25    25
browser |    25  100.0%         12     +  13852292  13852316              AB351024     1    25    25
browser |    25  100.0%         12     +  17855571  17855595              AB351024     1    25    25
browser |    23  100.0%         12     -  18404013  18404035              AB351024     3    25    25
browser |    25  100.0%         12     +  19527174  19527198              AB351024     1    25    25
browser |    25  100.0%         12     +  20100800  20100824              AB351024     1    25    25
browser |    25  100.0%         12     +  20637774  20637798              AB351024     1    25    25
browser |    25  100.0%         12     -  29449895  29449919              AB351024     1    25    25
browser |    25  100.0%         12     +  31213499  31213523              AB351024     1    25    25
browser |    25  100.0%         12     -  36730154  36730178              AB351024     1    25    25
browser |    25  100.0%         12     -  37680237  37680261              AB351024     1    25    25
browser |    25  100.0%         12     -  45648430  45648454              AB351024     1    25    25
browser |    25  100.0%         12     +  45961009  45961033              AB351024     1    25    25
browser |    24  100.0%         12     -  48183728  48183751              AB351024     1    24    25
browser |    25  100.0%         12     +  51080820  51080844              AB351024     1    25    25
browser |    25  100.0%         12     +  51082318  51082342              AB351024     1    25    25
browser |    24  100.0%         12     -  52403042  52403065              AB351024     1    24    25
browser |    25  100.0%         12     +  57439469  57439493              AB351024     1    25    25
browser |    25  100.0%         12     +  58342424  58342448              AB351024     1    25    25
browser |    24  100.0%         12     -  58382135  58382158              AB351024     1    24    25
browser |    25  100.0%         12     +  64511564  64511588              AB351024     1    25    25
browser |    25  100.0%         12     +  67566829  67566853              AB351024     1    25    25
browser |    25  100.0%         12     -  67583235  67583259              AB351024     1    25    25
browser |    25  100.0%         12     -  69193980  69194004              AB351024     1    25    25
browser |    25  100.0%         12     -  72318367  72318391              AB351024     1    25    25
browser |    25  100.0%         12     -  75832688  75832712              AB351024     1    25    25
browser |    24  100.0%         12     -  80653590  80653613              AB351024     1    24    25
browser |    25  100.0%         12     +  81873686  81873710              AB351024     1    25    25
browser |    25  100.0%         12     +  88460877  88460901              AB351024     1    25    25
browser |    25  100.0%         12     +  96077697  96077721              AB351024     1    25    25
browser |    25  100.0%         12     +  96617388  96617412              AB351024     1    25    25
browser |    24  100.0%         12     - 101693492 101693515              AB351024     1    24    25
browser |    25  100.0%         12     + 101814701 101814725              AB351024     1    25    25
browser |    25  100.0%         12     - 109286149 109286173              AB351024     1    25    25
browser |    24  100.0%         12     + 112498202 112498225              AB351024     1    24    25
browser |    25  100.0%         13     -   4076890   4076914              AB351024     1    25    25
browser |    25  100.0%         13     -   7007658   7007682              AB351024     1    25    25
browser |    25  100.0%         13     +  10566825  10566849              AB351024     1    25    25
browser |    25  100.0%         13     +  12546013  12546037              AB351024     1    25    25
browser |    25  100.0%         13     -  12799206  12799230              AB351024     1    25    25
browser |    25  100.0%         13     -  13164199  13164223              AB351024     1    25    25
browser |    24  100.0%         13     -  14133306  14133329              AB351024     1    24    25
browser |    24  100.0%         13     +  14220492  14220515              AB351024     1    24    25
browser |    25  100.0%         13     -  14883054  14883078              AB351024     1    25    25
browser |    24  100.0%         13     +  16135623  16135646              AB351024     1    24    25
browser |    25  100.0%         13     -  16605479  16605503              AB351024     1    25    25
browser |    24  100.0%         13     -  18911376  18911399              AB351024     1    24    25
browser |    24  100.0%         13     -  23830915  23830938              AB351024     1    24    25
browser |    24  100.0%         13     +  23841323  23841346              AB351024     1    24    25
browser |    25  100.0%         13     -  25252771  25252795              AB351024     1    25    25
browser |    25  100.0%         13     -  30684285  30684309              AB351024     1    25    25
browser |    25  100.0%         13     +  39042182  39042206              AB351024     1    25    25
browser |    25  100.0%         13     +  43696245  43696269              AB351024     1    25    25
browser |    25  100.0%         13     +  44642483  44642507              AB351024     1    25    25
browser |    25  100.0%         13     -  44867156  44867180              AB351024     1    25    25
browser |    25  100.0%         13     +  46594312  46594336              AB351024     1    25    25
browser |    25  100.0%         13     -  48664522  48664546              AB351024     1    25    25
browser |    24  100.0%         13     -  50600962  50600985              AB351024     1    24    25
browser |    25  100.0%         13     +  51822707  51822731              AB351024     1    25    25
browser |    24  100.0%         13     +  53294723  53294746              AB351024     2    25    25
browser |    25  100.0%         13     -  54974286  54974310              AB351024     1    25    25
browser |    25  100.0%         13     +  62461965  62461989              AB351024     1    25    25
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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

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