AB349706
 

Information on mRNA AB349706

Description: Mus musculus non-coding RNA, oocyte_piRNA522, 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: AB349706
Position: chr12:56797702-56797723

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 |    22  100.0%         12     -  56797702  56797723              AB349706     1    22    22
browser |    22  100.0%          1     -   5880387   5880408              AB349706     1    22    22
browser |    22  100.0%          1     -   6506416   6506437              AB349706     1    22    22
browser |    22  100.0%          1     +   8065211   8065232              AB349706     1    22    22
browser |    22  100.0%          1     +   8227652   8227673              AB349706     1    22    22
browser |    22  100.0%          1     +   8858686   8858707              AB349706     1    22    22
browser |    22  100.0%          1     -  10805903  10805924              AB349706     1    22    22
browser |    22  100.0%          1     -  12019727  12019748              AB349706     1    22    22
browser |    22  100.0%          1     +  16809722  16809743              AB349706     1    22    22
browser |    22  100.0%          1     +  18028316  18028337              AB349706     1    22    22
browser |    22  100.0%          1     +  18588346  18588367              AB349706     1    22    22
browser |    22  100.0%          1     +  19693930  19693951              AB349706     1    22    22
browser |    22  100.0%          1     -  22071280  22071301              AB349706     1    22    22
browser |    22  100.0%          1     +  23341487  23341508              AB349706     1    22    22
browser |    22  100.0%          1     -  26392176  26392197              AB349706     1    22    22
browser |    22  100.0%          1     +  26454338  26454359              AB349706     1    22    22
browser |    22  100.0%          1     -  26513992  26514013              AB349706     1    22    22
browser |    22  100.0%          1     +  27220486  27220507              AB349706     1    22    22
browser |    22  100.0%          1     +  29695210  29695231              AB349706     1    22    22
browser |    22  100.0%          1     -  29987122  29987143              AB349706     1    22    22
browser |    22  100.0%          1     +  34387819  34387840              AB349706     1    22    22
browser |    22  100.0%          1     +  35828815  35828836              AB349706     1    22    22
browser |    22  100.0%          1     +  38745204  38745225              AB349706     1    22    22
browser |    22  100.0%          1     +  40738495  40738516              AB349706     1    22    22
browser |    22  100.0%          1     +  45774568  45774589              AB349706     1    22    22
browser |    22  100.0%          1     -  47265836  47265857              AB349706     1    22    22
browser |    22  100.0%          1     -  48401177  48401198              AB349706     1    22    22
browser |    22  100.0%          1     -  58368342  58368363              AB349706     1    22    22
browser |    22  100.0%          1     -  58856650  58856671              AB349706     1    22    22
browser |    22  100.0%          1     -  60769836  60769857              AB349706     1    22    22
browser |    22  100.0%          1     -  62579100  62579121              AB349706     1    22    22
browser |    22  100.0%          1     -  64223162  64223183              AB349706     1    22    22
browser |    22  100.0%          1     -  81547711  81547732              AB349706     1    22    22
browser |    22  100.0%          1     +  82480065  82480086              AB349706     1    22    22
browser |    22  100.0%          1     -  83209315  83209336              AB349706     1    22    22
browser |    22  100.0%          1     -  87067193  87067214              AB349706     1    22    22
browser |    22  100.0%          1     +  87389142  87389163              AB349706     1    22    22
browser |    22  100.0%          1     +  89128070  89128091              AB349706     1    22    22
browser |    22  100.0%          1     -  91404766  91404787              AB349706     1    22    22
browser |    22  100.0%          1     +  93885552  93885573              AB349706     1    22    22
browser |    22  100.0%          1     +  95624140  95624161              AB349706     1    22    22
browser |    22  100.0%          1     +  97101751  97101772              AB349706     1    22    22
browser |    22  100.0%          1     -  98529963  98529984              AB349706     1    22    22
browser |    22  100.0%          1     - 101911701 101911722              AB349706     1    22    22
browser |    22  100.0%          1     + 102960653 102960674              AB349706     1    22    22
browser |    22  100.0%          1     - 103138730 103138751              AB349706     1    22    22
browser |    22  100.0%          1     + 103407286 103407307              AB349706     1    22    22
browser |    22  100.0%          1     + 103517815 103517836              AB349706     1    22    22
browser |    22  100.0%          1     - 104221226 104221247              AB349706     1    22    22
browser |    22  100.0%          1     + 104293520 104293541              AB349706     1    22    22
browser |    22  100.0%          1     - 108342418 108342439              AB349706     1    22    22
browser |    22  100.0%          1     + 109542395 109542416              AB349706     1    22    22
browser |    22  100.0%          1     + 110258060 110258081              AB349706     1    22    22
browser |    22  100.0%          1     - 111187187 111187208              AB349706     1    22    22
browser |    22  100.0%          1     + 111632363 111632384              AB349706     1    22    22
browser |    22  100.0%          1     - 112197907 112197928              AB349706     1    22    22
browser |    22  100.0%          1     + 112858472 112858493              AB349706     1    22    22
browser |    22  100.0%          1     + 112945070 112945091              AB349706     1    22    22
browser |    22  100.0%          1     + 114114301 114114322              AB349706     1    22    22
browser |    22  100.0%          1     - 115817028 115817049              AB349706     1    22    22
browser |    22  100.0%          1     - 116581835 116581856              AB349706     1    22    22
browser |    22  100.0%          1     - 117635493 117635514              AB349706     1    22    22
browser |    22  100.0%          1     - 120502487 120502508              AB349706     1    22    22
browser |    22  100.0%          1     - 125276936 125276957              AB349706     1    22    22
browser |    22  100.0%          1     - 159803161 159803182              AB349706     1    22    22
browser |    22  100.0%          1     - 160647354 160647375              AB349706     1    22    22
browser |    22  100.0%          1     + 162669383 162669404              AB349706     1    22    22
browser |    22  100.0%          1     + 166181024 166181045              AB349706     1    22    22
browser |    22  100.0%          1     - 166596034 166596055              AB349706     1    22    22
browser |    22  100.0%          1     + 169944617 169944638              AB349706     1    22    22
browser |    22  100.0%          1     + 172094584 172094605              AB349706     1    22    22
browser |    22  100.0%          1     - 174874566 174874587              AB349706     1    22    22
browser |    22  100.0%          1     - 176376460 176376481              AB349706     1    22    22
browser |    22  100.0%          1     + 177886882 177886903              AB349706     1    22    22
browser |    22  100.0%          1     + 178002935 178002956              AB349706     1    22    22
browser |    22  100.0%          1     + 179722830 179722851              AB349706     1    22    22
browser |    22  100.0%          1     - 181096917 181096938              AB349706     1    22    22
browser |    22  100.0%          1     + 181321724 181321745              AB349706     1    22    22
browser |    22  100.0%          1     + 183297542 183297563              AB349706     1    22    22
browser |    22  100.0%          1     + 191840964 191840985              AB349706     1    22    22
browser |    22  100.0%          1     + 195003919 195003940              AB349706     1    22    22
browser |    22  100.0%         10     -   3556757   3556778              AB349706     1    22    22
browser |    22  100.0%         10     +   8476308   8476329              AB349706     1    22    22
browser |    22  100.0%         10     +  11571287  11571308              AB349706     1    22    22
browser |    22  100.0%         10     -  19420470  19420491              AB349706     1    22    22
browser |    22  100.0%         10     +  19674322  19674343              AB349706     1    22    22
browser |    21  100.0%         10     -  19892198  19892218              AB349706     1    21    22
browser |    22  100.0%         10     +  21088507  21088528              AB349706     1    22    22
browser |    22  100.0%         10     -  21524043  21524064              AB349706     1    22    22
browser |    22  100.0%         10     -  22404935  22404956              AB349706     1    22    22
browser |    22  100.0%         10     -  22564989  22565010              AB349706     1    22    22
browser |    22  100.0%         10     -  23753044  23753065              AB349706     1    22    22
browser |    22  100.0%         10     +  24563601  24563622              AB349706     1    22    22
browser |    22  100.0%         10     +  25845580  25845601              AB349706     1    22    22
browser |    22  100.0%         10     +  30358652  30358673              AB349706     1    22    22
browser |    22  100.0%         10     +  30691248  30691269              AB349706     1    22    22
browser |    22  100.0%         10     +  30965933  30965954              AB349706     1    22    22
browser |    22  100.0%         10     +  31359875  31359896              AB349706     1    22    22
browser |    22  100.0%         10     +  33764226  33764247              AB349706     1    22    22
browser |    22  100.0%         10     -  34623647  34623668              AB349706     1    22    22
browser |    22  100.0%         10     +  41717802  41717823              AB349706     1    22    22
browser |    22  100.0%         10     -  43648756  43648777              AB349706     1    22    22
browser |    22  100.0%         10     -  45434928  45434949              AB349706     1    22    22
browser |    22  100.0%         10     +  47547952  47547973              AB349706     1    22    22
browser |    22  100.0%         10     +  51760360  51760381              AB349706     1    22    22
browser |    22  100.0%         10     -  55595555  55595576              AB349706     1    22    22
browser |    22  100.0%         10     -  65479450  65479471              AB349706     1    22    22
browser |    22  100.0%         10     -  65790524  65790545              AB349706     1    22    22
browser |    22  100.0%         10     -  66564065  66564086              AB349706     1    22    22
browser |    22  100.0%         10     +  77857483  77857504              AB349706     1    22    22
browser |    22  100.0%         10     -  78657614  78657635              AB349706     1    22    22
browser |    20  100.0%         10     -  81671328  81671347              AB349706     1    20    22
browser |    22  100.0%         10     +  81804992  81805013              AB349706     1    22    22
browser |    22  100.0%         10     -  83253548  83253569              AB349706     1    22    22
browser |    22  100.0%         10     -  83307555  83307576              AB349706     1    22    22
browser |    22  100.0%         10     -  83512610  83512631              AB349706     1    22    22
browser |    22  100.0%         10     +  83624594  83624615              AB349706     1    22    22
browser |    22  100.0%         10     +  84581831  84581852              AB349706     1    22    22
browser |    22  100.0%         10     +  85552326  85552347              AB349706     1    22    22
browser |    22  100.0%         10     +  86979746  86979767              AB349706     1    22    22
browser |    22  100.0%         10     +  88488113  88488134              AB349706     1    22    22
browser |    22  100.0%         10     -  90164321  90164342              AB349706     1    22    22
browser |    22  100.0%         10     -  94203758  94203779              AB349706     1    22    22
browser |    22  100.0%         10     -  96034218  96034239              AB349706     1    22    22
browser |    22  100.0%         10     -  97164137  97164158              AB349706     1    22    22
browser |    22  100.0%         10     -  98937935  98937956              AB349706     1    22    22
browser |    22  100.0%         10     +  99176252  99176273              AB349706     1    22    22
browser |    22  100.0%         10     -  99385910  99385931              AB349706     1    22    22
browser |    22  100.0%         10     + 104392479 104392500              AB349706     1    22    22
browser |    22  100.0%         10     - 104659257 104659278              AB349706     1    22    22
browser |    22  100.0%         10     + 104672696 104672717              AB349706     1    22    22
browser |    22  100.0%         10     + 105014215 105014236              AB349706     1    22    22
browser |    22  100.0%         10     - 105512440 105512461              AB349706     1    22    22
browser |    22  100.0%         10     - 109156904 109156925              AB349706     1    22    22
browser |    22  100.0%         10     - 113564430 113564451              AB349706     1    22    22
browser |    22  100.0%         10     + 121001904 121001925              AB349706     1    22    22
browser |    22  100.0%         10     + 122342950 122342971              AB349706     1    22    22
browser |    22  100.0%         10     + 123696517 123696538              AB349706     1    22    22
browser |    22  100.0%         10     + 124413491 124413512              AB349706     1    22    22
browser |    22  100.0%         10     + 124442936 124442957              AB349706     1    22    22
browser |    22  100.0%         10     - 124520671 124520692              AB349706     1    22    22
browser |    22  100.0%         10     - 129230516 129230537              AB349706     1    22    22
browser |    22  100.0%         10     + 129762439 129762460              AB349706     1    22    22
browser |    22  100.0%         10     - 130400725 130400746              AB349706     1    22    22
browser |    22  100.0%         11     -   6097318   6097339              AB349706     1    22    22
browser |    22  100.0%         11     -   7531510   7531531              AB349706     1    22    22
browser |    22  100.0%         11     -   9663809   9663830              AB349706     1    22    22
browser |    22  100.0%         11     +  10711592  10711613              AB349706     1    22    22
browser |    22  100.0%         11     -  12461195  12461216              AB349706     1    22    22
browser |    22  100.0%         11     +  12513202  12513223              AB349706     1    22    22
browser |    22  100.0%         11     +  12746873  12746894              AB349706     1    22    22
browser |    22  100.0%         11     -  12907922  12907943              AB349706     1    22    22
browser |    22  100.0%         11     -  14848528  14848549              AB349706     1    22    22
browser |    22  100.0%         11     +  15178972  15178993              AB349706     1    22    22
browser |    22  100.0%         11     -  15236684  15236705              AB349706     1    22    22
browser |    22  100.0%         11     -  18762282  18762303              AB349706     1    22    22
browser |    22  100.0%         11     -  19519251  19519272              AB349706     1    22    22
browser |    22  100.0%         11     +  20467658  20467679              AB349706     1    22    22
browser |    22  100.0%         11     +  22529060  22529081              AB349706     1    22    22
browser |    22  100.0%         11     -  23174409  23174430              AB349706     1    22    22
browser |    22  100.0%         11     -  23196019  23196040              AB349706     1    22    22
browser |    22  100.0%         11     +  26506802  26506823              AB349706     1    22    22
browser |    22  100.0%         11     +  27081679  27081700              AB349706     1    22    22
browser |    22  100.0%         11     +  27085045  27085066              AB349706     1    22    22
browser |    22  100.0%         11     -  27905795  27905816              AB349706     1    22    22
browser |    22  100.0%         11     +  28048575  28048596              AB349706     1    22    22
browser |    22  100.0%         11     +  29075840  29075861              AB349706     1    22    22
browser |    22  100.0%         11     -  29233425  29233446              AB349706     1    22    22
browser |    22  100.0%         11     +  38373604  38373625              AB349706     1    22    22
browser |    22  100.0%         11     -  39960378  39960399              AB349706     1    22    22
browser |    22  100.0%         11     -  51559783  51559804              AB349706     1    22    22
browser |    22  100.0%         11     +  74021040  74021061              AB349706     1    22    22
browser |    22  100.0%         11     +  74432259  74432280              AB349706     1    22    22
browser |    22  100.0%         11     +  74776502  74776523              AB349706     1    22    22
browser |    22  100.0%         11     +  79764819  79764840              AB349706     1    22    22
browser |    22  100.0%         11     -  82227899  82227920              AB349706     1    22    22
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browser |    22  100.0%         11     -  85182222  85182243              AB349706     1    22    22
browser |    22  100.0%         11     +  86737718  86737739              AB349706     1    22    22
browser |    22  100.0%         11     -  88807609  88807630              AB349706     1    22    22
browser |    22  100.0%         11     -  90201993  90202014              AB349706     1    22    22
browser |    22  100.0%         11     -  90724353  90724374              AB349706     1    22    22
browser |    22  100.0%         11     +  90793795  90793816              AB349706     1    22    22
browser |    22  100.0%         11     -  90856826  90856847              AB349706     1    22    22
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browser |    22  100.0%         11     +  98505369  98505390              AB349706     1    22    22
browser |    22  100.0%         11     -  99606772  99606793              AB349706     1    22    22
browser |    22  100.0%         11     + 100555025 100555046              AB349706     1    22    22
browser |    22  100.0%         11     - 105923011 105923032              AB349706     1    22    22
browser |    22  100.0%         11     - 108293863 108293884              AB349706     1    22    22
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browser |    22  100.0%         11     + 111074611 111074632              AB349706     1    22    22
browser |    22  100.0%         11     - 111112298 111112319              AB349706     1    22    22
browser |    22  100.0%         11     + 113804301 113804322              AB349706     1    22    22
browser |    22  100.0%         11     - 115651552 115651573              AB349706     1    22    22
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browser |    22  100.0%         11     + 116677668 116677689              AB349706     1    22    22
browser |    22  100.0%         11     + 117391963 117391984              AB349706     1    22    22
browser |    22  100.0%         11     + 120213262 120213283              AB349706     1    22    22
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browser |    22  100.0%         12     +   3053657   3053678              AB349706     1    22    22
browser |    22  100.0%         12     -   3086825   3086846              AB349706     1    22    22
browser |    22  100.0%         12     -   3386635   3386656              AB349706     1    22    22
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browser |    22  100.0%         12     +   6854308   6854329              AB349706     1    22    22
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browser |    22  100.0%         12     -  11159483  11159504              AB349706     1    22    22
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browser |    22  100.0%         12     -  14649983  14650004              AB349706     1    22    22
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browser |    22  100.0%         12     -  19314066  19314087              AB349706     1    22    22
browser |    22  100.0%         12     +  22093250  22093271              AB349706     1    22    22
browser |    22  100.0%         12     +  24446752  24446773              AB349706     1    22    22
browser |    22  100.0%         12     +  24743375  24743396              AB349706     1    22    22
browser |    22  100.0%         12     -  31413974  31413995              AB349706     1    22    22
browser |    22  100.0%         12     +  32079276  32079297              AB349706     1    22    22
browser |    22  100.0%         12     +  39483102  39483123              AB349706     1    22    22
browser |    22  100.0%         12     +  40453366  40453387              AB349706     1    22    22
browser |    22  100.0%         12     +  41414787  41414808              AB349706     1    22    22
browser |    22  100.0%         12     -  44817753  44817774              AB349706     1    22    22
browser |    22  100.0%         12     +  48580238  48580259              AB349706     1    22    22
browser |    22  100.0%         12     -  52780814  52780835              AB349706     1    22    22
browser |    22  100.0%         12     -  65853828  65853849              AB349706     1    22    22
browser |    22  100.0%         12     -  66459628  66459649              AB349706     1    22    22
browser |    22  100.0%         12     -  68674381  68674402              AB349706     1    22    22
browser |    22  100.0%         12     -  70713761  70713782              AB349706     1    22    22
browser |    22  100.0%         12     -  70970610  70970631              AB349706     1    22    22
browser |    22  100.0%         12     -  79614440  79614461              AB349706     1    22    22
browser |    22  100.0%         12     +  80465345  80465366              AB349706     1    22    22
browser |    22  100.0%         12     -  82511767  82511788              AB349706     1    22    22
browser |    22  100.0%         12     -  85453622  85453643              AB349706     1    22    22
browser |    22  100.0%         12     +  93477607  93477628              AB349706     1    22    22
browser |    22  100.0%         12     -  94009109  94009130              AB349706     1    22    22
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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