AB345587
 

Information on mRNA AB345587

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA10788, 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: n/a
Development stage: growing stage
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB345587
Position: chr12:56959200-56959228

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 |    28  100.0%         12     +  56959200  56959228              AB345587     1    28    28
browser |    28  100.0%          1     -   4629323   4629351              AB345587     1    28    28
browser |    28  100.0%          1     -   5636445   5636473              AB345587     1    28    28
browser |    28  100.0%          1     +   5817908   5817936              AB345587     1    28    28
browser |    28  100.0%          1     +   7890623   7890651              AB345587     1    28    28
browser |    28  100.0%          1     -  11439200  11439228              AB345587     1    28    28
browser |    28  100.0%          1     +  14032170  14032198              AB345587     1    28    28
browser |    28  100.0%          1     -  18324161  18324189              AB345587     1    28    28
browser |    28  100.0%          1     +  21653064  21653092              AB345587     1    28    28
browser |    28  100.0%          1     -  28496823  28496851              AB345587     1    28    28
browser |    28  100.0%          1     +  28929406  28929434              AB345587     1    28    28
browser |    28  100.0%          1     -  30728223  30728251              AB345587     1    28    28
browser |    28  100.0%          1     +  31045315  31045343              AB345587     1    28    28
browser |    28  100.0%          1     -  37321594  37321622              AB345587     1    28    28
browser |    28  100.0%          1     +  37813949  37813977              AB345587     1    28    28
browser |    28  100.0%          1     +  41128701  41128729              AB345587     1    28    28
browser |    28  100.0%          1     +  44331050  44331078              AB345587     1    28    28
browser |    28  100.0%          1     +  44400703  44400731              AB345587     1    28    28
browser |    28  100.0%          1     -  45651316  45651344              AB345587     1    28    28
browser |    28  100.0%          1     -  48711839  48711867              AB345587     1    28    28
browser |    28  100.0%          1     +  50200108  50200136              AB345587     1    28    28
browser |    28  100.0%          1     +  53275990  53276018              AB345587     1    28    28
browser |    28  100.0%          1     +  57348933  57348961              AB345587     1    28    28
browser |    28  100.0%          1     -  57626739  57626767              AB345587     1    28    28
browser |    28  100.0%          1     +  65748434  65748462              AB345587     1    28    28
browser |    28  100.0%          1     +  65855426  65855454              AB345587     1    28    28
browser |    28  100.0%          1     -  65930103  65930131              AB345587     1    28    28
browser |    28  100.0%          1     +  81961503  81961531              AB345587     1    28    28
browser |    28  100.0%          1     -  86246841  86246869              AB345587     1    28    28
browser |    28  100.0%          1     -  93038345  93038373              AB345587     1    28    28
browser |    28  100.0%          1     -  96896070  96896098              AB345587     1    28    28
browser |    28  100.0%          1     - 100458226 100458254              AB345587     1    28    28
browser |    28  100.0%          1     + 102078701 102078729              AB345587     1    28    28
browser |    28  100.0%          1     + 108066053 108066081              AB345587     1    28    28
browser |    28  100.0%          1     - 108875486 108875514              AB345587     1    28    28
browser |    28  100.0%          1     + 109061726 109061754              AB345587     1    28    28
browser |    28  100.0%          1     - 112495920 112495948              AB345587     1    28    28
browser |    28  100.0%          1     - 113609138 113609166              AB345587     1    28    28
browser |    28  100.0%          1     - 117561346 117561374              AB345587     1    28    28
browser |    28  100.0%          1     - 117676325 117676353              AB345587     1    28    28
browser |    28  100.0%          1     + 117919018 117919046              AB345587     1    28    28
browser |    28  100.0%          1     + 128816879 128816907              AB345587     1    28    28
browser |    28  100.0%          1     - 143724463 143724491              AB345587     1    28    28
browser |    28  100.0%          1     + 161361079 161361107              AB345587     1    28    28
browser |    28  100.0%          1     - 163299200 163299228              AB345587     1    28    28
browser |    28  100.0%          1     + 185037175 185037203              AB345587     1    28    28
browser |    28  100.0%          1     + 191235210 191235238              AB345587     1    28    28
browser |    27  100.0%         10     -   3270069   3270096              AB345587     1    27    28
browser |    28  100.0%         10     -   6520491   6520519              AB345587     1    28    28
browser |    28  100.0%         10     +   7192456   7192484              AB345587     1    28    28
browser |    28  100.0%         10     +   7316180   7316208              AB345587     1    28    28
browser |    28  100.0%         10     +   8512171   8512199              AB345587     1    28    28
browser |    28  100.0%         10     +   9723779   9723807              AB345587     1    28    28
browser |    28  100.0%         10     -  11778073  11778101              AB345587     1    28    28
browser |    28  100.0%         10     -  15058275  15058303              AB345587     1    28    28
browser |    27  100.0%         10     +  15812209  15812236              AB345587     2    28    28
browser |    28  100.0%         10     +  18115988  18116016              AB345587     1    28    28
browser |    28  100.0%         10     +  31627110  31627138              AB345587     1    28    28
browser |    28  100.0%         10     -  35600285  35600313              AB345587     1    28    28
browser |    28  100.0%         10     -  37728893  37728921              AB345587     1    28    28
browser |    28  100.0%         10     +  38467318  38467346              AB345587     1    28    28
browser |    28  100.0%         10     -  47513534  47513562              AB345587     1    28    28
browser |    28  100.0%         10     -  47909801  47909829              AB345587     1    28    28
browser |    28  100.0%         10     +  50368411  50368439              AB345587     1    28    28
browser |    28  100.0%         10     +  54465845  54465873              AB345587     1    28    28
browser |    28  100.0%         10     +  62445843  62445871              AB345587     1    28    28
browser |    28  100.0%         10     -  73385518  73385546              AB345587     1    28    28
browser |    28  100.0%         10     -  73691986  73692014              AB345587     1    28    28
browser |    28  100.0%         10     +  74712699  74712727              AB345587     1    28    28
browser |    26  100.0%         10     +  76757122  76757148              AB345587     3    28    28
browser |    28  100.0%         10     -  82409783  82409811              AB345587     1    28    28
browser |    28  100.0%         10     -  85608021  85608049              AB345587     1    28    28
browser |    28  100.0%         10     +  88800845  88800873              AB345587     1    28    28
browser |    28  100.0%         10     -  92588888  92588916              AB345587     1    28    28
browser |    28  100.0%         10     + 100415873 100415901              AB345587     1    28    28
browser |    28  100.0%         10     + 103910855 103910883              AB345587     1    28    28
browser |    28  100.0%         10     - 104412336 104412364              AB345587     1    28    28
browser |    28  100.0%         10     + 110837243 110837271              AB345587     1    28    28
browser |    28  100.0%         10     - 124303650 124303678              AB345587     1    28    28
browser |    28  100.0%         11     +   6482628   6482656              AB345587     1    28    28
browser |    28  100.0%         11     -   7986359   7986387              AB345587     1    28    28
browser |    28  100.0%         11     +  13824168  13824196              AB345587     1    28    28
browser |    28  100.0%         11     +  15811304  15811332              AB345587     1    28    28
browser |    28  100.0%         11     +  15834604  15834632              AB345587     1    28    28
browser |    28  100.0%         11     +  16179511  16179539              AB345587     1    28    28
browser |    28  100.0%         11     -  19742456  19742484              AB345587     1    28    28
browser |    28  100.0%         11     -  20460583  20460611              AB345587     1    28    28
browser |    28  100.0%         11     -  27366471  27366499              AB345587     1    28    28
browser |    28  100.0%         11     -  29115415  29115443              AB345587     1    28    28
browser |    28  100.0%         11     +  29231494  29231522              AB345587     1    28    28
browser |    28  100.0%         11     +  31725596  31725624              AB345587     1    28    28
browser |    28  100.0%         11     +  44276361  44276389              AB345587     1    28    28
browser |    28  100.0%         11     +  67021825  67021853              AB345587     1    28    28
browser |    28  100.0%         11     -  70934393  70934421              AB345587     1    28    28
browser |    28  100.0%         11     -  70959113  70959141              AB345587     1    28    28
browser |    28  100.0%         11     -  73839588  73839616              AB345587     1    28    28
browser |    28  100.0%         11     -  79126751  79126779              AB345587     1    28    28
browser |    28  100.0%         11     -  85331858  85331886              AB345587     1    28    28
browser |    28  100.0%         11     +  90399691  90399719              AB345587     1    28    28
browser |    28  100.0%         11     - 104751928 104751956              AB345587     1    28    28
browser |    28  100.0%         11     + 116651349 116651377              AB345587     1    28    28
browser |    28  100.0%         12     +   3109508   3109536              AB345587     1    28    28
browser |    28  100.0%         12     +   4839020   4839048              AB345587     1    28    28
browser |    28  100.0%         12     +  17294660  17294688              AB345587     1    28    28
browser |    28  100.0%         12     +  17979791  17979819              AB345587     1    28    28
browser |    28  100.0%         12     -  19850938  19850966              AB345587     1    28    28
browser |    27  100.0%         12     -  20694126  20694153              AB345587     2    28    28
browser |    28  100.0%         12     -  22426621  22426649              AB345587     1    28    28
browser |    28  100.0%         12     +  24396845  24396873              AB345587     1    28    28
browser |    28  100.0%         12     -  26157984  26158012              AB345587     1    28    28
browser |    28  100.0%         12     -  27283651  27283679              AB345587     1    28    28
browser |    28  100.0%         12     +  32647414  32647442              AB345587     1    28    28
browser |    28  100.0%         12     +  36667135  36667163              AB345587     1    28    28
browser |    28  100.0%         12     +  40232893  40232921              AB345587     1    28    28
browser |    28  100.0%         12     +  42921081  42921109              AB345587     1    28    28
browser |    28  100.0%         12     -  44202329  44202357              AB345587     1    28    28
browser |    28  100.0%         12     -  52222048  52222076              AB345587     1    28    28
browser |    28  100.0%         12     +  54406278  54406306              AB345587     1    28    28
browser |    28  100.0%         12     -  54917765  54917793              AB345587     1    28    28
browser |    28  100.0%         12     +  63345541  63345569              AB345587     1    28    28
browser |    28  100.0%         12     -  64202075  64202103              AB345587     1    28    28
browser |    28  100.0%         12     +  65731255  65731283              AB345587     1    28    28
browser |    28  100.0%         12     -  65832726  65832754              AB345587     1    28    28
browser |    28  100.0%         12     +  65880605  65880633              AB345587     1    28    28
browser |    28  100.0%         12     +  76701083  76701111              AB345587     1    28    28
browser |    28  100.0%         12     +  79162308  79162336              AB345587     1    28    28
browser |    28  100.0%         12     +  90734736  90734764              AB345587     1    28    28
browser |    27  100.0%         12     +  91195435  91195462              AB345587     1    27    28
browser |    28  100.0%         12     +  96904606  96904634              AB345587     1    28    28
browser |    28  100.0%         12     + 105595536 105595564              AB345587     1    28    28
browser |    28  100.0%         12     - 109788431 109788459              AB345587     1    28    28
browser |    28  100.0%         12     + 112852351 112852379              AB345587     1    28    28
browser |    28  100.0%         12     + 114906114 114906142              AB345587     1    28    28
browser |    28  100.0%         12     + 115364741 115364769              AB345587     1    28    28
browser |    28  100.0%         12     + 118759620 118759648              AB345587     1    28    28
browser |    28  100.0%         13     -   4879083   4879111              AB345587     1    28    28
browser |    28  100.0%         13     +   4922041   4922069              AB345587     1    28    28
browser |    28  100.0%         13     -   5031408   5031436              AB345587     1    28    28
browser |    28  100.0%         13     -   6318378   6318406              AB345587     1    28    28
browser |    28  100.0%         13     +  10828406  10828434              AB345587     1    28    28
browser |    28  100.0%         13     -  11013044  11013072              AB345587     1    28    28
browser |    28  100.0%         13     +  11143054  11143082              AB345587     1    28    28
browser |    28  100.0%         13     -  15274499  15274527              AB345587     1    28    28
browser |    28  100.0%         13     +  24411751  24411779              AB345587     1    28    28
browser |    28  100.0%         13     +  27473180  27473208              AB345587     1    28    28
browser |    28  100.0%         13     -  28383875  28383903              AB345587     1    28    28
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browser |    28  100.0%         13     -  33960054  33960082              AB345587     1    28    28
browser |    28  100.0%         13     +  50060355  50060383              AB345587     1    28    28
browser |    28  100.0%         13     -  50658138  50658166              AB345587     1    28    28
browser |    28  100.0%         13     -  50712505  50712533              AB345587     1    28    28
browser |    28  100.0%         13     +  51187599  51187627              AB345587     1    28    28
browser |    28  100.0%         13     -  54570149  54570177              AB345587     1    28    28
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browser |    28  100.0%         14     -   4398958   4398986              AB345587     1    28    28
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browser |    28  100.0%         14     - 119681476 119681504              AB345587     1    28    28
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browser |    28  100.0%         15     -   6836239   6836267              AB345587     1    28    28
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View details of parts of alignment within browser window
.
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