AB345588
 

Information on mRNA AB345588

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA10789, 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: AB345588
Position: chr12:56959199-56959225

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 |    26  100.0%         12     +  56959199  56959225              AB345588     1    26    26
browser |    26  100.0%          1     -   4629326   4629352              AB345588     1    26    26
browser |    26  100.0%          1     -   5636448   5636474              AB345588     1    26    26
browser |    26  100.0%          1     -  11102120  11102146              AB345588     1    26    26
browser |    26  100.0%          1     -  11439203  11439229              AB345588     1    26    26
browser |    26  100.0%          1     +  14032169  14032195              AB345588     1    26    26
browser |    26  100.0%          1     +  21653063  21653089              AB345588     1    26    26
browser |    26  100.0%          1     +  27176766  27176792              AB345588     1    26    26
browser |    26  100.0%          1     -  28496826  28496852              AB345588     1    26    26
browser |    26  100.0%          1     +  28929405  28929431              AB345588     1    26    26
browser |    26  100.0%          1     -  30728226  30728252              AB345588     1    26    26
browser |    26  100.0%          1     +  31045314  31045340              AB345588     1    26    26
browser |    26  100.0%          1     +  31510296  31510322              AB345588     1    26    26
browser |    26  100.0%          1     +  34955121  34955147              AB345588     1    26    26
browser |    26  100.0%          1     -  37321597  37321623              AB345588     1    26    26
browser |    26  100.0%          1     +  37813948  37813974              AB345588     1    26    26
browser |    26  100.0%          1     +  41128700  41128726              AB345588     1    26    26
browser |    26  100.0%          1     +  44331049  44331075              AB345588     1    26    26
browser |    26  100.0%          1     -  47996380  47996406              AB345588     1    26    26
browser |    26  100.0%          1     +  48009576  48009602              AB345588     1    26    26
browser |    26  100.0%          1     -  48711842  48711868              AB345588     1    26    26
browser |    26  100.0%          1     +  52630141  52630167              AB345588     1    26    26
browser |    26  100.0%          1     +  53275989  53276015              AB345588     1    26    26
browser |    26  100.0%          1     -  57626742  57626768              AB345588     1    26    26
browser |    26  100.0%          1     -  59388165  59388191              AB345588     1    26    26
browser |    26  100.0%          1     +  65748433  65748459              AB345588     1    26    26
browser |    26  100.0%          1     +  65855425  65855451              AB345588     1    26    26
browser |    26  100.0%          1     -  65930106  65930132              AB345588     1    26    26
browser |    26  100.0%          1     -  67146310  67146336              AB345588     1    26    26
browser |    26  100.0%          1     +  75980865  75980891              AB345588     1    26    26
browser |    26  100.0%          1     -  93038348  93038374              AB345588     1    26    26
browser |    26  100.0%          1     -  96896073  96896099              AB345588     1    26    26
browser |    26  100.0%          1     + 102078700 102078726              AB345588     1    26    26
browser |    26  100.0%          1     + 108885671 108885697              AB345588     1    26    26
browser |    26  100.0%          1     + 109061725 109061751              AB345588     1    26    26
browser |    26  100.0%          1     - 112495923 112495949              AB345588     1    26    26
browser |    26  100.0%          1     - 113609141 113609167              AB345588     1    26    26
browser |    26  100.0%          1     - 117676328 117676354              AB345588     1    26    26
browser |    26  100.0%          1     - 121708260 121708286              AB345588     1    26    26
browser |    26  100.0%          1     + 128816878 128816904              AB345588     1    26    26
browser |    26  100.0%          1     + 129019306 129019332              AB345588     1    26    26
browser |    26  100.0%          1     - 136737280 136737306              AB345588     1    26    26
browser |    26  100.0%          1     - 143724466 143724492              AB345588     1    26    26
browser |    26  100.0%          1     + 161361078 161361104              AB345588     1    26    26
browser |    26  100.0%          1     - 163299203 163299229              AB345588     1    26    26
browser |    26  100.0%          1     + 171658696 171658722              AB345588     1    26    26
browser |    26  100.0%          1     - 177955925 177955951              AB345588     1    26    26
browser |    26  100.0%          1     + 185037174 185037200              AB345588     1    26    26
browser |    26  100.0%          1     + 191235209 191235235              AB345588     1    26    26
browser |    26  100.0%         10     -   3270071   3270097              AB345588     1    26    26
browser |    26  100.0%         10     +   7192455   7192481              AB345588     1    26    26
browser |    26  100.0%         10     +   7316179   7316205              AB345588     1    26    26
browser |    26  100.0%         10     +   8512170   8512196              AB345588     1    26    26
browser |    26  100.0%         10     +   9723778   9723804              AB345588     1    26    26
browser |    26  100.0%         10     -  11778076  11778102              AB345588     1    26    26
browser |    26  100.0%         10     -  15058278  15058304              AB345588     1    26    26
browser |    26  100.0%         10     -  28888940  28888966              AB345588     1    26    26
browser |    26  100.0%         10     +  31627109  31627135              AB345588     1    26    26
browser |    26  100.0%         10     +  32813806  32813832              AB345588     1    26    26
browser |    26  100.0%         10     -  35600288  35600314              AB345588     1    26    26
browser |    26  100.0%         10     -  37728896  37728922              AB345588     1    26    26
browser |    26  100.0%         10     -  39639440  39639466              AB345588     1    26    26
browser |    26  100.0%         10     +  43754476  43754502              AB345588     1    26    26
browser |    26  100.0%         10     -  47513537  47513563              AB345588     1    26    26
browser |    26  100.0%         10     -  47558270  47558296              AB345588     1    26    26
browser |    26  100.0%         10     +  50368410  50368436              AB345588     1    26    26
browser |    26  100.0%         10     +  54465844  54465870              AB345588     1    26    26
browser |    26  100.0%         10     -  73385521  73385547              AB345588     1    26    26
browser |    26  100.0%         10     +  74712698  74712724              AB345588     1    26    26
browser |    26  100.0%         10     -  82409786  82409812              AB345588     1    26    26
browser |    26  100.0%         10     +  82776206  82776232              AB345588     1    26    26
browser |    26  100.0%         10     +  88800844  88800870              AB345588     1    26    26
browser |    26  100.0%         10     -  91651700  91651726              AB345588     1    26    26
browser |    26  100.0%         10     +  92356011  92356037              AB345588     1    26    26
browser |    26  100.0%         10     -  92588891  92588917              AB345588     1    26    26
browser |    26  100.0%         10     + 103910854 103910880              AB345588     1    26    26
browser |    26  100.0%         10     - 122143265 122143291              AB345588     1    26    26
browser |    26  100.0%         10     - 124303653 124303679              AB345588     1    26    26
browser |    26  100.0%         11     -   7986362   7986388              AB345588     1    26    26
browser |    26  100.0%         11     -   9036310   9036336              AB345588     1    26    26
browser |    26  100.0%         11     +  15811303  15811329              AB345588     1    26    26
browser |    26  100.0%         11     +  15834603  15834629              AB345588     1    26    26
browser |    26  100.0%         11     +  16179510  16179536              AB345588     1    26    26
browser |    26  100.0%         11     -  20460586  20460612              AB345588     1    26    26
browser |    26  100.0%         11     -  29115418  29115444              AB345588     1    26    26
browser |    26  100.0%         11     +  29231493  29231519              AB345588     1    26    26
browser |    26  100.0%         11     +  31163976  31164002              AB345588     1    26    26
browser |    26  100.0%         11     +  31725595  31725621              AB345588     1    26    26
browser |    26  100.0%         11     +  43551506  43551532              AB345588     1    26    26
browser |    26  100.0%         11     +  44276360  44276386              AB345588     1    26    26
browser |    26  100.0%         11     +  67021824  67021850              AB345588     1    26    26
browser |    26  100.0%         11     -  70934396  70934422              AB345588     1    26    26
browser |    26  100.0%         11     -  70959116  70959142              AB345588     1    26    26
browser |    26  100.0%         11     -  73839591  73839617              AB345588     1    26    26
browser |    26  100.0%         11     -  85331861  85331887              AB345588     1    26    26
browser |    26  100.0%         11     +  90399690  90399716              AB345588     1    26    26
browser |    26  100.0%         11     - 104751931 104751957              AB345588     1    26    26
browser |    26  100.0%         11     - 108715695 108715721              AB345588     1    26    26
browser |    26  100.0%         11     + 116651348 116651374              AB345588     1    26    26
browser |    26  100.0%         12     +   4839019   4839045              AB345588     1    26    26
browser |    26  100.0%         12     +  17294659  17294685              AB345588     1    26    26
browser |    26  100.0%         12     +  17979790  17979816              AB345588     1    26    26
browser |    26  100.0%         12     -  19850941  19850967              AB345588     1    26    26
browser |    26  100.0%         12     -  23585635  23585661              AB345588     1    26    26
browser |    26  100.0%         12     +  24396844  24396870              AB345588     1    26    26
browser |    26  100.0%         12     +  25642876  25642902              AB345588     1    26    26
browser |    26  100.0%         12     -  26157987  26158013              AB345588     1    26    26
browser |    26  100.0%         12     +  32647413  32647439              AB345588     1    26    26
browser |    26  100.0%         12     +  32953286  32953312              AB345588     1    26    26
browser |    26  100.0%         12     +  36667134  36667160              AB345588     1    26    26
browser |    26  100.0%         12     +  42921080  42921106              AB345588     1    26    26
browser |    26  100.0%         12     -  44202332  44202358              AB345588     1    26    26
browser |    26  100.0%         12     -  52222051  52222077              AB345588     1    26    26
browser |    26  100.0%         12     -  54917768  54917794              AB345588     1    26    26
browser |    26  100.0%         12     +  63345540  63345566              AB345588     1    26    26
browser |    26  100.0%         12     -  64202078  64202104              AB345588     1    26    26
browser |    26  100.0%         12     +  65731254  65731280              AB345588     1    26    26
browser |    26  100.0%         12     +  65880604  65880630              AB345588     1    26    26
browser |    26  100.0%         12     +  74746266  74746292              AB345588     1    26    26
browser |    26  100.0%         12     +  88479591  88479617              AB345588     1    26    26
browser |    26  100.0%         12     +  90734735  90734761              AB345588     1    26    26
browser |    26  100.0%         12     +  91195434  91195460              AB345588     1    26    26
browser |    26  100.0%         12     +  96904605  96904631              AB345588     1    26    26
browser |    26  100.0%         12     + 105595535 105595561              AB345588     1    26    26
browser |    26  100.0%         12     + 112852350 112852376              AB345588     1    26    26
browser |    26  100.0%         12     + 114906113 114906139              AB345588     1    26    26
browser |    26  100.0%         12     + 115364740 115364766              AB345588     1    26    26
browser |    26  100.0%         12     + 118759619 118759645              AB345588     1    26    26
browser |    26  100.0%         13     -   4513555   4513581              AB345588     1    26    26
browser |    26  100.0%         13     -   4879086   4879112              AB345588     1    26    26
browser |    26  100.0%         13     +   4922040   4922066              AB345588     1    26    26
browser |    26  100.0%         13     -   5031411   5031437              AB345588     1    26    26
browser |    26  100.0%         13     -   6318381   6318407              AB345588     1    26    26
browser |    26  100.0%         13     -   8073385   8073411              AB345588     1    26    26
browser |    26  100.0%         13     +  10828405  10828431              AB345588     1    26    26
browser |    26  100.0%         13     -  11013047  11013073              AB345588     1    26    26
browser |    26  100.0%         13     +  11143053  11143079              AB345588     1    26    26
browser |    26  100.0%         13     -  15274502  15274528              AB345588     1    26    26
browser |    26  100.0%         13     +  23391031  23391057              AB345588     1    26    26
browser |    26  100.0%         13     +  24411750  24411776              AB345588     1    26    26
browser |    26  100.0%         13     +  27473179  27473205              AB345588     1    26    26
browser |    26  100.0%         13     -  33960057  33960083              AB345588     1    26    26
browser |    26  100.0%         13     +  39863626  39863652              AB345588     1    26    26
browser |    26  100.0%         13     +  50060354  50060380              AB345588     1    26    26
browser |    26  100.0%         13     -  50658141  50658167              AB345588     1    26    26
browser |    26  100.0%         13     -  50712508  50712534              AB345588     1    26    26
browser |    26  100.0%         13     +  51187598  51187624              AB345588     1    26    26
browser |    26  100.0%         13     +  52205556  52205582              AB345588     1    26    26
browser |    26  100.0%         13     -  54570152  54570178              AB345588     1    26    26
browser |    26  100.0%         13     +  54919936  54919962              AB345588     1    26    26
browser |    26  100.0%         13     +  62697491  62697517              AB345588     1    26    26
browser |    26  100.0%         13     -  62811010  62811036              AB345588     1    26    26
browser |    26  100.0%         13     -  64647935  64647961              AB345588     1    26    26
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browser |    26  100.0%         13     -  66147532  66147558              AB345588     1    26    26
browser |    26  100.0%         13     -  75358192  75358218              AB345588     1    26    26
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browser |    26  100.0%         13     - 104085146 104085172              AB345588     1    26    26
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browser |    26  100.0%         13     + 106276148 106276174              AB345588     1    26    26
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browser |    26  100.0%         13     + 118208251 118208277              AB345588     1    26    26
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browser |    26  100.0%         14     -   4398961   4398987              AB345588     1    26    26
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browser |    26  100.0%         14     - 110200988 110201014              AB345588     1    26    26
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browser |    26  100.0%         14     - 114426977 114427003              AB345588     1    26    26
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browser |    26  100.0%         15     -   6836242   6836268              AB345588     1    26    26
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browser |    26  100.0%         15     -  29132803  29132829              AB345588     1    26    26
browser |    26  100.0%         15     -  32785545  32785571              AB345588     1    26    26
browser |    26  100.0%         15     -  33660590  33660616              AB345588     1    26    26
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browser |    26  100.0%         15     -  38464123  38464149              AB345588     1    26    26
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View details of parts of alignment within browser window
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Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

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

Display Conventions and Configuration

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

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

To use the filter:

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

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

Methods

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

Credits

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

References

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

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

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