AB337316
 

Information on mRNA AB337316

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA2517, 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: AB337316
Position: chrX:15604212-15604233

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%          X     -  15604212  15604233              AB337316     1    22    23
browser |    22  100.0%          1     +   5610549   5610570              AB337316     1    22    23
browser |    22  100.0%          1     +   5820346   5820367              AB337316     1    22    23
browser |    22  100.0%          1     -   5870861   5870882              AB337316     1    22    23
browser |    22  100.0%          1     +   6389815   6389836              AB337316     1    22    23
browser |    22  100.0%          1     +   8315570   8315591              AB337316     1    22    23
browser |    22  100.0%          1     -  10585348  10585369              AB337316     1    22    23
browser |    22  100.0%          1     +  10820881  10820902              AB337316     1    22    23
browser |    22  100.0%          1     +  10988273  10988294              AB337316     1    22    23
browser |    22  100.0%          1     -  11944124  11944145              AB337316     1    22    23
browser |    22  100.0%          1     -  14021241  14021262              AB337316     1    22    23
browser |    22  100.0%          1     +  16394977  16394998              AB337316     1    22    23
browser |    22  100.0%          1     -  16485849  16485870              AB337316     1    22    23
browser |    22  100.0%          1     -  16765697  16765718              AB337316     1    22    23
browser |    22  100.0%          1     -  17133247  17133268              AB337316     1    22    23
browser |    22  100.0%          1     -  18414192  18414213              AB337316     1    22    23
browser |    22  100.0%          1     -  18770492  18770513              AB337316     1    22    23
browser |    22  100.0%          1     +  19015568  19015589              AB337316     1    22    23
browser |    22  100.0%          1     -  19341934  19341955              AB337316     1    22    23
browser |    22  100.0%          1     -  20729302  20729323              AB337316     1    22    23
browser |    22  100.0%          1     +  24898515  24898536              AB337316     1    22    23
browser |    22  100.0%          1     +  26001356  26001377              AB337316     1    22    23
browser |    22  100.0%          1     +  26145485  26145506              AB337316     1    22    23
browser |    22  100.0%          1     -  27632770  27632791              AB337316     1    22    23
browser |    22  100.0%          1     +  31471143  31471164              AB337316     1    22    23
browser |    22  100.0%          1     -  33046762  33046783              AB337316     1    22    23
browser |    22  100.0%          1     +  33273213  33273234              AB337316     1    22    23
browser |    22  100.0%          1     -  33382224  33382245              AB337316     1    22    23
browser |    22  100.0%          1     -  38917319  38917340              AB337316     1    22    23
browser |    22  100.0%          1     -  39168543  39168564              AB337316     1    22    23
browser |    22  100.0%          1     +  44975746  44975767              AB337316     1    22    23
browser |    22  100.0%          1     +  46419882  46419903              AB337316     1    22    23
browser |    22  100.0%          1     +  47365966  47365987              AB337316     1    22    23
browser |    22  100.0%          1     -  80341422  80341443              AB337316     1    22    23
browser |    22  100.0%          1     -  92503654  92503675              AB337316     1    22    23
browser |    22  100.0%          1     -  94443321  94443342              AB337316     1    22    23
browser |    22  100.0%          1     -  95481620  95481641              AB337316     1    22    23
browser |    22  100.0%          1     +  98450806  98450827              AB337316     1    22    23
browser |    22  100.0%          1     +  99022103  99022124              AB337316     1    22    23
browser |    22  100.0%          1     - 100501899 100501920              AB337316     1    22    23
browser |    22  100.0%          1     - 101348454 101348475              AB337316     1    22    23
browser |    22  100.0%          1     - 102519398 102519419              AB337316     1    22    23
browser |    22  100.0%          1     - 103434222 103434243              AB337316     1    22    23
browser |    22  100.0%          1     + 110247013 110247034              AB337316     1    22    23
browser |    22  100.0%          1     + 115071850 115071871              AB337316     1    22    23
browser |    22  100.0%          1     + 119685469 119685490              AB337316     1    22    23
browser |    22  100.0%          1     + 122675843 122675864              AB337316     1    22    23
browser |    22  100.0%          1     - 123207017 123207038              AB337316     1    22    23
browser |    22  100.0%          1     - 145082684 145082705              AB337316     1    22    23
browser |    22  100.0%          1     - 145092853 145092874              AB337316     1    22    23
browser |    22  100.0%          1     - 150058046 150058067              AB337316     1    22    23
browser |    22  100.0%          1     - 150160997 150161018              AB337316     1    22    23
browser |    21  100.0%          1     + 162881706 162881726              AB337316     1    21    23
browser |    22  100.0%          1     - 166038650 166038671              AB337316     1    22    23
browser |    22  100.0%          1     - 173571141 173571162              AB337316     1    22    23
browser |    22  100.0%          1     + 174404675 174404696              AB337316     1    22    23
browser |    22  100.0%          1     - 176918571 176918592              AB337316     1    22    23
browser |    22  100.0%          1     + 183941516 183941537              AB337316     1    22    23
browser |    22  100.0%          1     + 194770167 194770188              AB337316     1    22    23
browser |    22  100.0%          1     - 194825363 194825384              AB337316     1    22    23
browser |    22  100.0%         10     -   6483702   6483723              AB337316     1    22    23
browser |    22  100.0%         10     -  10233944  10233965              AB337316     1    22    23
browser |    22  100.0%         10     -  10514983  10515004              AB337316     1    22    23
browser |    22  100.0%         10     +  11399250  11399271              AB337316     1    22    23
browser |    22  100.0%         10     -  16694814  16694835              AB337316     1    22    23
browser |    22  100.0%         10     +  17030150  17030171              AB337316     1    22    23
browser |    22  100.0%         10     -  21899805  21899826              AB337316     1    22    23
browser |    22  100.0%         10     -  23936431  23936452              AB337316     1    22    23
browser |    21  100.0%         10     -  27476007  27476027              AB337316     1    21    23
browser |    22  100.0%         10     -  28316846  28316867              AB337316     1    22    23
browser |    22  100.0%         10     -  29716693  29716714              AB337316     1    22    23
browser |    22  100.0%         10     +  30756918  30756939              AB337316     1    22    23
browser |    22  100.0%         10     +  34644926  34644947              AB337316     1    22    23
browser |    22  100.0%         10     +  35364319  35364340              AB337316     1    22    23
browser |    22  100.0%         10     -  35414716  35414737              AB337316     1    22    23
browser |    22  100.0%         10     -  38264789  38264810              AB337316     1    22    23
browser |    22  100.0%         10     +  39809395  39809416              AB337316     1    22    23
browser |    22  100.0%         10     -  40829160  40829181              AB337316     1    22    23
browser |    22  100.0%         10     -  46758109  46758130              AB337316     1    22    23
browser |    22  100.0%         10     +  47374430  47374451              AB337316     1    22    23
browser |    22  100.0%         10     +  49164545  49164566              AB337316     1    22    23
browser |    22  100.0%         10     -  50103965  50103986              AB337316     1    22    23
browser |    22  100.0%         10     -  51776109  51776130              AB337316     1    22    23
browser |    22  100.0%         10     +  74669061  74669082              AB337316     1    22    23
browser |    22  100.0%         10     -  79057062  79057083              AB337316     1    22    23
browser |    23  100.0%         10     +  83232547  83232569              AB337316     1    23    23
browser |    22  100.0%         10     + 101580431 101580452              AB337316     1    22    23
browser |    22  100.0%         11     +   6929643   6929664              AB337316     1    22    23
browser |    22  100.0%         11     -   8801825   8801846              AB337316     1    22    23
browser |    22  100.0%         11     -   9821184   9821205              AB337316     1    22    23
browser |    22  100.0%         11     -  10024625  10024646              AB337316     1    22    23
browser |    22  100.0%         11     -  10195197  10195218              AB337316     1    22    23
browser |    22  100.0%         11     +  12109008  12109029              AB337316     1    22    23
browser |    22  100.0%         11     +  13233134  13233155              AB337316     1    22    23
browser |    22  100.0%         11     -  15053580  15053601              AB337316     1    22    23
browser |    22  100.0%         11     -  16515309  16515330              AB337316     1    22    23
browser |    22  100.0%         11     -  19272232  19272253              AB337316     1    22    23
browser |    22  100.0%         11     -  22158642  22158663              AB337316     1    22    23
browser |    22  100.0%         11     -  22306716  22306737              AB337316     1    22    23
browser |    22  100.0%         11     -  24343163  24343184              AB337316     1    22    23
browser |    22  100.0%         11     -  25863506  25863527              AB337316     1    22    23
browser |    22  100.0%         11     -  26959166  26959187              AB337316     1    22    23
browser |    22  100.0%         11     +  28717939  28717960              AB337316     1    22    23
browser |    22  100.0%         11     +  29038310  29038331              AB337316     1    22    23
browser |    22  100.0%         11     -  30410537  30410558              AB337316     1    22    23
browser |    22  100.0%         11     +  31049606  31049627              AB337316     1    22    23
browser |    22  100.0%         11     -  39748674  39748695              AB337316     1    22    23
browser |    22  100.0%         11     +  39936109  39936130              AB337316     1    22    23
browser |    22  100.0%         11     +  41965994  41966015              AB337316     1    22    23
browser |    22  100.0%         11     +  55732536  55732557              AB337316     1    22    23
browser |    22  100.0%         11     +  73388970  73388991              AB337316     1    22    23
browser |    22  100.0%         11     -  74132797  74132818              AB337316     1    22    23
browser |    22  100.0%         11     - 108593434 108593455              AB337316     1    22    23
browser |    22  100.0%         12     -   4704447   4704468              AB337316     1    22    23
browser |    22  100.0%         12     +  10825026  10825047              AB337316     1    22    23
browser |    22  100.0%         12     +  11718110  11718131              AB337316     1    22    23
browser |    22  100.0%         12     +  35010945  35010966              AB337316     1    22    23
browser |    22  100.0%         12     +  37614341  37614362              AB337316     1    22    23
browser |    22  100.0%         12     +  37716207  37716228              AB337316     1    22    23
browser |    22  100.0%         12     -  42139863  42139884              AB337316     1    22    23
browser |    22  100.0%         12     -  45899039  45899060              AB337316     1    22    23
browser |    22  100.0%         12     +  50092173  50092194              AB337316     1    22    23
browser |    22  100.0%         12     -  50175292  50175313              AB337316     1    22    23
browser |    22  100.0%         12     -  60596011  60596032              AB337316     1    22    23
browser |    22  100.0%         12     +  65229539  65229560              AB337316     1    22    23
browser |    22  100.0%         12     +  81404193  81404214              AB337316     1    22    23
browser |    22  100.0%         12     - 101158641 101158662              AB337316     1    22    23
browser |    22  100.0%         12     + 101244454 101244475              AB337316     1    22    23
browser |    21  100.0%         12     - 109124100 109124120              AB337316     2    22    23
browser |    22  100.0%         12     - 113498731 113498752              AB337316     1    22    23
browser |    22  100.0%         12     - 113988052 113988073              AB337316     1    22    23
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browser |    22  100.0%         13     -   7614827   7614848              AB337316     1    22    23
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browser |    22  100.0%         13     -  28338676  28338697              AB337316     1    22    23
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browser |    22  100.0%         13     -  77129891  77129912              AB337316     1    22    23
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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