AB352940
 

Information on mRNA AB352940

Description: Mus musculus non-coding RNA, oocyte_piRNA3756, 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: AB352940
Position: chrX:15617824-15617847

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 |    24  100.0%          X     +  15617824  15617847              AB352940     1    24    24
browser |    24  100.0%          1     -   3207121   3207144              AB352940     1    24    24
browser |    24  100.0%          1     +   3377831   3377854              AB352940     1    24    24
browser |    24  100.0%          1     +   3378820   3378843              AB352940     1    24    24
browser |    24  100.0%          1     -   4149821   4149844              AB352940     1    24    24
browser |    24  100.0%          1     -   4283235   4283258              AB352940     1    24    24
browser |    24  100.0%          1     +   5506525   5506548              AB352940     1    24    24
browser |    24  100.0%          1     +   5623698   5623721              AB352940     1    24    24
browser |    24  100.0%          1     +   5896481   5896504              AB352940     1    24    24
browser |    24  100.0%          1     +   6993283   6993306              AB352940     1    24    24
browser |    24  100.0%          1     -   8104383   8104406              AB352940     1    24    24
browser |    24  100.0%          1     -   8283005   8283028              AB352940     1    24    24
browser |    24  100.0%          1     +   8671330   8671353              AB352940     1    24    24
browser |    24  100.0%          1     +   8765146   8765169              AB352940     1    24    24
browser |    24  100.0%          1     +   8788520   8788543              AB352940     1    24    24
browser |    24  100.0%          1     +   9099163   9099186              AB352940     1    24    24
browser |    24  100.0%          1     +   9195190   9195213              AB352940     1    24    24
browser |    24  100.0%          1     +   9251864   9251887              AB352940     1    24    24
browser |    24  100.0%          1     -  10857395  10857418              AB352940     1    24    24
browser |    24  100.0%          1     +  13163046  13163069              AB352940     1    24    24
browser |    24  100.0%          1     +  15030498  15030521              AB352940     1    24    24
browser |    24  100.0%          1     -  15059129  15059152              AB352940     1    24    24
browser |    24  100.0%          1     +  15096375  15096398              AB352940     1    24    24
browser |    24  100.0%          1     +  15304314  15304337              AB352940     1    24    24
browser |    24  100.0%          1     -  15807119  15807142              AB352940     1    24    24
browser |    24  100.0%          1     -  16020595  16020618              AB352940     1    24    24
browser |    24  100.0%          1     -  17399453  17399476              AB352940     1    24    24
browser |    24  100.0%          1     -  17769483  17769506              AB352940     1    24    24
browser |    24  100.0%          1     -  20385901  20385924              AB352940     1    24    24
browser |    24  100.0%          1     -  22125048  22125071              AB352940     1    24    24
browser |    24  100.0%          1     -  22537668  22537691              AB352940     1    24    24
browser |    24  100.0%          1     -  22955609  22955632              AB352940     1    24    24
browser |    24  100.0%          1     -  22986524  22986547              AB352940     1    24    24
browser |    24  100.0%          1     -  80458238  80458261              AB352940     1    24    24
browser |    24  100.0%          1     +  80656868  80656891              AB352940     1    24    24
browser |    24  100.0%          1     -  80665780  80665803              AB352940     1    24    24
browser |    24  100.0%          1     -  81536599  81536622              AB352940     1    24    24
browser |    24  100.0%          1     +  81901938  81901961              AB352940     1    24    24
browser |    24  100.0%          1     +  82529900  82529923              AB352940     1    24    24
browser |    24  100.0%          1     -  83434866  83434889              AB352940     1    24    24
browser |    24  100.0%          1     +  84105460  84105483              AB352940     1    24    24
browser |    24  100.0%          1     +  84248101  84248124              AB352940     1    24    24
browser |    24  100.0%          1     +  84684568  84684591              AB352940     1    24    24
browser |    24  100.0%          1     -  84992621  84992644              AB352940     1    24    24
browser |    24  100.0%          1     +  85207194  85207217              AB352940     1    24    24
browser |    24  100.0%          1     -  87956678  87956701              AB352940     1    24    24
browser |    24  100.0%          1     +  90036131  90036154              AB352940     1    24    24
browser |    24  100.0%          1     -  92340259  92340282              AB352940     1    24    24
browser |    24  100.0%          1     -  94056740  94056763              AB352940     1    24    24
browser |    24  100.0%          1     -  94069803  94069826              AB352940     1    24    24
browser |    24  100.0%          1     -  94164003  94164026              AB352940     1    24    24
browser |    24  100.0%          1     -  94316151  94316174              AB352940     1    24    24
browser |    24  100.0%          1     -  94403230  94403253              AB352940     1    24    24
browser |    24  100.0%          1     -  94457316  94457339              AB352940     1    24    24
browser |    24  100.0%          1     -  95160423  95160446              AB352940     1    24    24
browser |    24  100.0%          1     -  95563258  95563281              AB352940     1    24    24
browser |    24  100.0%          1     +  95717136  95717159              AB352940     1    24    24
browser |    24  100.0%          1     +  95741973  95741996              AB352940     1    24    24
browser |    24  100.0%          1     +  96007148  96007171              AB352940     1    24    24
browser |    24  100.0%          1     +  96125028  96125051              AB352940     1    24    24
browser |    24  100.0%          1     +  96506020  96506043              AB352940     1    24    24
browser |    24  100.0%          1     -  98573028  98573051              AB352940     1    24    24
browser |    24  100.0%          1     +  98727878  98727901              AB352940     1    24    24
browser |    24  100.0%          1     +  99116970  99116993              AB352940     1    24    24
browser |    24  100.0%          1     + 100569939 100569962              AB352940     1    24    24
browser |    24  100.0%          1     + 157426820 157426843              AB352940     1    24    24
browser |    24  100.0%          1     - 157705124 157705147              AB352940     1    24    24
browser |    24  100.0%          1     - 157761428 157761451              AB352940     1    24    24
browser |    24  100.0%          1     + 157979885 157979908              AB352940     1    24    24
browser |    24  100.0%          1     - 159123555 159123578              AB352940     1    24    24
browser |    24  100.0%          1     + 160255541 160255564              AB352940     1    24    24
browser |    24  100.0%          1     - 162091916 162091939              AB352940     1    24    24
browser |    24  100.0%          1     - 162823171 162823194              AB352940     1    24    24
browser |    24  100.0%          1     + 162988879 162988902              AB352940     1    24    24
browser |    24  100.0%          1     + 163070203 163070226              AB352940     1    24    24
browser |    24  100.0%          1     - 163634664 163634687              AB352940     1    24    24
browser |    24  100.0%          1     - 164551689 164551712              AB352940     1    24    24
browser |    24  100.0%          1     + 164859558 164859581              AB352940     1    24    24
browser |    24  100.0%          1     + 165540149 165540172              AB352940     1    24    24
browser |    24  100.0%          1     - 166368788 166368811              AB352940     1    24    24
browser |    24  100.0%          1     + 166522239 166522262              AB352940     1    24    24
browser |    24  100.0%          1     - 166567254 166567277              AB352940     1    24    24
browser |    24  100.0%          1     - 167302684 167302707              AB352940     1    24    24
browser |    24  100.0%          1     + 168816985 168817008              AB352940     1    24    24
browser |    24  100.0%          1     - 168935129 168935152              AB352940     1    24    24
browser |    24  100.0%          1     + 168969515 168969538              AB352940     1    24    24
browser |    24  100.0%          1     + 169118385 169118408              AB352940     1    24    24
browser |    24  100.0%          1     + 172550326 172550349              AB352940     1    24    24
browser |    24  100.0%          1     - 173720540 173720563              AB352940     1    24    24
browser |    24  100.0%          1     - 174535755 174535778              AB352940     1    24    24
browser |    24  100.0%          1     + 188107505 188107528              AB352940     1    24    24
browser |    24  100.0%          1     - 190083474 190083497              AB352940     1    24    24
browser |    24  100.0%          1     + 191881920 191881943              AB352940     1    24    24
browser |    24  100.0%          1     - 192147934 192147957              AB352940     1    24    24
browser |    24  100.0%          1     + 193768566 193768589              AB352940     1    24    24
browser |    24  100.0%          1     - 194732336 194732359              AB352940     1    24    24
browser |    24  100.0%          1     + 194778058 194778081              AB352940     1    24    24
browser |    24  100.0%         10     +   5345120   5345143              AB352940     1    24    24
browser |    24  100.0%         10     +   6179528   6179551              AB352940     1    24    24
browser |    24  100.0%         10     +   6610803   6610826              AB352940     1    24    24
browser |    24  100.0%         10     +   8148634   8148657              AB352940     1    24    24
browser |    24  100.0%         10     -   8187121   8187144              AB352940     1    24    24
browser |    24  100.0%         10     -   8258470   8258493              AB352940     1    24    24
browser |    24  100.0%         10     -   9316836   9316859              AB352940     1    24    24
browser |    24  100.0%         10     +   9318885   9318908              AB352940     1    24    24
browser |    24  100.0%         10     +  10466633  10466656              AB352940     1    24    24
browser |    24  100.0%         10     +  10700075  10700098              AB352940     1    24    24
browser |    24  100.0%         10     -  11786579  11786602              AB352940     1    24    24
browser |    24  100.0%         10     +  12148446  12148469              AB352940     1    24    24
browser |    24  100.0%         10     +  13788833  13788856              AB352940     1    24    24
browser |    24  100.0%         10     -  15257216  15257239              AB352940     1    24    24
browser |    24  100.0%         10     +  15303664  15303687              AB352940     1    24    24
browser |    24  100.0%         10     -  15340375  15340398              AB352940     1    24    24
browser |    24  100.0%         10     -  15442828  15442851              AB352940     1    24    24
browser |    24  100.0%         10     -  15471101  15471124              AB352940     1    24    24
browser |    24  100.0%         10     -  15495619  15495642              AB352940     1    24    24
browser |    24  100.0%         10     -  15650660  15650683              AB352940     1    24    24
browser |    24  100.0%         10     -  15840206  15840229              AB352940     1    24    24
browser |    24  100.0%         10     +  16620479  16620502              AB352940     1    24    24
browser |    24  100.0%         10     +  17018884  17018907              AB352940     1    24    24
browser |    24  100.0%         10     +  17339429  17339452              AB352940     1    24    24
browser |    24  100.0%         10     -  21501136  21501159              AB352940     1    24    24
browser |    24  100.0%         10     +  21800659  21800682              AB352940     1    24    24
browser |    24  100.0%         10     +  22406851  22406874              AB352940     1    24    24
browser |    24  100.0%         10     +  22503473  22503496              AB352940     1    24    24
browser |    24  100.0%         10     -  23403949  23403972              AB352940     1    24    24
browser |    24  100.0%         10     -  27137910  27137933              AB352940     1    24    24
browser |    24  100.0%         10     -  27230253  27230276              AB352940     1    24    24
browser |    24  100.0%         10     -  29311048  29311071              AB352940     1    24    24
browser |    24  100.0%         10     +  81588100  81588123              AB352940     1    24    24
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browser |    24  100.0%         10     -  83749418  83749441              AB352940     1    24    24
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browser |    24  100.0%         10     -  87010413  87010436              AB352940     1    24    24
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browser |    24  100.0%         10     -  88392199  88392222              AB352940     1    24    24
browser |    24  100.0%         10     -  89794914  89794937              AB352940     1    24    24
browser |    24  100.0%         10     -  91764978  91765001              AB352940     1    24    24
browser |    24  100.0%         10     +  92312143  92312166              AB352940     1    24    24
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browser |    24  100.0%         10     -  92745288  92745311              AB352940     1    24    24
browser |    24  100.0%         10     -  92890376  92890399              AB352940     1    24    24
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browser |    24  100.0%         10     -  97007834  97007857              AB352940     1    24    24
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browser |    24  100.0%         10     -  99555129  99555152              AB352940     1    24    24
browser |    24  100.0%         10     -  99721059  99721082              AB352940     1    24    24
browser |    24  100.0%         10     - 100223181 100223204              AB352940     1    24    24
browser |    24  100.0%         10     - 101460943 101460966              AB352940     1    24    24
browser |    24  100.0%         10     - 101569739 101569762              AB352940     1    24    24
browser |    24  100.0%         10     + 102157426 102157449              AB352940     1    24    24
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browser |    24  100.0%         11     -   7568113   7568136              AB352940     1    24    24
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browser |    24  100.0%         11     -   9088364   9088387              AB352940     1    24    24
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browser |    24  100.0%         11     - 104540370 104540393              AB352940     1    24    24
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browser |    24  100.0%         11     + 111536819 111536842              AB352940     1    24    24
browser |    24  100.0%         12     +   4809913   4809936              AB352940     1    24    24
browser |    24  100.0%         12     +   5767311   5767334              AB352940     1    24    24
browser |    24  100.0%         12     -   5878835   5878858              AB352940     1    24    24
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browser |    24  100.0%         12     -   6656800   6656823              AB352940     1    24    24
browser |    24  100.0%         12     -   6716935   6716958              AB352940     1    24    24
browser |    24  100.0%         12     -   7047671   7047694              AB352940     1    24    24
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browser |    24  100.0%         12     +   7989264   7989287              AB352940     1    24    24
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browser |    24  100.0%         12     -   9351479   9351502              AB352940     1    24    24
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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