AB350824
 

Information on mRNA AB350824

Description: Mus musculus non-coding RNA, oocyte_piRNA1640, 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: AB350824
Position: chr12:56959199-56959224

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  56959224              AB350824     1    26    27
browser |    26  100.0%          1     -   4629327   4629352              AB350824     1    26    27
browser |    26  100.0%          1     -   5636449   5636474              AB350824     1    26    27
browser |    26  100.0%          1     +   5817907   5817932              AB350824     1    26    27
browser |    26  100.0%          1     +   7890622   7890647              AB350824     1    26    27
browser |    26  100.0%          1     -  11102121  11102146              AB350824     1    26    27
browser |    26  100.0%          1     -  11439204  11439229              AB350824     1    26    27
browser |    26  100.0%          1     +  14032169  14032194              AB350824     1    26    27
browser |    26  100.0%          1     -  18324165  18324190              AB350824     1    26    27
browser |    26  100.0%          1     +  21653063  21653088              AB350824     1    26    27
browser |    26  100.0%          1     +  27176766  27176791              AB350824     1    26    27
browser |    26  100.0%          1     -  28496827  28496852              AB350824     1    26    27
browser |    26  100.0%          1     +  28929405  28929430              AB350824     1    26    27
browser |    26  100.0%          1     -  30728227  30728252              AB350824     1    26    27
browser |    26  100.0%          1     +  31045314  31045339              AB350824     1    26    27
browser |    26  100.0%          1     +  31510296  31510321              AB350824     1    26    27
browser |    26  100.0%          1     +  34955121  34955146              AB350824     1    26    27
browser |    26  100.0%          1     -  37321598  37321623              AB350824     1    26    27
browser |    26  100.0%          1     +  37813948  37813973              AB350824     1    26    27
browser |    26  100.0%          1     +  41128700  41128725              AB350824     1    26    27
browser |    26  100.0%          1     +  44331049  44331074              AB350824     1    26    27
browser |    26  100.0%          1     +  44400702  44400727              AB350824     1    26    27
browser |    26  100.0%          1     -  45651320  45651345              AB350824     1    26    27
browser |    26  100.0%          1     -  47996381  47996406              AB350824     1    26    27
browser |    26  100.0%          1     +  48009576  48009601              AB350824     1    26    27
browser |    26  100.0%          1     -  48711843  48711868              AB350824     1    26    27
browser |    26  100.0%          1     +  50200107  50200132              AB350824     1    26    27
browser |    26  100.0%          1     -  57626743  57626768              AB350824     1    26    27
browser |    26  100.0%          1     -  59388166  59388191              AB350824     1    26    27
browser |    26  100.0%          1     -  65930107  65930132              AB350824     1    26    27
browser |    26  100.0%          1     -  67146311  67146336              AB350824     1    26    27
browser |    26  100.0%          1     +  81961502  81961527              AB350824     1    26    27
browser |    26  100.0%          1     -  86246845  86246870              AB350824     1    26    27
browser |    26  100.0%          1     -  93038349  93038374              AB350824     1    26    27
browser |    26  100.0%          1     -  96896074  96896099              AB350824     1    26    27
browser |    26  100.0%          1     - 100458230 100458255              AB350824     1    26    27
browser |    26  100.0%          1     + 102078700 102078725              AB350824     1    26    27
browser |    26  100.0%          1     + 108066052 108066077              AB350824     1    26    27
browser |    26  100.0%          1     - 108875490 108875515              AB350824     1    26    27
browser |    26  100.0%          1     + 108885671 108885696              AB350824     1    26    27
browser |    26  100.0%          1     + 109061725 109061750              AB350824     1    26    27
browser |    26  100.0%          1     - 112495924 112495949              AB350824     1    26    27
browser |    26  100.0%          1     - 113609142 113609167              AB350824     1    26    27
browser |    26  100.0%          1     - 117561350 117561375              AB350824     1    26    27
browser |    26  100.0%          1     - 117676329 117676354              AB350824     1    26    27
browser |    26  100.0%          1     + 117919017 117919042              AB350824     1    26    27
browser |    26  100.0%          1     - 121708261 121708286              AB350824     1    26    27
browser |    26  100.0%          1     + 128816878 128816903              AB350824     1    26    27
browser |    26  100.0%          1     + 129019306 129019331              AB350824     1    26    27
browser |    26  100.0%          1     - 136737281 136737306              AB350824     1    26    27
browser |    26  100.0%          1     - 143724467 143724492              AB350824     1    26    27
browser |    26  100.0%          1     + 161361078 161361103              AB350824     1    26    27
browser |    26  100.0%          1     - 163299204 163299229              AB350824     1    26    27
browser |    26  100.0%          1     + 171658696 171658721              AB350824     1    26    27
browser |    26  100.0%          1     - 177955926 177955951              AB350824     1    26    27
browser |    26  100.0%          1     + 185037174 185037199              AB350824     1    26    27
browser |    26  100.0%          1     + 191235209 191235234              AB350824     1    26    27
browser |    26  100.0%         10     -   3270072   3270097              AB350824     1    26    27
browser |    26  100.0%         10     -   6520495   6520520              AB350824     1    26    27
browser |    26  100.0%         10     +   7192455   7192480              AB350824     1    26    27
browser |    26  100.0%         10     +   7316179   7316204              AB350824     1    26    27
browser |    26  100.0%         10     +   8512170   8512195              AB350824     1    26    27
browser |    26  100.0%         10     +   9723778   9723803              AB350824     1    26    27
browser |    26  100.0%         10     -  11778077  11778102              AB350824     1    26    27
browser |    26  100.0%         10     -  15058279  15058304              AB350824     1    26    27
browser |    26  100.0%         10     +  18115987  18116012              AB350824     1    26    27
browser |    26  100.0%         10     -  28888941  28888966              AB350824     1    26    27
browser |    26  100.0%         10     +  31627109  31627134              AB350824     1    26    27
browser |    26  100.0%         10     +  32813806  32813831              AB350824     1    26    27
browser |    26  100.0%         10     -  35600289  35600314              AB350824     1    26    27
browser |    26  100.0%         10     -  37728897  37728922              AB350824     1    26    27
browser |    26  100.0%         10     +  38467317  38467342              AB350824     1    26    27
browser |    26  100.0%         10     -  39639441  39639466              AB350824     1    26    27
browser |    26  100.0%         10     +  43754476  43754501              AB350824     1    26    27
browser |    26  100.0%         10     -  47513538  47513563              AB350824     1    26    27
browser |    26  100.0%         10     -  47558271  47558296              AB350824     1    26    27
browser |    26  100.0%         10     +  50368410  50368435              AB350824     1    26    27
browser |    26  100.0%         10     +  54465844  54465869              AB350824     1    26    27
browser |    26  100.0%         10     +  62445842  62445867              AB350824     1    26    27
browser |    26  100.0%         10     -  73385522  73385547              AB350824     1    26    27
browser |    26  100.0%         10     -  73691990  73692015              AB350824     1    26    27
browser |    26  100.0%         10     +  74712698  74712723              AB350824     1    26    27
browser |    26  100.0%         10     -  82409787  82409812              AB350824     1    26    27
browser |    26  100.0%         10     +  82776206  82776231              AB350824     1    26    27
browser |    26  100.0%         10     -  85608025  85608050              AB350824     1    26    27
browser |    26  100.0%         10     +  88800844  88800869              AB350824     1    26    27
browser |    26  100.0%         10     -  91651701  91651726              AB350824     1    26    27
browser |    26  100.0%         10     +  92356011  92356036              AB350824     1    26    27
browser |    26  100.0%         10     -  92588892  92588917              AB350824     1    26    27
browser |    26  100.0%         10     + 100415872 100415897              AB350824     1    26    27
browser |    26  100.0%         10     + 103910854 103910879              AB350824     1    26    27
browser |    26  100.0%         10     - 104412340 104412365              AB350824     1    26    27
browser |    26  100.0%         10     + 110837242 110837267              AB350824     1    26    27
browser |    26  100.0%         10     - 122143266 122143291              AB350824     1    26    27
browser |    26  100.0%         10     - 124303654 124303679              AB350824     1    26    27
browser |    26  100.0%         11     +   6482627   6482652              AB350824     1    26    27
browser |    26  100.0%         11     -   7986363   7986388              AB350824     1    26    27
browser |    26  100.0%         11     -   9036311   9036336              AB350824     1    26    27
browser |    26  100.0%         11     +  13824167  13824192              AB350824     1    26    27
browser |    26  100.0%         11     +  15811303  15811328              AB350824     1    26    27
browser |    26  100.0%         11     +  15834603  15834628              AB350824     1    26    27
browser |    26  100.0%         11     +  16179510  16179535              AB350824     1    26    27
browser |    26  100.0%         11     -  19742460  19742485              AB350824     1    26    27
browser |    26  100.0%         11     -  20460587  20460612              AB350824     1    26    27
browser |    26  100.0%         11     -  27366475  27366500              AB350824     1    26    27
browser |    26  100.0%         11     -  29115419  29115444              AB350824     1    26    27
browser |    26  100.0%         11     +  29231493  29231518              AB350824     1    26    27
browser |    26  100.0%         11     +  31163976  31164001              AB350824     1    26    27
browser |    26  100.0%         11     +  31725595  31725620              AB350824     1    26    27
browser |    26  100.0%         11     +  43551506  43551531              AB350824     1    26    27
browser |    26  100.0%         11     +  44276360  44276385              AB350824     1    26    27
browser |    26  100.0%         11     +  67021824  67021849              AB350824     1    26    27
browser |    26  100.0%         11     -  70934397  70934422              AB350824     1    26    27
browser |    26  100.0%         11     -  70959117  70959142              AB350824     1    26    27
browser |    26  100.0%         11     -  73839592  73839617              AB350824     1    26    27
browser |    26  100.0%         11     -  79126755  79126780              AB350824     1    26    27
browser |    26  100.0%         11     -  85331862  85331887              AB350824     1    26    27
browser |    26  100.0%         11     +  90399690  90399715              AB350824     1    26    27
browser |    26  100.0%         11     - 104751932 104751957              AB350824     1    26    27
browser |    26  100.0%         11     - 108715696 108715721              AB350824     1    26    27
browser |    26  100.0%         11     + 116651348 116651373              AB350824     1    26    27
browser |    26  100.0%         12     +   3109507   3109532              AB350824     1    26    27
browser |    26  100.0%         12     +   4839019   4839044              AB350824     1    26    27
browser |    26  100.0%         12     +  17294659  17294684              AB350824     1    26    27
browser |    26  100.0%         12     +  17979790  17979815              AB350824     1    26    27
browser |    26  100.0%         12     -  19850942  19850967              AB350824     1    26    27
browser |    26  100.0%         12     -  22426625  22426650              AB350824     1    26    27
browser |    26  100.0%         12     -  23585636  23585661              AB350824     1    26    27
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browser |    26  100.0%         12     -  26157988  26158013              AB350824     1    26    27
browser |    26  100.0%         12     -  27283655  27283680              AB350824     1    26    27
browser |    26  100.0%         12     +  32647413  32647438              AB350824     1    26    27
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browser |    26  100.0%         12     +  36667134  36667159              AB350824     1    26    27
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browser |    26  100.0%         12     -  44202333  44202358              AB350824     1    26    27
browser |    26  100.0%         12     -  52222052  52222077              AB350824     1    26    27
browser |    26  100.0%         12     +  54406277  54406302              AB350824     1    26    27
browser |    26  100.0%         12     -  54917769  54917794              AB350824     1    26    27
browser |    26  100.0%         12     -  64202079  64202104              AB350824     1    26    27
browser |    26  100.0%         12     -  65832730  65832755              AB350824     1    26    27
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browser |    26  100.0%         12     +  79162307  79162332              AB350824     1    26    27
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browser |    26  100.0%         12     +  96904605  96904630              AB350824     1    26    27
browser |    26  100.0%         12     + 105595535 105595560              AB350824     1    26    27
browser |    26  100.0%         12     - 109788435 109788460              AB350824     1    26    27
browser |    26  100.0%         12     + 112852350 112852375              AB350824     1    26    27
browser |    25  100.0%         12     + 114489317 114489341              AB350824     3    27    27
browser |    26  100.0%         12     + 114906113 114906138              AB350824     1    26    27
browser |    26  100.0%         12     + 115364740 115364765              AB350824     1    26    27
browser |    26  100.0%         12     + 118759619 118759644              AB350824     1    26    27
browser |    26  100.0%         13     -   4513556   4513581              AB350824     1    26    27
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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