AB352580
 

Information on mRNA AB352580

Description: Mus musculus non-coding RNA, oocyte_piRNA3396, 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: AB352580
Position: chr12:56795816-56795844

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 |    29  100.0%         12     -  56795816  56795844              AB352580     1    29    29
browser |    29  100.0%          1     -   4628510   4628538              AB352580     1    29    29
browser |    29  100.0%          1     +   6241817   6241845              AB352580     1    29    29
browser |    29  100.0%          1     -   6501780   6501808              AB352580     1    29    29
browser |    29  100.0%          1     +   8069837   8069865              AB352580     1    29    29
browser |    29  100.0%          1     +   8232282   8232310              AB352580     1    29    29
browser |    29  100.0%          1     -  10801270  10801298              AB352580     1    29    29
browser |    29  100.0%          1     -  11958528  11958556              AB352580     1    29    29
browser |    29  100.0%          1     +  16814351  16814379              AB352580     1    29    29
browser |    29  100.0%          1     +  18590225  18590253              AB352580     1    29    29
browser |    29  100.0%          1     +  19698559  19698587              AB352580     1    29    29
browser |    29  100.0%          1     +  23344219  23344247              AB352580     1    29    29
browser |    29  100.0%          1     -  26389437  26389465              AB352580     1    29    29
browser |    29  100.0%          1     -  29982989  29983017              AB352580     1    29    29
browser |    29  100.0%          1     +  35833444  35833472              AB352580     1    29    29
browser |    29  100.0%          1     +  38746826  38746854              AB352580     1    29    29
browser |    29  100.0%          1     +  45777300  45777328              AB352580     1    29    29
browser |    29  100.0%          1     +  48132234  48132262              AB352580     1    29    29
browser |    29  100.0%          1     -  48394677  48394705              AB352580     1    29    29
browser |    29  100.0%          1     +  52632084  52632112              AB352580     1    29    29
browser |    29  100.0%          1     -  53169968  53169996              AB352580     1    29    29
browser |    29  100.0%          1     +  55821209  55821237              AB352580     1    29    29
browser |    29  100.0%          1     +  56817251  56817279              AB352580     1    29    29
browser |    29  100.0%          1     -  58363706  58363734              AB352580     1    29    29
browser |    29  100.0%          1     -  60765200  60765228              AB352580     1    29    29
browser |    29  100.0%          1     -  62574464  62574492              AB352580     1    29    29
browser |    29  100.0%          1     -  64218529  64218557              AB352580     1    29    29
browser |    29  100.0%          1     +  64428151  64428179              AB352580     1    29    29
browser |    29  100.0%          1     -  65000662  65000690              AB352580     1    29    29
browser |    29  100.0%          1     -  66057973  66058001              AB352580     1    29    29
browser |    29  100.0%          1     -  69738416  69738444              AB352580     1    29    29
browser |    29  100.0%          1     +  79920658  79920686              AB352580     1    29    29
browser |    29  100.0%          1     -  81543075  81543103              AB352580     1    29    29
browser |    29  100.0%          1     -  84974793  84974821              AB352580     1    29    29
browser |    29  100.0%          1     -  87062557  87062585              AB352580     1    29    29
browser |    29  100.0%          1     +  87393771  87393799              AB352580     1    29    29
browser |    29  100.0%          1     -  91400133  91400161              AB352580     1    29    29
browser |    29  100.0%          1     +  93887814  93887842              AB352580     1    29    29
browser |    29  100.0%          1     +  97105880  97105908              AB352580     1    29    29
browser |    29  100.0%          1     - 101907062 101907090              AB352580     1    29    29
browser |    29  100.0%          1     + 102965282 102965310              AB352580     1    29    29
browser |    29  100.0%          1     - 103134094 103134122              AB352580     1    29    29
browser |    29  100.0%          1     - 104218487 104218515              AB352580     1    29    29
browser |    29  100.0%          1     - 108337782 108337810              AB352580     1    29    29
browser |    29  100.0%          1     - 109057598 109057626              AB352580     1    29    29
browser |    29  100.0%          1     + 110260792 110260820              AB352580     1    29    29
browser |    29  100.0%          1     - 110866529 110866557              AB352580     1    29    29
browser |    29  100.0%          1     - 111182554 111182582              AB352580     1    29    29
browser |    29  100.0%          1     + 112861984 112862012              AB352580     1    29    29
browser |    29  100.0%          1     + 112949699 112949727              AB352580     1    29    29
browser |    29  100.0%          1     + 114117009 114117037              AB352580     1    29    29
browser |    29  100.0%          1     - 115814289 115814317              AB352580     1    29    29
browser |    29  100.0%          1     - 116577199 116577227              AB352580     1    29    29
browser |    29  100.0%          1     - 117630856 117630884              AB352580     1    29    29
browser |    29  100.0%          1     - 120499772 120499800              AB352580     1    29    29
browser |    29  100.0%          1     + 125250484 125250512              AB352580     1    29    29
browser |    29  100.0%          1     - 125275050 125275078              AB352580     1    29    29
browser |    29  100.0%          1     + 126356178 126356206              AB352580     1    29    29
browser |    29  100.0%          1     + 130465757 130465785              AB352580     1    29    29
browser |    29  100.0%          1     + 139656597 139656625              AB352580     1    29    29
browser |    29  100.0%          1     + 140750441 140750469              AB352580     1    29    29
browser |    29  100.0%          1     + 140969038 140969066              AB352580     1    29    29
browser |    29  100.0%          1     + 146002566 146002594              AB352580     1    29    29
browser |    29  100.0%          1     + 148154017 148154045              AB352580     1    29    29
browser |    29  100.0%          1     - 159798525 159798553              AB352580     1    29    29
browser |    29  100.0%          1     - 160644639 160644667              AB352580     1    29    29
browser |    29  100.0%          1     + 162674012 162674040              AB352580     1    29    29
browser |    29  100.0%          1     - 163297255 163297283              AB352580     1    29    29
browser |    29  100.0%          1     - 166591897 166591925              AB352580     1    29    29
browser |    29  100.0%          1     + 169375256 169375284              AB352580     1    29    29
browser |    29  100.0%          1     - 174870742 174870770              AB352580     1    29    29
browser |    29  100.0%          1     - 176371824 176371852              AB352580     1    29    29
browser |    29  100.0%          1     + 177891511 177891539              AB352580     1    29    29
browser |    29  100.0%          1     + 178007564 178007592              AB352580     1    29    29
browser |    29  100.0%          1     - 181092280 181092308              AB352580     1    29    29
browser |    29  100.0%          1     + 191843672 191843700              AB352580     1    29    29
browser |    29  100.0%         10     -   3267527   3267555              AB352580     1    29    29
browser |    29  100.0%         10     -   3552120   3552148              AB352580     1    29    29
browser |    29  100.0%         10     +   9726320   9726348              AB352580     1    29    29
browser |    29  100.0%         10     +  19676038  19676066              AB352580     1    29    29
browser |    29  100.0%         10     +  21091239  21091267              AB352580     1    29    29
browser |    29  100.0%         10     -  21519407  21519435              AB352580     1    29    29
browser |    29  100.0%         10     -  22560353  22560381              AB352580     1    29    29
browser |    29  100.0%         10     -  23748408  23748436              AB352580     1    29    29
browser |    29  100.0%         10     +  24566267  24566295              AB352580     1    29    29
browser |    29  100.0%         10     -  24978632  24978660              AB352580     1    29    29
browser |    29  100.0%         10     +  30695877  30695905              AB352580     1    29    29
browser |    29  100.0%         10     +  30970562  30970590              AB352580     1    29    29
browser |    29  100.0%         10     +  31364507  31364535              AB352580     1    29    29
browser |    29  100.0%         10     +  33765823  33765851              AB352580     1    29    29
browser |    29  100.0%         10     -  34619011  34619039              AB352580     1    29    29
browser |    29  100.0%         10     +  41722429  41722457              AB352580     1    29    29
browser |    29  100.0%         10     -  45432189  45432217              AB352580     1    29    29
browser |    29  100.0%         10     +  50370356  50370384              AB352580     1    29    29
browser |    29  100.0%         10     +  51762800  51762828              AB352580     1    29    29
browser |    29  100.0%         10     -  55592816  55592844              AB352580     1    29    29
browser |    29  100.0%         10     +  56602737  56602765              AB352580     1    29    29
browser |    29  100.0%         10     +  57019657  57019685              AB352580     1    29    29
browser |    29  100.0%         10     +  59221654  59221682              AB352580     1    29    29
browser |    29  100.0%         10     +  62447788  62447816              AB352580     1    29    29
browser |    29  100.0%         10     +  62945660  62945688              AB352580     1    29    29
browser |    29  100.0%         10     -  65787788  65787816              AB352580     1    29    29
browser |    29  100.0%         10     +  80815468  80815496              AB352580     1    29    29
browser |    29  100.0%         10     -  83507974  83508002              AB352580     1    29    29
browser |    29  100.0%         10     +  83627248  83627276              AB352580     1    29    29
browser |    29  100.0%         10     +  85555342  85555370              AB352580     1    29    29
browser |    29  100.0%         10     +  88802844  88802872              AB352580     1    29    29
browser |    29  100.0%         10     -  90161660  90161688              AB352580     1    29    29
browser |    29  100.0%         10     -  94199626  94199654              AB352580     1    29    29
browser |    29  100.0%         10     -  96029582  96029610              AB352580     1    29    29
browser |    29  100.0%         10     -  97157610  97157638              AB352580     1    29    29
browser |    29  100.0%         10     + 100418414 100418442              AB352580     1    29    29
browser |    29  100.0%         10     - 104656542 104656570              AB352580     1    29    29
browser |    29  100.0%         10     - 105509701 105509729              AB352580     1    29    29
browser |    29  100.0%         10     + 107841254 107841282              AB352580     1    29    29
browser |    29  100.0%         10     - 109152267 109152295              AB352580     1    29    29
browser |    29  100.0%         10     - 113559797 113559825              AB352580     1    29    29
browser |    29  100.0%         10     - 116443355 116443383              AB352580     1    29    29
browser |    29  100.0%         10     - 122203153 122203181              AB352580     1    29    29
browser |    29  100.0%         10     + 124418121 124418149              AB352580     1    29    29
browser |    29  100.0%         10     + 124445626 124445654              AB352580     1    29    29
browser |    29  100.0%         10     - 124517544 124517572              AB352580     1    29    29
browser |    29  100.0%         10     - 129225880 129225908              AB352580     1    29    29
browser |    29  100.0%         10     - 130397199 130397227              AB352580     1    29    29
browser |    29  100.0%         11     -   6092681   6092709              AB352580     1    29    29
browser |    29  100.0%         11     +   6484574   6484602              AB352580     1    29    29
browser |    29  100.0%         11     -   9659176   9659204              AB352580     1    29    29
browser |    29  100.0%         11     -  12458480  12458508              AB352580     1    29    29
browser |    29  100.0%         11     +  12517831  12517859              AB352580     1    29    29
browser |    29  100.0%         11     -  12905207  12905235              AB352580     1    29    29
browser |    29  100.0%         11     +  15183601  15183629              AB352580     1    29    29
browser |    29  100.0%         11     +  15836603  15836631              AB352580     1    29    29
browser |    29  100.0%         11     +  16181456  16181484              AB352580     1    29    29
browser |    29  100.0%         11     -  18757646  18757674              AB352580     1    29    29
browser |    29  100.0%         11     -  19517365  19517393              AB352580     1    29    29
browser |    29  100.0%         11     -  19739915  19739943              AB352580     1    29    29
browser |    29  100.0%         11     -  22286444  22286472              AB352580     1    29    29
browser |    29  100.0%         11     +  22531792  22531820              AB352580     1    29    29
browser |    29  100.0%         11     -  23169773  23169801              AB352580     1    29    29
browser |    29  100.0%         11     +  26509534  26509562              AB352580     1    29    29
browser |    29  100.0%         11     -  27902269  27902297              AB352580     1    29    29
browser |    29  100.0%         11     +  28053201  28053229              AB352580     1    29    29
browser |    29  100.0%         11     -  31398756  31398784              AB352580     1    29    29
browser |    29  100.0%         11     +  43553449  43553477              AB352580     1    29    29
browser |    29  100.0%         11     -  51557044  51557072              AB352580     1    29    29
browser |    29  100.0%         11     -  55132953  55132981              AB352580     1    29    29
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browser |    29  100.0%         11     -  65343803  65343831              AB352580     1    29    29
browser |    29  100.0%         11     -  66839845  66839873              AB352580     1    29    29
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browser |    29  100.0%         11     +  74434967  74434995              AB352580     1    29    29
browser |    29  100.0%         11     +  74781131  74781159              AB352580     1    29    29
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browser |    29  100.0%         11     -  85177586  85177614              AB352580     1    29    29
browser |    29  100.0%         11     -  88802978  88803006              AB352580     1    29    29
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browser |    29  100.0%         11     - 111107662 111107690              AB352580     1    29    29
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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