AB339609
 

Information on mRNA AB339609

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA4810, 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: AB339609
Position: chr12:56796226-56796246

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 |    21  100.0%         12     +  56796226  56796246              AB339609     1    21    23
browser |    21  100.0%          1     +   5878911   5878931              AB339609     1    21    23
browser |    21  100.0%          1     -   8066688   8066708              AB339609     1    21    23
browser |    21  100.0%          1     -   8229129   8229149              AB339609     1    21    23
browser |    21  100.0%          1     +  10804427  10804447              AB339609     1    21    23
browser |    21  100.0%          1     -  13623553  13623573              AB339609     1    21    23
browser |    21  100.0%          1     -  16811199  16811219              AB339609     1    21    23
browser |    21  100.0%          1     -  18029793  18029813              AB339609     1    21    23
browser |    21  100.0%          1     -  18589823  18589843              AB339609     1    21    23
browser |    21  100.0%          1     -  19695407  19695427              AB339609     1    21    23
browser |    21  100.0%          1     +  22069816  22069836              AB339609     1    21    23
browser |    21  100.0%          1     -  26455815  26455835              AB339609     1    21    23
browser |    21  100.0%          1     +  26512516  26512536              AB339609     1    21    23
browser |    21  100.0%          1     -  27221963  27221983              AB339609     1    21    23
browser |    21  100.0%          1     +  29985646  29985666              AB339609     1    21    23
browser |    21  100.0%          1     -  34389296  34389316              AB339609     1    21    23
browser |    21  100.0%          1     +  47264360  47264380              AB339609     1    21    23
browser |    21  100.0%          1     +  48399701  48399721              AB339609     1    21    23
browser |    21  100.0%          1     +  53171191  53171211              AB339609     1    21    23
browser |    21  100.0%          1     -  56814099  56814119              AB339609     1    21    23
browser |    21  100.0%          1     +  58366866  58366886              AB339609     1    21    23
browser |    21  100.0%          1     +  58855174  58855194              AB339609     1    21    23
browser |    21  100.0%          1     -  64424999  64425019              AB339609     1    21    23
browser |    21  100.0%          1     +  65003822  65003842              AB339609     1    21    23
browser |    21  100.0%          1     +  66061129  66061149              AB339609     1    21    23
browser |    21  100.0%          1     +  67794934  67794954              AB339609     1    21    23
browser |    21  100.0%          1     -  70278981  70279001              AB339609     1    21    23
browser |    21  100.0%          1     +  72169046  72169066              AB339609     1    21    23
browser |    21  100.0%          1     +  74696942  74696962              AB339609     1    21    23
browser |    21  100.0%          1     -  78999278  78999298              AB339609     1    21    23
browser |    21  100.0%          1     -  79917506  79917526              AB339609     1    21    23
browser |    21  100.0%          1     +  81546235  81546255              AB339609     1    21    23
browser |    21  100.0%          1     -  82481542  82481562              AB339609     1    21    23
browser |    21  100.0%          1     +  87065717  87065737              AB339609     1    21    23
browser |    21  100.0%          1     -  87390619  87390639              AB339609     1    21    23
browser |    21  100.0%          1     +  91403290  91403310              AB339609     1    21    23
browser |    21  100.0%          1     -  93887029  93887049              AB339609     1    21    23
browser |    21  100.0%          1     -  95625617  95625637              AB339609     1    21    23
browser |    21  100.0%          1     -  97103228  97103248              AB339609     1    21    23
browser |    21  100.0%          1     + 101910225 101910245              AB339609     1    21    23
browser |    21  100.0%          1     - 102962130 102962150              AB339609     1    21    23
browser |    21  100.0%          1     + 103137254 103137274              AB339609     1    21    23
browser |    21  100.0%          1     + 108340942 108340962              AB339609     1    21    23
browser |    21  100.0%          1     - 109543872 109543892              AB339609     1    21    23
browser |    21  100.0%          1     + 111185711 111185731              AB339609     1    21    23
browser |    21  100.0%          1     - 111633840 111633860              AB339609     1    21    23
browser |    21  100.0%          1     + 112196420 112196440              AB339609     1    21    23
browser |    21  100.0%          1     - 112859949 112859969              AB339609     1    21    23
browser |    21  100.0%          1     - 112946547 112946567              AB339609     1    21    23
browser |    21  100.0%          1     + 116580359 116580379              AB339609     1    21    23
browser |    21  100.0%          1     + 117634017 117634037              AB339609     1    21    23
browser |    21  100.0%          1     + 125275460 125275480              AB339609     1    21    23
browser |    21  100.0%          1     + 127490353 127490373              AB339609     1    21    23
browser |    21  100.0%          1     + 127807152 127807172              AB339609     1    21    23
browser |    21  100.0%          1     + 137203259 137203279              AB339609     1    21    23
browser |    21  100.0%          1     - 140747290 140747310              AB339609     1    21    23
browser |    21  100.0%          1     - 140965888 140965908              AB339609     1    21    23
browser |    21  100.0%          1     - 144262647 144262667              AB339609     1    21    23
browser |    21  100.0%          1     - 145999414 145999434              AB339609     1    21    23
browser |    21  100.0%          1     - 149271737 149271757              AB339609     1    21    23
browser |    21  100.0%          1     - 149460048 149460068              AB339609     1    21    23
browser |    21  100.0%          1     + 154779052 154779072              AB339609     1    21    23
browser |    21  100.0%          1     + 159801685 159801705              AB339609     1    21    23
browser |    21  100.0%          1     - 162670860 162670880              AB339609     1    21    23
browser |    21  100.0%          1     - 166182498 166182518              AB339609     1    21    23
browser |    21  100.0%          1     - 169372107 169372127              AB339609     1    21    23
browser |    21  100.0%          1     - 169946094 169946114              AB339609     1    21    23
browser |    21  100.0%          1     + 174873090 174873110              AB339609     1    21    23
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browser |    21  100.0%          1     - 177888359 177888379              AB339609     1    21    23
browser |    21  100.0%          1     - 178004412 178004432              AB339609     1    21    23
browser |    21  100.0%          1     - 179724307 179724327              AB339609     1    21    23
browser |    21  100.0%          1     + 181095441 181095461              AB339609     1    21    23
browser |    21  100.0%          1     - 181323201 181323221              AB339609     1    21    23
browser |    21  100.0%          1     - 183299020 183299040              AB339609     1    21    23
browser |    21  100.0%          1     - 195005396 195005416              AB339609     1    21    23
browser |    21  100.0%         10     +   3555281   3555301              AB339609     1    21    23
browser |    21  100.0%         10     -   8477785   8477805              AB339609     1    21    23
browser |    21  100.0%         10     -  11572764  11572784              AB339609     1    21    23
browser |    21  100.0%         10     +  19418994  19419014              AB339609     1    21    23
browser |    21  100.0%         10     -  19675636  19675656              AB339609     1    21    23
browser |    21  100.0%         10     +  19890721  19890741              AB339609     1    21    23
browser |    21  100.0%         10     +  21522567  21522587              AB339609     1    21    23
browser |    21  100.0%         10     +  22403458  22403478              AB339609     1    21    23
browser |    21  100.0%         10     +  22563513  22563533              AB339609     1    21    23
browser |    21  100.0%         10     +  23751568  23751588              AB339609     1    21    23
browser |    21  100.0%         10     +  24979640  24979660              AB339609     1    21    23
browser |    21  100.0%         10     -  25847057  25847077              AB339609     1    21    23
browser |    21  100.0%         10     -  30692725  30692745              AB339609     1    21    23
browser |    21  100.0%         10     -  30967410  30967430              AB339609     1    21    23
browser |    21  100.0%         10     -  31361353  31361373              AB339609     1    21    23
browser |    21  100.0%         10     +  34622171  34622191              AB339609     1    21    23
browser |    21  100.0%         10     -  41719279  41719299              AB339609     1    21    23
browser |    21  100.0%         10     +  43647443  43647463              AB339609     1    21    23
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browser |    21  100.0%         10     -  56599585  56599605              AB339609     1    21    23
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browser |    21  100.0%         10     -  62942507  62942527              AB339609     1    21    23
browser |    21  100.0%         10     +  65477974  65477994              AB339609     1    21    23
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browser |    21  100.0%         10     -  70629998  70630018              AB339609     1    21    23
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browser |    21  100.0%         10     -  77789349  77789369              AB339609     1    21    23
browser |    21  100.0%         10     +  78656138  78656158              AB339609     1    21    23
browser |    21  100.0%         10     +  81510723  81510743              AB339609     1    21    23
browser |    21  100.0%         10     +  81669851  81669871              AB339609     1    21    23
browser |    21  100.0%         10     -  81806469  81806489              AB339609     1    21    23
browser |    23  100.0%         10     +  83306079  83306101              AB339609     1    23    23
browser |    21  100.0%         10     +  83511134  83511154              AB339609     1    21    23
browser |    21  100.0%         10     -  85553803  85553823              AB339609     1    21    23
browser |    21  100.0%         10     -  88489590  88489610              AB339609     1    21    23
browser |    21  100.0%         10     +  94202282  94202302              AB339609     1    21    23
browser |    21  100.0%         10     +  96032742  96032762              AB339609     1    21    23
browser |    21  100.0%         10     +  97162661  97162681              AB339609     1    21    23
browser |    21  100.0%         10     -  99177729  99177749              AB339609     1    21    23
browser |    21  100.0%         10     - 104393956 104393976              AB339609     1    21    23
browser |    21  100.0%         10     - 104674173 104674193              AB339609     1    21    23
browser |    21  100.0%         10     - 105015692 105015712              AB339609     1    21    23
browser |    21  100.0%         10     - 107838102 107838122              AB339609     1    21    23
browser |    21  100.0%         10     + 109155428 109155448              AB339609     1    21    23
browser |    21  100.0%         10     - 110534873 110534893              AB339609     1    21    23
browser |    21  100.0%         10     + 113562954 113562974              AB339609     1    21    23
browser |    21  100.0%         10     + 116446515 116446535              AB339609     1    21    23
browser |    21  100.0%         10     - 117909296 117909316              AB339609     1    21    23
browser |    21  100.0%         10     - 121003381 121003401              AB339609     1    21    23
browser |    21  100.0%         10     + 122204124 122204144              AB339609     1    21    23
browser |    21  100.0%         10     - 122344416 122344436              AB339609     1    21    23
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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