AB339608
 

Information on mRNA AB339608

Description: Mus musculus non-coding RNA, oocyte_clustered_small_RNA4809, 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: AB339608
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              AB339608     1    21    22
browser |    21  100.0%          1     +   5878911   5878931              AB339608     1    21    22
browser |    21  100.0%          1     -   8066688   8066708              AB339608     1    21    22
browser |    21  100.0%          1     -   8229129   8229149              AB339608     1    21    22
browser |    21  100.0%          1     +  10804427  10804447              AB339608     1    21    22
browser |    21  100.0%          1     -  13623553  13623573              AB339608     1    21    22
browser |    21  100.0%          1     -  16811199  16811219              AB339608     1    21    22
browser |    21  100.0%          1     -  18029793  18029813              AB339608     1    21    22
browser |    21  100.0%          1     -  18589823  18589843              AB339608     1    21    22
browser |    21  100.0%          1     -  19695407  19695427              AB339608     1    21    22
browser |    21  100.0%          1     +  22069816  22069836              AB339608     1    21    22
browser |    21  100.0%          1     -  26455815  26455835              AB339608     1    21    22
browser |    21  100.0%          1     +  26512516  26512536              AB339608     1    21    22
browser |    21  100.0%          1     -  27221963  27221983              AB339608     1    21    22
browser |    21  100.0%          1     +  29985646  29985666              AB339608     1    21    22
browser |    21  100.0%          1     -  34389296  34389316              AB339608     1    21    22
browser |    21  100.0%          1     +  47264360  47264380              AB339608     1    21    22
browser |    21  100.0%          1     +  48399701  48399721              AB339608     1    21    22
browser |    21  100.0%          1     +  53171191  53171211              AB339608     1    21    22
browser |    21  100.0%          1     -  56814099  56814119              AB339608     1    21    22
browser |    21  100.0%          1     +  58366866  58366886              AB339608     1    21    22
browser |    21  100.0%          1     +  58855174  58855194              AB339608     1    21    22
browser |    21  100.0%          1     -  64424999  64425019              AB339608     1    21    22
browser |    21  100.0%          1     +  65003822  65003842              AB339608     1    21    22
browser |    21  100.0%          1     +  66061129  66061149              AB339608     1    21    22
browser |    21  100.0%          1     +  67794934  67794954              AB339608     1    21    22
browser |    21  100.0%          1     -  70278981  70279001              AB339608     1    21    22
browser |    21  100.0%          1     +  72169046  72169066              AB339608     1    21    22
browser |    21  100.0%          1     +  74696942  74696962              AB339608     1    21    22
browser |    21  100.0%          1     -  78999278  78999298              AB339608     1    21    22
browser |    21  100.0%          1     -  79917506  79917526              AB339608     1    21    22
browser |    21  100.0%          1     +  81546235  81546255              AB339608     1    21    22
browser |    21  100.0%          1     -  82481542  82481562              AB339608     1    21    22
browser |    21  100.0%          1     +  87065717  87065737              AB339608     1    21    22
browser |    21  100.0%          1     -  87390619  87390639              AB339608     1    21    22
browser |    21  100.0%          1     +  91403290  91403310              AB339608     1    21    22
browser |    21  100.0%          1     -  93887029  93887049              AB339608     1    21    22
browser |    21  100.0%          1     -  95625617  95625637              AB339608     1    21    22
browser |    21  100.0%          1     -  97103228  97103248              AB339608     1    21    22
browser |    21  100.0%          1     + 101910225 101910245              AB339608     1    21    22
browser |    21  100.0%          1     - 102962130 102962150              AB339608     1    21    22
browser |    21  100.0%          1     + 103137254 103137274              AB339608     1    21    22
browser |    21  100.0%          1     + 108340942 108340962              AB339608     1    21    22
browser |    21  100.0%          1     - 109543872 109543892              AB339608     1    21    22
browser |    21  100.0%          1     + 111185711 111185731              AB339608     1    21    22
browser |    21  100.0%          1     - 111633840 111633860              AB339608     1    21    22
browser |    21  100.0%          1     + 112196420 112196440              AB339608     1    21    22
browser |    21  100.0%          1     - 112859949 112859969              AB339608     1    21    22
browser |    21  100.0%          1     - 112946547 112946567              AB339608     1    21    22
browser |    21  100.0%          1     + 116580359 116580379              AB339608     1    21    22
browser |    21  100.0%          1     + 117634017 117634037              AB339608     1    21    22
browser |    21  100.0%          1     + 125275460 125275480              AB339608     1    21    22
browser |    21  100.0%          1     + 127490353 127490373              AB339608     1    21    22
browser |    21  100.0%          1     + 127807152 127807172              AB339608     1    21    22
browser |    21  100.0%          1     + 137203259 137203279              AB339608     1    21    22
browser |    21  100.0%          1     - 140747290 140747310              AB339608     1    21    22
browser |    21  100.0%          1     - 140965888 140965908              AB339608     1    21    22
browser |    21  100.0%          1     - 144262647 144262667              AB339608     1    21    22
browser |    21  100.0%          1     - 145999414 145999434              AB339608     1    21    22
browser |    21  100.0%          1     - 149271737 149271757              AB339608     1    21    22
browser |    21  100.0%          1     - 149460048 149460068              AB339608     1    21    22
browser |    21  100.0%          1     + 154779052 154779072              AB339608     1    21    22
browser |    21  100.0%          1     + 159801685 159801705              AB339608     1    21    22
browser |    21  100.0%          1     - 162670860 162670880              AB339608     1    21    22
browser |    21  100.0%          1     - 166182498 166182518              AB339608     1    21    22
browser |    21  100.0%          1     - 169372107 169372127              AB339608     1    21    22
browser |    21  100.0%          1     - 169946094 169946114              AB339608     1    21    22
browser |    21  100.0%          1     + 174873090 174873110              AB339608     1    21    22
browser |    21  100.0%          1     + 176374984 176375004              AB339608     1    21    22
browser |    21  100.0%          1     - 177888359 177888379              AB339608     1    21    22
browser |    21  100.0%          1     - 178004412 178004432              AB339608     1    21    22
browser |    21  100.0%          1     - 179724307 179724327              AB339608     1    21    22
browser |    21  100.0%          1     + 181095441 181095461              AB339608     1    21    22
browser |    21  100.0%          1     - 181323201 181323221              AB339608     1    21    22
browser |    21  100.0%          1     - 183299020 183299040              AB339608     1    21    22
browser |    21  100.0%          1     - 195005396 195005416              AB339608     1    21    22
browser |    21  100.0%         10     +   3555281   3555301              AB339608     1    21    22
browser |    21  100.0%         10     -   8477785   8477805              AB339608     1    21    22
browser |    21  100.0%         10     -  11572764  11572784              AB339608     1    21    22
browser |    21  100.0%         10     +  19418994  19419014              AB339608     1    21    22
browser |    21  100.0%         10     -  19675636  19675656              AB339608     1    21    22
browser |    21  100.0%         10     +  19890721  19890741              AB339608     1    21    22
browser |    21  100.0%         10     +  21522567  21522587              AB339608     1    21    22
browser |    21  100.0%         10     +  22403458  22403478              AB339608     1    21    22
browser |    21  100.0%         10     +  22563513  22563533              AB339608     1    21    22
browser |    21  100.0%         10     +  23751568  23751588              AB339608     1    21    22
browser |    21  100.0%         10     +  24979640  24979660              AB339608     1    21    22
browser |    21  100.0%         10     -  25847057  25847077              AB339608     1    21    22
browser |    21  100.0%         10     -  30692725  30692745              AB339608     1    21    22
browser |    21  100.0%         10     -  30967410  30967430              AB339608     1    21    22
browser |    21  100.0%         10     -  31361353  31361373              AB339608     1    21    22
browser |    21  100.0%         10     +  34622171  34622191              AB339608     1    21    22
browser |    21  100.0%         10     -  41719279  41719299              AB339608     1    21    22
browser |    21  100.0%         10     +  43647443  43647463              AB339608     1    21    22
browser |    21  100.0%         10     -  51761837  51761857              AB339608     1    21    22
browser |    21  100.0%         10     -  56599585  56599605              AB339608     1    21    22
browser |    21  100.0%         10     -  57016505  57016525              AB339608     1    21    22
browser |    21  100.0%         10     -  62942507  62942527              AB339608     1    21    22
browser |    21  100.0%         10     +  65477974  65477994              AB339608     1    21    22
browser |    21  100.0%         10     +  66562589  66562609              AB339608     1    21    22
browser |    21  100.0%         10     -  70629998  70630018              AB339608     1    21    22
browser |    21  100.0%         10     -  71529991  71530011              AB339608     1    21    22
browser |    21  100.0%         10     -  77789349  77789369              AB339608     1    21    22
browser |    21  100.0%         10     +  78656138  78656158              AB339608     1    21    22
browser |    21  100.0%         10     +  81510723  81510743              AB339608     1    21    22
browser |    21  100.0%         10     +  81669851  81669871              AB339608     1    21    22
browser |    21  100.0%         10     -  81806469  81806489              AB339608     1    21    22
browser |    22  100.0%         10     +  83306079  83306100              AB339608     1    22    22
browser |    21  100.0%         10     +  83511134  83511154              AB339608     1    21    22
browser |    21  100.0%         10     -  85553803  85553823              AB339608     1    21    22
browser |    21  100.0%         10     -  88489590  88489610              AB339608     1    21    22
browser |    21  100.0%         10     +  94202282  94202302              AB339608     1    21    22
browser |    21  100.0%         10     +  96032742  96032762              AB339608     1    21    22
browser |    21  100.0%         10     +  97162661  97162681              AB339608     1    21    22
browser |    21  100.0%         10     -  99177729  99177749              AB339608     1    21    22
browser |    21  100.0%         10     - 104393956 104393976              AB339608     1    21    22
browser |    21  100.0%         10     - 104674173 104674193              AB339608     1    21    22
browser |    21  100.0%         10     - 105015692 105015712              AB339608     1    21    22
browser |    21  100.0%         10     - 107838102 107838122              AB339608     1    21    22
browser |    21  100.0%         10     + 109155428 109155448              AB339608     1    21    22
browser |    21  100.0%         10     - 110534873 110534893              AB339608     1    21    22
browser |    21  100.0%         10     + 113562954 113562974              AB339608     1    21    22
browser |    21  100.0%         10     + 116446515 116446535              AB339608     1    21    22
browser |    21  100.0%         10     - 117909296 117909316              AB339608     1    21    22
browser |    21  100.0%         10     - 121003381 121003401              AB339608     1    21    22
browser |    21  100.0%         10     + 122204124 122204144              AB339608     1    21    22
browser |    21  100.0%         10     - 122344416 122344436              AB339608     1    21    22
browser |    21  100.0%         10     + 122673001 122673021              AB339608     1    21    22
browser |    21  100.0%         10     - 123697993 123698013              AB339608     1    21    22
browser |    21  100.0%         10     - 124414968 124414988              AB339608     1    21    22
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browser |    21  100.0%         10     - 129763916 129763936              AB339608     1    21    22
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browser |    21  100.0%         11     +   6095842   6095862              AB339608     1    21    22
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browser |    21  100.0%         11     +   9662333   9662353              AB339608     1    21    22
browser |    21  100.0%         11     -  10713069  10713089              AB339608     1    21    22
browser |    21  100.0%         11     -  12514679  12514699              AB339608     1    21    22
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browser |    21  100.0%         11     -  15180449  15180469              AB339608     1    21    22
browser |    21  100.0%         11     +  18760806  18760826              AB339608     1    21    22
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browser |    21  100.0%         11     -  20469135  20469155              AB339608     1    21    22
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browser |    21  100.0%         11     +  27904319  27904339              AB339608     1    21    22
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browser |    21  100.0%         11     -  38375081  38375101              AB339608     1    21    22
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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