DQ716464
 

Information on mRNA DQ716464

Description: Mus musculus piRNA piR-131786, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2006-06-08
Version: 1
mRNA sequence: DQ716464
Position: chr12:56796086-56796111

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     +  56796086  56796111              DQ716464     4    29    29
browser |    26  100.0%          1     +   5878771   5878796              DQ716464     4    29    29
browser |    26  100.0%          1     +   6504800   6504825              DQ716464     4    29    29
browser |    26  100.0%          1     -   8066823   8066848              DQ716464     4    29    29
browser |    26  100.0%          1     -   8229264   8229289              DQ716464     4    29    29
browser |    26  100.0%          1     +  10804287  10804312              DQ716464     4    29    29
browser |    26  100.0%          1     -  13623688  13623713              DQ716464     4    29    29
browser |    26  100.0%          1     -  16811334  16811359              DQ716464     4    29    29
browser |    26  100.0%          1     -  18029928  18029953              DQ716464     4    29    29
browser |    26  100.0%          1     -  18589958  18589983              DQ716464     4    29    29
browser |    26  100.0%          1     -  19695542  19695567              DQ716464     4    29    29
browser |    26  100.0%          1     +  22069676  22069701              DQ716464     4    29    29
browser |    26  100.0%          1     -  26455950  26455975              DQ716464     4    29    29
browser |    26  100.0%          1     +  26512376  26512401              DQ716464     4    29    29
browser |    26  100.0%          1     +  29985506  29985531              DQ716464     4    29    29
browser |    28  100.0%          1     +  47264217  47264244              DQ716464     1    28    29
browser |    26  100.0%          1     +  48399561  48399586              DQ716464     4    29    29
browser |    26  100.0%          1     +  53171051  53171076              DQ716464     4    29    29
browser |    26  100.0%          1     -  55820381  55820406              DQ716464     4    29    29
browser |    26  100.0%          1     -  56814234  56814259              DQ716464     4    29    29
browser |    26  100.0%          1     +  58366726  58366751              DQ716464     4    29    29
browser |    26  100.0%          1     +  58855034  58855059              DQ716464     4    29    29
browser |    26  100.0%          1     -  64425134  64425159              DQ716464     4    29    29
browser |    26  100.0%          1     +  66060989  66061014              DQ716464     4    29    29
browser |    26  100.0%          1     +  67794794  67794819              DQ716464     4    29    29
browser |    26  100.0%          1     -  70279116  70279141              DQ716464     4    29    29
browser |    26  100.0%          1     +  72168906  72168931              DQ716464     4    29    29
browser |    26  100.0%          1     +  74696802  74696827              DQ716464     4    29    29
browser |    29  100.0%          1     -  76594230  76594258              DQ716464     1    29    29
browser |    29  100.0%          1     -  78999413  78999441              DQ716464     1    29    29
browser |    26  100.0%          1     -  79917641  79917666              DQ716464     4    29    29
browser |    26  100.0%          1     +  81546095  81546120              DQ716464     4    29    29
browser |    26  100.0%          1     -  82481677  82481702              DQ716464     4    29    29
browser |    26  100.0%          1     +  87065577  87065602              DQ716464     4    29    29
browser |    26  100.0%          1     -  87390754  87390779              DQ716464     4    29    29
browser |    26  100.0%          1     +  91403150  91403175              DQ716464     4    29    29
browser |    26  100.0%          1     -  93887164  93887189              DQ716464     4    29    29
browser |    28  100.0%          1     -  95625753  95625780              DQ716464     1    28    29
browser |    26  100.0%          1     -  97103363  97103388              DQ716464     4    29    29
browser |    26  100.0%          1     + 101910085 101910110              DQ716464     4    29    29
browser |    26  100.0%          1     - 102962265 102962290              DQ716464     4    29    29
browser |    26  100.0%          1     + 103137114 103137139              DQ716464     4    29    29
browser |    26  100.0%          1     + 108340802 108340827              DQ716464     4    29    29
browser |    26  100.0%          1     - 109544007 109544032              DQ716464     4    29    29
browser |    26  100.0%          1     + 111185571 111185596              DQ716464     4    29    29
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browser |    26  100.0%          1     - 112860084 112860109              DQ716464     4    29    29
browser |    26  100.0%          1     + 116580219 116580244              DQ716464     4    29    29
browser |    26  100.0%          1     + 117633877 117633902              DQ716464     4    29    29
browser |    26  100.0%          1     + 125275320 125275345              DQ716464     4    29    29
browser |    26  100.0%          1     + 127490213 127490238              DQ716464     4    29    29
browser |    26  100.0%          1     + 127807012 127807037              DQ716464     4    29    29
browser |    26  100.0%          1     - 130464929 130464954              DQ716464     4    29    29
browser |    26  100.0%          1     + 137203119 137203144              DQ716464     4    29    29
browser |    26  100.0%          1     - 140747425 140747450              DQ716464     4    29    29
browser |    26  100.0%          1     - 140966023 140966048              DQ716464     4    29    29
browser |    26  100.0%          1     - 144262782 144262807              DQ716464     4    29    29
browser |    26  100.0%          1     - 145999549 145999574              DQ716464     4    29    29
browser |    26  100.0%          1     - 149271872 149271897              DQ716464     4    29    29
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browser |    26  100.0%          1     - 181323336 181323361              DQ716464     4    29    29
browser |    26  100.0%          1     - 183299155 183299180              DQ716464     4    29    29
browser |    26  100.0%          1     - 195005531 195005556              DQ716464     4    29    29
browser |    26  100.0%         10     +   3555141   3555166              DQ716464     4    29    29
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browser |    26  100.0%         10     -  19675771  19675796              DQ716464     4    29    29
browser |    26  100.0%         10     +  19890581  19890606              DQ716464     4    29    29
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browser |    26  100.0%         10     +  22563373  22563398              DQ716464     4    29    29
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browser |    28  100.0%         10     +  43647300  43647327              DQ716464     1    28    29
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browser |    26  100.0%         10     -  77789484  77789509              DQ716464     4    29    29
browser |    26  100.0%         10     +  81510583  81510608              DQ716464     4    29    29
browser |    26  100.0%         10     +  81669711  81669736              DQ716464     4    29    29
browser |    26  100.0%         10     -  81806604  81806629              DQ716464     4    29    29
browser |    26  100.0%         10     +  83305939  83305964              DQ716464     4    29    29
browser |    26  100.0%         10     +  83510994  83511019              DQ716464     4    29    29
browser |    26  100.0%         10     -  85553938  85553963              DQ716464     4    29    29
browser |    26  100.0%         10     +  94202142  94202167              DQ716464     4    29    29
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browser |    26  100.0%         10     +  97162521  97162546              DQ716464     4    29    29
browser |    26  100.0%         10     -  99177864  99177889              DQ716464     4    29    29
browser |    26  100.0%         10     - 104394091 104394116              DQ716464     4    29    29
browser |    26  100.0%         10     - 104674308 104674333              DQ716464     4    29    29
browser |    26  100.0%         10     - 105015827 105015852              DQ716464     4    29    29
browser |    26  100.0%         10     - 107838237 107838262              DQ716464     4    29    29
browser |    26  100.0%         10     + 109155288 109155313              DQ716464     4    29    29
browser |    26  100.0%         10     - 110535008 110535033              DQ716464     4    29    29
browser |    26  100.0%         10     + 113562814 113562839              DQ716464     4    29    29
browser |    26  100.0%         10     - 117909431 117909456              DQ716464     4    29    29
browser |    26  100.0%         10     - 121003516 121003541              DQ716464     4    29    29
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browser |    28  100.0%         11     -  27086492  27086519              DQ716464     1    28    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