DQ546860

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Information on mRNA DQ546860

Description: Mus musculus piRNA piR-14972, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
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: 2008-11-02
Version: 1
mRNA sequence: DQ546860
Position: chr12:56797403-56797434
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 |    32  100.0%         12     -  56797403  56797434              DQ546860     1    32    32
browser |    32  100.0%          1     -   5880088   5880119              DQ546860     1    32    32
browser |    32  100.0%          1     -   6506117   6506148              DQ546860     1    32    32
browser |    32  100.0%          1     +   8065500   8065531              DQ546860     1    32    32
browser |    32  100.0%          1     +   8227941   8227972              DQ546860     1    32    32
browser |    32  100.0%          1     -   8731128   8731159              DQ546860     1    32    32
browser |    32  100.0%          1     -  10805604  10805635              DQ546860     1    32    32
browser |    32  100.0%          1     -  12019428  12019459              DQ546860     1    32    32
browser |    32  100.0%          1     +  13622365  13622396              DQ546860     1    32    32
browser |    32  100.0%          1     +  16810011  16810042              DQ546860     1    32    32
browser |    32  100.0%          1     +  18028605  18028636              DQ546860     1    32    32
browser |    32  100.0%          1     +  18588635  18588666              DQ546860     1    32    32
browser |    32  100.0%          1     +  19694219  19694250              DQ546860     1    32    32
browser |    32  100.0%          1     -  22070981  22071012              DQ546860     1    32    32
browser |    32  100.0%          1     +  26454627  26454658              DQ546860     1    32    32
browser |    32  100.0%          1     -  26513693  26513724              DQ546860     1    32    32
browser |    32  100.0%          1     +  27220775  27220806              DQ546860     1    32    32
browser |    32  100.0%          1     -  29986823  29986854              DQ546860     1    32    32
browser |    32  100.0%          1     +  34388108  34388139              DQ546860     1    32    32
browser |    32  100.0%          1     +  35829104  35829135              DQ546860     1    32    32
browser |    32  100.0%          1     +  40738784  40738815              DQ546860     1    32    32
browser |    32  100.0%          1     -  47265537  47265568              DQ546860     1    32    32
browser |    32  100.0%          1     -  48400878  48400909              DQ546860     1    32    32
browser |    32  100.0%          1     -  53172368  53172399              DQ546860     1    32    32
browser |    32  100.0%          1     +  55819057  55819088              DQ546860     1    32    32
browser |    32  100.0%          1     +  56812911  56812942              DQ546860     1    32    32
browser |    32  100.0%          1     -  58368043  58368074              DQ546860     1    32    32
browser |    32  100.0%          1     -  58856351  58856382              DQ546860     1    32    32
browser |    32  100.0%          1     +  58971464  58971495              DQ546860     1    32    32
browser |    32  100.0%          1     -  60769537  60769568              DQ546860     1    32    32
browser |    32  100.0%          1     -  62578801  62578832              DQ546860     1    32    32
browser |    32  100.0%          1     -  64222863  64222894              DQ546860     1    32    32
browser |    32  100.0%          1     +  64423811  64423842              DQ546860     1    32    32
browser |    32  100.0%          1     -  81547412  81547443              DQ546860     1    32    32
browser |    32  100.0%          1     +  82480354  82480385              DQ546860     1    32    32
browser |    32  100.0%          1     -  83209016  83209047              DQ546860     1    32    32
browser |    32  100.0%          1     -  87066894  87066925              DQ546860     1    32    32
browser |    32  100.0%          1     +  87389431  87389462              DQ546860     1    32    32
browser |    32  100.0%          1     +  89128359  89128390              DQ546860     1    32    32
browser |    32  100.0%          1     -  91404467  91404498              DQ546860     1    32    32
browser |    32  100.0%          1     +  93885841  93885872              DQ546860     1    32    32
browser |    32  100.0%          1     +  95624429  95624460              DQ546860     1    32    32
browser |    32  100.0%          1     +  97102040  97102071              DQ546860     1    32    32
browser |    32  100.0%          1     - 101911402 101911433              DQ546860     1    32    32
browser |    32  100.0%          1     + 102960942 102960973              DQ546860     1    32    32
browser |    32  100.0%          1     - 103138431 103138462              DQ546860     1    32    32
browser |    32  100.0%          1     - 108342119 108342150              DQ546860     1    32    32
browser |    32  100.0%          1     + 109542684 109542715              DQ546860     1    32    32
browser |    32  100.0%          1     - 111186888 111186919              DQ546860     1    32    32
browser |    32  100.0%          1     + 111632652 111632683              DQ546860     1    32    32
browser |    32  100.0%          1     - 112197608 112197639              DQ546860     1    32    32
browser |    32  100.0%          1     + 112858761 112858792              DQ546860     1    32    32
browser |    32  100.0%          1     + 112945359 112945390              DQ546860     1    32    32
browser |    32  100.0%          1     - 116581536 116581567              DQ546860     1    32    32
browser |    32  100.0%          1     + 125246147 125246178              DQ546860     1    32    32
browser |    32  100.0%          1     + 126353325 126353356              DQ546860     1    32    32
browser |    32  100.0%          1     - 127491530 127491561              DQ546860     1    32    32
browser |    32  100.0%          1     - 127808329 127808360              DQ546860     1    32    32
browser |    32  100.0%          1     + 130463606 130463637              DQ546860     1    32    32
browser |    32  100.0%          1     - 137204436 137204467              DQ546860     1    32    32
browser |    32  100.0%          1     + 140746102 140746133              DQ546860     1    32    32
browser |    32  100.0%          1     + 140964700 140964731              DQ546860     1    32    32
browser |    32  100.0%          1     - 146163169 146163200              DQ546860     1    32    32
browser |    32  100.0%          1     - 146278472 146278503              DQ546860     1    32    32
browser |    32  100.0%          1     - 148048549 148048580              DQ546860     1    32    32
browser |    32  100.0%          1     - 159802862 159802893              DQ546860     1    32    32
browser |    32  100.0%          1     + 162669672 162669703              DQ546860     1    32    32
browser |    32  100.0%          1     - 166595735 166595766              DQ546860     1    32    32
browser |    32  100.0%          1     - 174874267 174874298              DQ546860     1    32    32
browser |    32  100.0%          1     - 176376161 176376192              DQ546860     1    32    32
browser |    32  100.0%          1     + 177887171 177887202              DQ546860     1    32    32
browser |    32  100.0%          1     + 178003224 178003255              DQ546860     1    32    32
browser |    32  100.0%          1     + 179723119 179723150              DQ546860     1    32    32
browser |    32  100.0%          1     - 181096618 181096649              DQ546860     1    32    32
browser |    32  100.0%          1     + 181322013 181322044              DQ546860     1    32    32
browser |    32  100.0%          1     + 183297831 183297862              DQ546860     1    32    32
browser |    32  100.0%          1     + 195004208 195004239              DQ546860     1    32    32
browser |    32  100.0%         10     -   3556458   3556489              DQ546860     1    32    32
browser |    32  100.0%         10     +   8476597   8476628              DQ546860     1    32    32
browser |    32  100.0%         10     +  11571576  11571607              DQ546860     1    32    32
browser |    32  100.0%         10     -  19420171  19420202              DQ546860     1    32    32
browser |    32  100.0%         10     +  19674611  19674642              DQ546860     1    32    32
browser |    32  100.0%         10     -  19891898  19891929              DQ546860     1    32    32
browser |    32  100.0%         10     -  21523744  21523775              DQ546860     1    32    32
browser |    32  100.0%         10     -  22404636  22404667              DQ546860     1    32    32
browser |    32  100.0%         10     -  22564690  22564721              DQ546860     1    32    32
browser |    32  100.0%         10     -  23752745  23752776              DQ546860     1    32    32
browser |    32  100.0%         10     -  24980817  24980848              DQ546860     1    32    32
browser |    32  100.0%         10     +  25845869  25845900              DQ546860     1    32    32
browser |    32  100.0%         10     +  30358941  30358972              DQ546860     1    32    32
browser |    32  100.0%         10     +  30691537  30691568              DQ546860     1    32    32
browser |    32  100.0%         10     +  30966222  30966253              DQ546860     1    32    32
browser |    32  100.0%         10     +  31360164  31360195              DQ546860     1    32    32
browser |    32  100.0%         10     -  34616570  34616601              DQ546860     1    32    32
browser |    32  100.0%         10     -  34623348  34623379              DQ546860     1    32    32
browser |    32  100.0%         10     +  41718091  41718122              DQ546860     1    32    32
browser |    32  100.0%         10     -  43648457  43648488              DQ546860     1    32    32
browser |    32  100.0%         10     +  47548241  47548272              DQ546860     1    32    32
browser |    32  100.0%         10     +  51760649  51760680              DQ546860     1    32    32
browser |    32  100.0%         10     +  56598397  56598428              DQ546860     1    32    32
browser |    32  100.0%         10     +  57015317  57015348              DQ546860     1    32    32
browser |    32  100.0%         10     +  62941319  62941350              DQ546860     1    32    32
browser |    32  100.0%         10     -  65479151  65479182              DQ546860     1    32    32
browser |    32  100.0%         10     -  66563766  66563797              DQ546860     1    32    32
browser |    32  100.0%         10     +  77788161  77788192              DQ546860     1    32    32
browser |    32  100.0%         10     -  78657315  78657346              DQ546860     1    32    32
browser |    32  100.0%         10     -  81511899  81511930              DQ546860     1    32    32
browser |    32  100.0%         10     -  81671027  81671058              DQ546860     1    32    32
browser |    32  100.0%         10     +  81805281  81805312              DQ546860     1    32    32
browser |    32  100.0%         10     -  83307256  83307287              DQ546860     1    32    32
browser |    32  100.0%         10     -  83512311  83512342              DQ546860     1    32    32
browser |    32  100.0%         10     +  85552615  85552646              DQ546860     1    32    32
browser |    32  100.0%         10     +  88488402  88488433              DQ546860     1    32    32
browser |    32  100.0%         10     -  94203459  94203490              DQ546860     1    32    32
browser |    32  100.0%         10     -  96033919  96033950              DQ546860     1    32    32
browser |    32  100.0%         10     -  97163838  97163869              DQ546860     1    32    32
browser |    32  100.0%         10     +  99176541  99176572              DQ546860     1    32    32
browser |    32  100.0%         10     -  99385611  99385642              DQ546860     1    32    32
browser |    32  100.0%         10     + 104392768 104392799              DQ546860     1    32    32
browser |    32  100.0%         10     + 104672985 104673016              DQ546860     1    32    32
browser |    32  100.0%         10     + 105014504 105014535              DQ546860     1    32    32
browser |    32  100.0%         10     + 107836914 107836945              DQ546860     1    32    32
browser |    32  100.0%         10     - 109156605 109156636              DQ546860     1    32    32
browser |    32  100.0%         10     - 113564131 113564162              DQ546860     1    32    32
browser |    32  100.0%         10     + 117908108 117908139              DQ546860     1    32    32
browser |    32  100.0%         10     + 121002193 121002224              DQ546860     1    32    32
browser |    32  100.0%         10     - 122205301 122205332              DQ546860     1    32    32
browser |    32  100.0%         10     - 122674178 122674209              DQ546860     1    32    32
browser |    32  100.0%         10     + 123696806 123696837              DQ546860     1    32    32
browser |    32  100.0%         10     + 124413780 124413811              DQ546860     1    32    32
browser |    32  100.0%         10     - 124520372 124520403              DQ546860     1    32    32
browser |    32  100.0%         10     - 129230217 129230248              DQ546860     1    32    32
browser |    32  100.0%         10     + 129762728 129762759              DQ546860     1    32    32
browser |    32  100.0%         10     - 130400426 130400457              DQ546860     1    32    32
browser |    32  100.0%         11     -   6097019   6097050              DQ546860     1    32    32
browser |    32  100.0%         11     -   9663510   9663541              DQ546860     1    32    32
browser |    32  100.0%         11     +  10711881  10711912              DQ546860     1    32    32
browser |    32  100.0%         11     +  12513491  12513522              DQ546860     1    32    32
browser |    32  100.0%         11     +  15179261  15179292              DQ546860     1    32    32
browser |    32  100.0%         11     -  15236385  15236416              DQ546860     1    32    32
browser |    32  100.0%         11     -  18761983  18762014              DQ546860     1    32    32
browser |    32  100.0%         11     -  19518952  19518983              DQ546860     1    32    32
browser |    32  100.0%         11     +  20467947  20467978              DQ546860     1    32    32
browser |    32  100.0%         11     -  23174110  23174141              DQ546860     1    32    32
browser |    32  100.0%         11     -  27905496  27905527              DQ546860     1    32    32
browser |    32  100.0%         11     +  28048864  28048895              DQ546860     1    32    32
browser |    32  100.0%         11     -  31403090  31403121              DQ546860     1    32    32
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browser |    32  100.0%         11     -  39960079  39960110              DQ546860     1    32    32
browser |    32  100.0%         11     +  51330079  51330110              DQ546860     1    32    32
browser |    32  100.0%         11     -  54472927  54472958              DQ546860     1    32    32
browser |    32  100.0%         11     -  55137290  55137321              DQ546860     1    32    32
browser |    32  100.0%         11     +  61312832  61312863              DQ546860     1    32    32
browser |    32  100.0%         11     +  63360121  63360152              DQ546860     1    32    32
browser |    32  100.0%         11     -  65348137  65348168              DQ546860     1    32    32
browser |    32  100.0%         11     -  66843596  66843627              DQ546860     1    32    32
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browser |    32  100.0%         11     -  90856527  90856558              DQ546860     1    32    32
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browser |    32  100.0%         11     +  98505658  98505689              DQ546860     1    32    32
browser |    32  100.0%         11     + 100555314 100555345              DQ546860     1    32    32
browser |    32  100.0%         11     - 106186854 106186885              DQ546860     1    32    32
browser |    32  100.0%         11     + 111074900 111074931              DQ546860     1    32    32
browser |    32  100.0%         11     - 111111999 111112030              DQ546860     1    32    32
browser |    32  100.0%         11     + 113804590 113804621              DQ546860     1    32    32
browser |    32  100.0%         11     - 115651253 115651284              DQ546860     1    32    32
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browser |    32  100.0%         12     -  94008810  94008841              DQ546860     1    32    32
browser |    32  100.0%         12     -  94240332  94240363              DQ546860     1    32    32
browser |    32  100.0%         12     -  96199733  96199764              DQ546860     1    32    32
browser |    32  100.0%         12     +  98323057  98323088              DQ546860     1    32    32
browser |    32  100.0%         12     - 105272009 105272040              DQ546860     1    32    32
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browser |    32  100.0%         12     - 113163068 113163099              DQ546860     1    32    32
browser |    32  100.0%         12     + 114598608 114598639              DQ546860     1    32    32
browser |    32  100.0%         12     + 118319674 118319705              DQ546860     1    32    32
browser |    32  100.0%         12     + 119556090 119556121              DQ546860     1    32    32
browser |    32  100.0%         13     +   4390015   4390046              DQ546860     1    32    32
browser |    32  100.0%         13     +   5329594   5329625              DQ546860     1    32    32
browser |    32  100.0%         13     -   8004704   8004735              DQ546860     1    32    32
browser |    32  100.0%         13     -   9488218   9488249              DQ546860     1    32    32
browser |    32  100.0%         13     -  10944734  10944765              DQ546860     1    32    32
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View details of parts of alignment within browser window.
Data schema/format description and download
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:
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.
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.
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