DQ723396
 

Information on mRNA DQ723396

Description: Mus musculus piRNA piR-138718, 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: DQ723396
Position: chrX:15612858-15612887

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 |    30  100.0%          X     +  15612858  15612887              DQ723396     1    30    30
browser |    30  100.0%          1     +   7347838   7347867              DQ723396     1    30    30
browser |    30  100.0%          1     +   7437745   7437774              DQ723396     1    30    30
browser |    30  100.0%          1     -  10608008  10608037              DQ723396     1    30    30
browser |    30  100.0%          1     +  11568835  11568864              DQ723396     1    30    30
browser |    30  100.0%          1     +  15343214  15343243              DQ723396     1    30    30
browser |    30  100.0%          1     +  18014055  18014084              DQ723396     1    30    30
browser |    30  100.0%          1     +  18550053  18550082              DQ723396     1    30    30
browser |    30  100.0%          1     -  20385808  20385837              DQ723396     1    30    30
browser |    30  100.0%          1     -  21265830  21265859              DQ723396     1    30    30
browser |    30  100.0%          1     -  21718073  21718102              DQ723396     1    30    30
browser |    30  100.0%          1     +  22201004  22201033              DQ723396     1    30    30
browser |    30  100.0%          1     +  22261619  22261648              DQ723396     1    30    30
browser |    30  100.0%          1     -  22301265  22301294              DQ723396     1    30    30
browser |    30  100.0%          1     +  22544100  22544129              DQ723396     1    30    30
browser |    30  100.0%          1     +  23841319  23841348              DQ723396     1    30    30
browser |    30  100.0%          1     -  24286508  24286537              DQ723396     1    30    30
browser |    30  100.0%          1     +  25922499  25922528              DQ723396     1    30    30
browser |    30  100.0%          1     -  27901608  27901637              DQ723396     1    30    30
browser |    30  100.0%          1     +  28746984  28747013              DQ723396     1    30    30
browser |    30  100.0%          1     -  29881840  29881869              DQ723396     1    30    30
browser |    30  100.0%          1     -  31924098  31924127              DQ723396     1    30    30
browser |    30  100.0%          1     +  32043505  32043534              DQ723396     1    30    30
browser |    30  100.0%          1     -  32201820  32201849              DQ723396     1    30    30
browser |    30  100.0%          1     +  35247498  35247527              DQ723396     1    30    30
browser |    30  100.0%          1     +  35462330  35462359              DQ723396     1    30    30
browser |    30  100.0%          1     -  35516628  35516657              DQ723396     1    30    30
browser |    30  100.0%          1     +  44551834  44551863              DQ723396     1    30    30
browser |    30  100.0%          1     -  45345470  45345499              DQ723396     1    30    30
browser |    30  100.0%          1     -  49443248  49443277              DQ723396     1    30    30
browser |    30  100.0%          1     -  50051760  50051789              DQ723396     1    30    30
browser |    30  100.0%          1     -  50559423  50559452              DQ723396     1    30    30
browser |    30  100.0%          1     -  54351158  54351187              DQ723396     1    30    30
browser |    30  100.0%          1     -  81489950  81489979              DQ723396     1    30    30
browser |    30  100.0%          1     -  83619728  83619757              DQ723396     1    30    30
browser |    30  100.0%          1     -  88138338  88138367              DQ723396     1    30    30
browser |    30  100.0%          1     +  91953235  91953264              DQ723396     1    30    30
browser |    30  100.0%          1     -  95748528  95748557              DQ723396     1    30    30
browser |    30  100.0%          1     +  96113488  96113517              DQ723396     1    30    30
browser |    30  100.0%          1     +  97444393  97444422              DQ723396     1    30    30
browser |    30  100.0%          1     -  99239213  99239242              DQ723396     1    30    30
browser |    30  100.0%          1     +  99784153  99784182              DQ723396     1    30    30
browser |    30  100.0%          1     + 100401194 100401223              DQ723396     1    30    30
browser |    30  100.0%          1     - 100674145 100674174              DQ723396     1    30    30
browser |    30  100.0%          1     + 101365380 101365409              DQ723396     1    30    30
browser |    30  100.0%          1     + 101511219 101511248              DQ723396     1    30    30
browser |    30  100.0%          1     + 101759389 101759418              DQ723396     1    30    30
browser |    30  100.0%          1     - 102171823 102171852              DQ723396     1    30    30
browser |    30  100.0%          1     + 102502818 102502847              DQ723396     1    30    30
browser |    30  100.0%          1     - 102762138 102762167              DQ723396     1    30    30
browser |    30  100.0%          1     + 104288788 104288817              DQ723396     1    30    30
browser |    30  100.0%          1     - 105399278 105399307              DQ723396     1    30    30
browser |    30  100.0%          1     + 105537000 105537029              DQ723396     1    30    30
browser |    30  100.0%          1     - 107048918 107048947              DQ723396     1    30    30
browser |    30  100.0%          1     + 107446595 107446624              DQ723396     1    30    30
browser |    30  100.0%          1     + 107603348 107603377              DQ723396     1    30    30
browser |    30  100.0%          1     - 108215385 108215414              DQ723396     1    30    30
browser |    30  100.0%          1     + 109264129 109264158              DQ723396     1    30    30
browser |    30  100.0%          1     + 111495908 111495937              DQ723396     1    30    30
browser |    30  100.0%          1     + 113494384 113494413              DQ723396     1    30    30
browser |    30  100.0%          1     - 113905280 113905309              DQ723396     1    30    30
browser |    30  100.0%          1     - 114034978 114035007              DQ723396     1    30    30
browser |    30  100.0%          1     - 116321403 116321432              DQ723396     1    30    30
browser |    30  100.0%          1     - 120747093 120747122              DQ723396     1    30    30
browser |    30  100.0%          1     - 122900730 122900759              DQ723396     1    30    30
browser |    30  100.0%          1     - 158533220 158533249              DQ723396     1    30    30
browser |    30  100.0%          1     - 161041410 161041439              DQ723396     1    30    30
browser |    30  100.0%          1     - 162583920 162583949              DQ723396     1    30    30
browser |    30  100.0%          1     - 162823078 162823107              DQ723396     1    30    30
browser |    28  100.0%          1     - 166330088 166330115              DQ723396     3    30    30
browser |    30  100.0%          1     - 166363183 166363212              DQ723396     1    30    30
browser |    30  100.0%          1     + 167595239 167595268              DQ723396     1    30    30
browser |    30  100.0%          1     - 168293723 168293752              DQ723396     1    30    30
browser |    30  100.0%          1     - 168467580 168467609              DQ723396     1    30    30
browser |    28  100.0%          1     + 172789049 172789076              DQ723396     1    28    30
browser |    30  100.0%          1     + 173269474 173269503              DQ723396     1    30    30
browser |    30  100.0%          1     - 173988478 173988507              DQ723396     1    30    30
browser |    30  100.0%          1     - 175079670 175079699              DQ723396     1    30    30
browser |    30  100.0%          1     - 175860445 175860474              DQ723396     1    30    30
browser |    30  100.0%          1     + 177686914 177686943              DQ723396     1    30    30
browser |    30  100.0%          1     + 183411104 183411133              DQ723396     1    30    30
browser |    30  100.0%          1     - 183602370 183602399              DQ723396     1    30    30
browser |    28  100.0%          1     + 184166279 184166306              DQ723396     1    28    30
browser |    30  100.0%          1     - 185703943 185703972              DQ723396     1    30    30
browser |    30  100.0%          1     - 194690990 194691019              DQ723396     1    30    30
browser |    28  100.0%          1     - 194874900 194874927              DQ723396     1    28    30
browser |    30  100.0%          1     + 194988495 194988524              DQ723396     1    30    30
browser |    30  100.0%         10     +   3162325   3162354              DQ723396     1    30    30
browser |    30  100.0%         10     +   3173874   3173903              DQ723396     1    30    30
browser |    30  100.0%         10     -   4451713   4451742              DQ723396     1    30    30
browser |    30  100.0%         10     +   5326865   5326894              DQ723396     1    30    30
browser |    30  100.0%         10     +   8582749   8582778              DQ723396     1    30    30
browser |    30  100.0%         10     -   9888125   9888154              DQ723396     1    30    30
browser |    30  100.0%         10     -  10706393  10706422              DQ723396     1    30    30
browser |    30  100.0%         10     -  14703330  14703359              DQ723396     1    30    30
browser |    30  100.0%         10     +  15571953  15571982              DQ723396     1    30    30
browser |    30  100.0%         10     -  18626748  18626777              DQ723396     1    30    30
browser |    30  100.0%         10     +  20169355  20169384              DQ723396     1    30    30
browser |    30  100.0%         10     -  20519260  20519289              DQ723396     1    30    30
browser |    30  100.0%         10     +  23323430  23323459              DQ723396     1    30    30
browser |    30  100.0%         10     +  24187600  24187629              DQ723396     1    30    30
browser |    30  100.0%         10     +  30354843  30354872              DQ723396     1    30    30
browser |    30  100.0%         10     +  36465299  36465328              DQ723396     1    30    30
browser |    30  100.0%         10     +  37400744  37400773              DQ723396     1    30    30
browser |    30  100.0%         10     +  37650523  37650552              DQ723396     1    30    30
browser |    30  100.0%         10     +  38224659  38224688              DQ723396     1    30    30
browser |    30  100.0%         10     -  38613025  38613054              DQ723396     1    30    30
browser |    30  100.0%         10     +  38636724  38636753              DQ723396     1    30    30
browser |    30  100.0%         10     +  39186105  39186134              DQ723396     1    30    30
browser |    30  100.0%         10     +  39528945  39528974              DQ723396     1    30    30
browser |    28  100.0%         10     -  46602140  46602167              DQ723396     1    28    30
browser |    30  100.0%         10     -  47883140  47883169              DQ723396     1    30    30
browser |    30  100.0%         10     -  64038103  64038132              DQ723396     1    30    30
browser |    30  100.0%         10     -  66005598  66005627              DQ723396     1    30    30
browser |    30  100.0%         10     -  68143280  68143309              DQ723396     1    30    30
browser |    30  100.0%         10     -  71505620  71505649              DQ723396     1    30    30
browser |    30  100.0%         10     -  74244630  74244659              DQ723396     1    30    30
browser |    30  100.0%         10     -  75262313  75262342              DQ723396     1    30    30
browser |    30  100.0%         10     -  81274840  81274869              DQ723396     1    30    30
browser |    30  100.0%         10     +  86436525  86436554              DQ723396     1    30    30
browser |    30  100.0%         10     -  87523303  87523332              DQ723396     1    30    30
browser |    30  100.0%         10     -  87599040  87599069              DQ723396     1    30    30
browser |    30  100.0%         10     +  88887705  88887734              DQ723396     1    30    30
browser |    30  100.0%         10     -  90060815  90060844              DQ723396     1    30    30
browser |    30  100.0%         10     -  90257978  90258007              DQ723396     1    30    30
browser |    30  100.0%         10     -  90632535  90632564              DQ723396     1    30    30
browser |    30  100.0%         10     +  91476255  91476284              DQ723396     1    30    30
browser |    30  100.0%         10     +  97130700  97130729              DQ723396     1    30    30
browser |    30  100.0%         10     -  99616215  99616244              DQ723396     1    30    30
browser |    28  100.0%         10     + 101169820 101169847              DQ723396     1    28    30
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browser |    30  100.0%         10     - 103540430 103540459              DQ723396     1    30    30
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browser |    30  100.0%         10     + 106194865 106194894              DQ723396     1    30    30
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browser |    30  100.0%         10     - 109458983 109459012              DQ723396     1    30    30
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browser |    30  100.0%         10     - 114825570 114825599              DQ723396     1    30    30
browser |    30  100.0%         10     - 118310143 118310172              DQ723396     1    30    30
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browser |    30  100.0%         11     +   3690375   3690404              DQ723396     1    30    30
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browser |    30  100.0%         11     +   8335024   8335053              DQ723396     1    30    30
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browser |    30  100.0%          Y     +  80752088  80752117              DQ723396     1    30    30
browser |    30  100.0%          Y     +  82857095  82857124              DQ723396     1    30    30
browser |    30  100.0%          Y     +  84697895  84697924              DQ723396     1    30    30

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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