DQ709412
 

Information on mRNA DQ709412

Description: Mus musculus piRNA piR-124734, 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: DQ709412
Position: chr12:56798655-56798680

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     -  56798655  56798680              DQ709412     1    26    26
browser |    26  100.0%          1     +   6238629   6238654              DQ709412     1    26    26
browser |    26  100.0%          1     +   6242980   6243005              DQ709412     1    26    26
browser |    26  100.0%          1     -   6500637   6500662              DQ709412     1    26    26
browser |    26  100.0%          1     -   6507405   6507430              DQ709412     1    26    26
browser |    26  100.0%          1     +   8226709   8226734              DQ709412     1    26    26
browser |    26  100.0%          1     +   8233413   8233438              DQ709412     1    26    26
browser |    26  100.0%          1     -  11957372  11957397              DQ709412     1    26    26
browser |    26  100.0%          1     -  11961583  11961608              DQ709412     1    26    26
browser |    26  100.0%          1     +  14069079  14069104              DQ709412     1    26    26
browser |    26  100.0%          1     +  18587358  18587383              DQ709412     1    26    26
browser |    26  100.0%          1     +  18591379  18591404              DQ709412     1    26    26
browser |    26  100.0%          1     +  19692894  19692919              DQ709412     1    26    26
browser |    26  100.0%          1     +  19699739  19699764              DQ709412     1    26    26
browser |    26  100.0%          1     -  26388298  26388323              DQ709412     1    26    26
browser |    26  100.0%          1     -  26393150  26393175              DQ709412     1    26    26
browser |    26  100.0%          1     +  26453365  26453390              DQ709412     1    26    26
browser |    26  100.0%          1     +  26460106  26460131              DQ709412     1    26    26
browser |    26  100.0%          1     +  27219527  27219552              DQ709412     1    26    26
browser |    26  100.0%          1     +  27226284  27226309              DQ709412     1    26    26
browser |    26  100.0%          1     +  34386833  34386858              DQ709412     1    26    26
browser |    26  100.0%          1     +  34390393  34390418              DQ709412     1    26    26
browser |    26  100.0%          1     +  34954440  34954465              DQ709412     1    26    26
browser |    26  100.0%          1     -  53168778  53168803              DQ709412     1    26    26
browser |    26  100.0%          1     -  53173607  53173632              DQ709412     1    26    26
browser |    26  100.0%          1     -  54658151  54658176              DQ709412     1    26    26
browser |    26  100.0%          1     -  58362539  58362564              DQ709412     1    26    26
browser |    26  100.0%          1     -  58369294  58369319              DQ709412     1    26    26
browser |    26  100.0%          1     -  58850879  58850904              DQ709412     1    26    26
browser |    26  100.0%          1     -  58857713  58857738              DQ709412     1    26    26
browser |    26  100.0%          1     -  62573234  62573259              DQ709412     1    26    26
browser |    26  100.0%          1     -  62580058  62580083              DQ709412     1    26    26
browser |    26  100.0%          1     -  64999503  64999528              DQ709412     1    26    26
browser |    26  100.0%          1     -  81541916  81541941              DQ709412     1    26    26
browser |    26  100.0%          1     -  81548643  81548668              DQ709412     1    26    26
browser |    26  100.0%          1     +  89127126  89127151              DQ709412     1    26    26
browser |    26  100.0%          1     +  89130924  89130949              DQ709412     1    26    26
browser |    26  100.0%          1     +  97100707  97100732              DQ709412     1    26    26
browser |    26  100.0%          1     +  97108880  97108905              DQ709412     1    26    26
browser |    26  100.0%          1     + 102959703 102959728              DQ709412     1    26    26
browser |    26  100.0%          1     + 102966461 102966486              DQ709412     1    26    26
browser |    26  100.0%          1     - 103132923 103132948              DQ709412     1    26    26
browser |    26  100.0%          1     - 103139676 103139701              DQ709412     1    26    26
browser |    26  100.0%          1     + 103516766 103516791              DQ709412     1    26    26
browser |    26  100.0%          1     + 103521735 103521760              DQ709412     1    26    26
browser |    26  100.0%          1     - 104217335 104217360              DQ709412     1    26    26
browser |    26  100.0%          1     - 104222224 104222249              DQ709412     1    26    26
browser |    26  100.0%          1     - 107966565 107966590              DQ709412     1    26    26
browser |    26  100.0%          1     - 107968301 107968326              DQ709412     1    26    26
browser |    26  100.0%          1     - 109056438 109056463              DQ709412     1    26    26
browser |    26  100.0%          1     - 109061342 109061367              DQ709412     1    26    26
browser |    26  100.0%          1     + 109541447 109541472              DQ709412     1    26    26
browser |    26  100.0%          1     + 109548205 109548230              DQ709412     1    26    26
browser |    26  100.0%          1     + 110257125 110257150              DQ709412     1    26    26
browser |    26  100.0%          1     + 110261933 110261958              DQ709412     1    26    26
browser |    26  100.0%          1     - 110865371 110865396              DQ709412     1    26    26
browser |    26  100.0%          1     - 110869849 110869874              DQ709412     1    26    26
browser |    26  100.0%          1     + 114113311 114113336              DQ709412     1    26    26
browser |    26  100.0%          1     + 114118230 114118255              DQ709412     1    26    26
browser |    26  100.0%          1     - 115813020 115813045              DQ709412     1    26    26
browser |    26  100.0%          1     - 115817998 115818023              DQ709412     1    26    26
browser |    26  100.0%          1     - 116576028 116576053              DQ709412     1    26    26
browser |    26  100.0%          1     - 116582790 116582815              DQ709412     1    26    26
browser |    26  100.0%          1     + 126352091 126352116              DQ709412     1    26    26
browser |    26  100.0%          1     + 126357374 126357399              DQ709412     1    26    26
browser |    26  100.0%          1     - 159797373 159797398              DQ709412     1    26    26
browser |    26  100.0%          1     - 159804102 159804127              DQ709412     1    26    26
browser |    26  100.0%          1     - 160643500 160643525              DQ709412     1    26    26
browser |    26  100.0%          1     - 160648292 160648317              DQ709412     1    26    26
browser |    26  100.0%          1     - 163520569 163520594              DQ709412     1    26    26
browser |    26  100.0%          1     + 178001955 178001980              DQ709412     1    26    26
browser |    26  100.0%          1     + 178008706 178008731              DQ709412     1    26    26
browser |    26  100.0%          1     - 181091123 181091148              DQ709412     1    26    26
browser |    26  100.0%          1     - 181097852 181097877              DQ709412     1    26    26
browser |    26  100.0%          1     + 191840020 191840045              DQ709412     1    26    26
browser |    26  100.0%          1     + 194336441 194336466              DQ709412     1    26    26
browser |    26  100.0%         10     -   3550976   3551001              DQ709412     1    26    26
browser |    26  100.0%         10     +  21087398  21087423              DQ709412     1    26    26
browser |    26  100.0%         10     +  21092398  21092423              DQ709412     1    26    26
browser |    26  100.0%         10     -  21518218  21518243              DQ709412     1    26    26
browser |    26  100.0%         10     -  21525069  21525094              DQ709412     1    26    26
browser |    26  100.0%         10     -  22559152  22559177              DQ709412     1    26    26
browser |    26  100.0%         10     -  22566080  22566105              DQ709412     1    26    26
browser |    26  100.0%         10     +  24562654  24562679              DQ709412     1    26    26
browser |    26  100.0%         10     +  24567455  24567480              DQ709412     1    26    26
browser |    26  100.0%         10     -  24977496  24977521              DQ709412     1    26    26
browser |    26  100.0%         10     -  24982107  24982132              DQ709412     1    26    26
browser |    26  100.0%         10     +  25844599  25844624              DQ709412     1    26    26
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browser |    26  100.0%         10     +  30964904  30964929              DQ709412     1    26    26
browser |    26  100.0%         10     +  30971764  30971789              DQ709412     1    26    26
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browser |    26  100.0%         10     +  33767032  33767057              DQ709412     1    26    26
browser |    26  100.0%         10     -  34617853  34617878              DQ709412     1    26    26
browser |    26  100.0%         10     -  34624602  34624627              DQ709412     1    26    26
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browser |    26  100.0%         10     -  45430938  45430963              DQ709412     1    26    26
browser |    26  100.0%         10     -  45435963  45435988              DQ709412     1    26    26
browser |    26  100.0%         10     +  54465165  54465190              DQ709412     1    26    26
browser |    26  100.0%         10     -  65786578  65786603              DQ709412     1    26    26
browser |    26  100.0%         10     -  65791598  65791623              DQ709412     1    26    26
browser |    26  100.0%         10     +  80812166  80812191              DQ709412     1    26    26
browser |    26  100.0%         10     +  80816629  80816654              DQ709412     1    26    26
browser |    26  100.0%         10     -  83506818  83506843              DQ709412     1    26    26
browser |    26  100.0%         10     -  83513543  83513568              DQ709412     1    26    26
browser |    26  100.0%         10     +  83623635  83623660              DQ709412     1    26    26
browser |    26  100.0%         10     +  83628406  83628431              DQ709412     1    26    26
browser |    26  100.0%         10     +  84580802  84580827              DQ709412     1    26    26
browser |    26  100.0%         10     +  84585750  84585775              DQ709412     1    26    26
browser |    26  100.0%         10     -  90160523  90160548              DQ709412     1    26    26
browser |    26  100.0%         10     -  90165291  90165316              DQ709412     1    26    26
browser |    26  100.0%         10     -  95993116  95993141              DQ709412     1    26    26
browser |    26  100.0%         10     -  95997965  95997990              DQ709412     1    26    26
browser |    26  100.0%         10     -  96028430  96028455              DQ709412     1    26    26
browser |    26  100.0%         10     -  96035245  96035270              DQ709412     1    26    26
browser |    26  100.0%         10     +  97377937  97377962              DQ709412     1    26    26
browser |    26  100.0%         10     -  98934087  98934112              DQ709412     1    26    26
browser |    26  100.0%         10     -  98938969  98938994              DQ709412     1    26    26
browser |    26  100.0%         10     - 104655344 104655369              DQ709412     1    26    26
browser |    26  100.0%         10     - 104660346 104660371              DQ709412     1    26    26
browser |    26  100.0%         10     + 104671752 104671777              DQ709412     1    26    26
browser |    26  100.0%         10     + 104678487 104678512              DQ709412     1    26    26
browser |    26  100.0%         10     - 104857649 104857674              DQ709412     1    26    26
browser |    26  100.0%         10     - 105508495 105508520              DQ709412     1    26    26
browser |    26  100.0%         10     - 105513423 105513448              DQ709412     1    26    26
browser |    26  100.0%         10     + 107835689 107835714              DQ709412     1    26    26
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browser |    26  100.0%         10     + 121000933 121000958              DQ709412     1    26    26
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browser |    26  100.0%         10     - 122206576 122206601              DQ709412     1    26    26
browser |    26  100.0%         10     + 124441959 124441984              DQ709412     1    26    26
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browser |    26  100.0%         11     +   3999264   3999289              DQ709412     1    26    26
browser |    26  100.0%         11     +   5312893   5312918              DQ709412     1    26    26
browser |    26  100.0%         11     -   9658018   9658043              DQ709412     1    26    26
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browser |    26  100.0%         11     -  12457341  12457366              DQ709412     1    26    26
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View details of parts of alignment within browser window
.
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