DQ706478
 

Information on mRNA DQ706478

Description: Mus musculus piRNA piR-121800, 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: DQ706478
Position: chr12:56959381-56959401

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     +  56959381  56959401              DQ706478     1    21    21
browser |    21  100.0%          1     +   5818086   5818106              DQ706478     1    21    21
browser |    21  100.0%          1     +   8195080   8195100              DQ706478     1    21    21
browser |    21  100.0%          1     +   8859223   8859243              DQ706478     1    21    21
browser |    21  100.0%          1     -  11439027  11439047              DQ706478     1    21    21
browser |    21  100.0%          1     +  14032350  14032370              DQ706478     1    21    21
browser |    21  100.0%          1     -  18323999  18324019              DQ706478     1    21    21
browser |    21  100.0%          1     -  22070744  22070764              DQ706478     1    21    21
browser |    21  100.0%          1     -  28496650  28496670              DQ706478     1    21    21
browser |    21  100.0%          1     +  29695747  29695767              DQ706478     1    21    21
browser |    21  100.0%          1     -  30728050  30728070              DQ706478     1    21    21
browser |    21  100.0%          1     +  31045496  31045516              DQ706478     1    21    21
browser |    21  100.0%          1     +  40739032  40739052              DQ706478     1    21    21
browser |    21  100.0%          1     +  41128882  41128902              DQ706478     1    21    21
browser |    21  100.0%          1     +  44400884  44400904              DQ706478     1    21    21
browser |    21  100.0%          1     +  48009758  48009778              DQ706478     1    21    21
browser |    21  100.0%          1     +  53276171  53276191              DQ706478     1    21    21
browser |    21  100.0%          1     -  65929930  65929950              DQ706478     1    21    21
browser |    21  100.0%          1     -  67146134  67146154              DQ706478     1    21    21
browser |    21  100.0%          1     +  68651299  68651319              DQ706478     1    21    21
browser |    21  100.0%          1     -  72169987  72170007              DQ706478     1    21    21
browser |    21  100.0%          1     +  75981047  75981067              DQ706478     1    21    21
browser |    21  100.0%          1     +  76567201  76567221              DQ706478     1    21    21
browser |    21  100.0%          1     +  78998436  78998456              DQ706478     1    21    21
browser |    21  100.0%          1     -  86246668  86246688              DQ706478     1    21    21
browser |    21  100.0%          1     -  96895897  96895917              DQ706478     1    21    21
browser |    21  100.0%          1     + 102078882 102078902              DQ706478     1    21    21
browser |    21  100.0%          1     + 103407821 103407841              DQ706478     1    21    21
browser |    21  100.0%          1     + 108066234 108066254              DQ706478     1    21    21
browser |    21  100.0%          1     + 109061907 109061927              DQ706478     1    21    21
browser |    21  100.0%          1     - 112197371 112197391              DQ706478     1    21    21
browser |    21  100.0%          1     - 117561173 117561193              DQ706478     1    21    21
browser |    21  100.0%          1     - 117676152 117676172              DQ706478     1    21    21
browser |    21  100.0%          1     + 117919199 117919219              DQ706478     1    21    21
browser |    21  100.0%          1     + 129019488 129019508              DQ706478     1    21    21
browser |    21  100.0%          1     - 136737104 136737124              DQ706478     1    21    21
browser |    21  100.0%          1     - 143724290 143724310              DQ706478     1    21    21
browser |    21  100.0%          1     + 171658878 171658898              DQ706478     1    21    21
browser |    21  100.0%         10     +   7316361   7316381              DQ706478     1    21    21
browser |    21  100.0%         10     +   8512352   8512372              DQ706478     1    21    21
browser |    21  100.0%         10     -  11777900  11777920              DQ706478     1    21    21
browser |    21  100.0%         10     +  18116158  18116178              DQ706478     1    21    21
browser |    21  100.0%         10     -  19891661  19891681              DQ706478     1    21    21
browser |    21  100.0%         10     -  22404399  22404419              DQ706478     1    21    21
browser |    21  100.0%         10     -  34616333  34616353              DQ706478     1    21    21
browser |    21  100.0%         10     -  35600112  35600132              DQ706478     1    21    21
browser |    21  100.0%         10     -  37728720  37728740              DQ706478     1    21    21
browser |    21  100.0%         10     +  43754658  43754678              DQ706478     1    21    21
browser |    21  100.0%         10     -  47513362  47513382              DQ706478     1    21    21
browser |    21  100.0%         10     -  47909628  47909648              DQ706478     1    21    21
browser |    21  100.0%         10     -  81511662  81511682              DQ706478     1    21    21
browser |    21  100.0%         10     -  81670790  81670810              DQ706478     1    21    21
browser |    21  100.0%         10     -  83252508  83252528              DQ706478     1    21    21
browser |    21  100.0%         10     -  83307019  83307039              DQ706478     1    21    21
browser |    21  100.0%         10     +  86980283  86980303              DQ706478     1    21    21
browser |    21  100.0%         10     -  91651524  91651544              DQ706478     1    21    21
browser |    21  100.0%         10     + 122343487 122343507              DQ706478     1    21    21
browser |    21  100.0%         10     + 123697054 123697074              DQ706478     1    21    21
browser |    21  100.0%         11     +   6748784   6748804              DQ706478     1    21    21
browser |    21  100.0%         11     -   9036134   9036154              DQ706478     1    21    21
browser |    21  100.0%         11     +  12747410  12747430              DQ706478     1    21    21
browser |    21  100.0%         11     +  13824350  13824370              DQ706478     1    21    21
browser |    21  100.0%         11     -  14847992  14848012              DQ706478     1    21    21
browser |    21  100.0%         11     +  15811485  15811505              DQ706478     1    21    21
browser |    21  100.0%         11     -  16155577  16155597              DQ706478     1    21    21
browser |    21  100.0%         11     -  20460406  20460426              DQ706478     1    21    21
browser |    21  100.0%         11     +  27085579  27085599              DQ706478     1    21    21
browser |    21  100.0%         11     -  29115242  29115262              DQ706478     1    21    21
browser |    21  100.0%         11     +  29231675  29231695              DQ706478     1    21    21
browser |    21  100.0%         11     +  38374141  38374161              DQ706478     1    21    21
browser |    21  100.0%         11     +  44276542  44276562              DQ706478     1    21    21
browser |    21  100.0%         11     +  67022006  67022026              DQ706478     1    21    21
browser |    21  100.0%         11     +  79765353  79765373              DQ706478     1    21    21
browser |    21  100.0%         11     -  85331649  85331669              DQ706478     1    21    21
browser |    21  100.0%         11     -  85331685  85331705              DQ706478     1    21    21
browser |    21  100.0%         11     +  90399868  90399888              DQ706478     1    21    21
browser |    21  100.0%         11     - 104751755 104751775              DQ706478     1    21    21
browser |    21  100.0%         12     -   3086292   3086312              DQ706478     1    21    21
browser |    21  100.0%         12     +   4839201   4839221              DQ706478     1    21    21
browser |    21  100.0%         12     +   6854845   6854865              DQ706478     1    21    21
browser |    21  100.0%         12     +  14492685  14492705              DQ706478     1    21    21
browser |    21  100.0%         12     +  17979972  17979992              DQ706478     1    21    21
browser |    21  100.0%         12     +  18011622  18011642              DQ706478     1    21    21
browser |    21  100.0%         12     +  18182060  18182080              DQ706478     1    21    21
browser |    21  100.0%         12     -  18330379  18330399              DQ706478     1    21    21
browser |    21  100.0%         12     +  18518855  18518875              DQ706478     1    21    21
browser |    21  100.0%         12     +  19826323  19826343              DQ706478     1    21    21
browser |    21  100.0%         12     -  19850765  19850785              DQ706478     1    21    21
browser |    21  100.0%         12     -  20693956  20693976              DQ706478     1    21    21
browser |    21  100.0%         12     +  21655581  21655601              DQ706478     1    21    21
browser |    21  100.0%         12     +  22093787  22093807              DQ706478     1    21    21
browser |    21  100.0%         12     -  22426448  22426468              DQ706478     1    21    21
browser |    21  100.0%         12     -  23585459  23585479              DQ706478     1    21    21
browser |    21  100.0%         12     -  26157811  26157831              DQ706478     1    21    21
browser |    21  100.0%         12     +  33798683  33798703              DQ706478     1    21    21
browser |    21  100.0%         12     +  42921262  42921282              DQ706478     1    21    21
browser |    21  100.0%         12     -  60758972  60758992              DQ706478     1    21    21
browser |    21  100.0%         12     +  63337877  63337897              DQ706478     1    21    21
browser |    21  100.0%         12     -  70970074  70970094              DQ706478     1    21    21
browser |    21  100.0%         12     +  72686874  72686894              DQ706478     1    21    21
browser |    21  100.0%         12     +  76701264  76701284              DQ706478     1    21    21
browser |    21  100.0%         12     +  91195616  91195636              DQ706478     1    21    21
browser |    21  100.0%         12     - 105271772 105271792              DQ706478     1    21    21
browser |    21  100.0%         12     + 105595717 105595737              DQ706478     1    21    21
browser |    21  100.0%         12     - 109788258 109788278              DQ706478     1    21    21
browser |    21  100.0%         12     + 114489497 114489517              DQ706478     1    21    21
browser |    21  100.0%         12     + 114906295 114906315              DQ706478     1    21    21
browser |    21  100.0%         12     + 115523663 115523683              DQ706478     1    21    21
browser |    21  100.0%         13     -   3066860   3066880              DQ706478     1    21    21
browser |    21  100.0%         13     +   3666263   3666283              DQ706478     1    21    21
browser |    21  100.0%         13     -   4878910   4878930              DQ706478     1    21    21
browser |    21  100.0%         13     -   4953027   4953047              DQ706478     1    21    21
browser |    21  100.0%         13     -   8073209   8073229              DQ706478     1    21    21
browser |    21  100.0%         13     -   8318607   8318627              DQ706478     1    21    21
browser |    21  100.0%         13     +  11143235  11143255              DQ706478     1    21    21
browser |    21  100.0%         13     -  23828224  23828244              DQ706478     1    21    21
browser |    21  100.0%         13     +  27473361  27473381              DQ706478     1    21    21
browser |    21  100.0%         13     -  33959881  33959901              DQ706478     1    21    21
browser |    21  100.0%         13     -  50712332  50712352              DQ706478     1    21    21
browser |    21  100.0%         13     +  65667892  65667912              DQ706478     1    21    21
browser |    21  100.0%         13     -  77381450  77381470              DQ706478     1    21    21
browser |    21  100.0%         13     -  81233212  81233232              DQ706478     1    21    21
browser |    21  100.0%         13     +  82260640  82260660              DQ706478     1    21    21
browser |    21  100.0%         13     -  82356403  82356423              DQ706478     1    21    21
browser |    21  100.0%         13     -  86561942  86561962              DQ706478     1    21    21
browser |    21  100.0%         13     -  88923438  88923458              DQ706478     1    21    21
browser |    21  100.0%         13     - 104084970 104084990              DQ706478     1    21    21
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browser |    21  100.0%         14     -  85241262  85241282              DQ706478     1    21    21
browser |    21  100.0%         14     -  85417747  85417767              DQ706478     1    21    21
browser |    21  100.0%         14     -  89819919  89819939              DQ706478     1    21    21
browser |    21  100.0%         14     -  95804221  95804241              DQ706478     1    21    21
browser |    21  100.0%         14     -  98993682  98993702              DQ706478     1    21    21
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browser |    21  100.0%         14     + 103874500 103874520              DQ706478     1    21    21
browser |    21  100.0%         14     + 106589240 106589260              DQ706478     1    21    21
browser |    21  100.0%         14     - 107064498 107064518              DQ706478     1    21    21
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browser |    21  100.0%         14     + 112501444 112501464              DQ706478     1    21    21
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browser |    21  100.0%         15     +   3197240   3197260              DQ706478     1    21    21
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browser |    21  100.0%         19     +  45176752  45176772              DQ706478     1    21    21
browser |    21  100.0%  1_GL456211v1_random     -    136381    136401              DQ706478     1    21    21
browser |    21  100.0%          2     -   9030547   9030567              DQ706478     1    21    21
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browser |    21  100.0%          2     +  78148653  78148673              DQ706478     1    21    21
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browser |    21  100.0%          2     -  82950837  82950857              DQ706478     1    21    21
browser |    21  100.0%          2     - 106398383 106398403              DQ706478     1    21    21
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browser |    21  100.0%          2     - 138776264 138776284              DQ706478     1    21    21
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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