DQ717533
 

Information on mRNA DQ717533

Description: Mus musculus piRNA piR-132855, 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: DQ717533
Position: chr12:56960137-56960160

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 |    24  100.0%         12     -  56960137  56960160              DQ717533     1    24    24
browser |    24  100.0%          1     +   4627761   4627784              DQ717533     1    24    24
browser |    24  100.0%          1     -   7681953   7681976              DQ717533     1    24    24
browser |    22  100.0%          1     +   8248986   8249007              DQ717533     1    22    24
browser |    24  100.0%          1     +   8728995   8729018              DQ717533     1    24    24
browser |    24  100.0%          1     -   8860124   8860147              DQ717533     1    24    24
browser |    24  100.0%          1     +  11100208  11100231              DQ717533     1    24    24
browser |    24  100.0%          1     +  11438151  11438174              DQ717533     1    24    24
browser |    24  100.0%          1     +  12017280  12017303              DQ717533     1    24    24
browser |    24  100.0%          1     -  14033244  14033267              DQ717533     1    24    24
browser |    24  100.0%          1     -  29697663  29697686              DQ717533     1    24    24
browser |    24  100.0%          1     +  30727291  30727314              DQ717533     1    24    24
browser |    24  100.0%          1     +  37318328  37318351              DQ717533     1    24    24
browser |    24  100.0%          1     -  41129773  41129796              DQ717533     1    24    24
browser |    24  100.0%          1     +  47263030  47263053              DQ717533     1    24    24
browser |    24  100.0%          1     -  47829589  47829612              DQ717533     1    24    24
browser |    24  100.0%          1     +  58789094  58789117              DQ717533     1    24    24
browser |    24  100.0%          1     -  76595422  76595445              DQ717533     1    24    24
browser |    24  100.0%          1     -  77648052  77648075              DQ717533     1    24    24
browser |    24  100.0%          1     -  95626925  95626948              DQ717533     1    24    24
browser |    24  100.0%          1     +  98528524  98528547              DQ717533     1    24    24
browser |    24  100.0%          1     + 108873421 108873444              DQ717533     1    24    24
browser |    24  100.0%          1     - 108887758 108887781              DQ717533     1    24    24
browser |    24  100.0%          1     - 111637739 111637762              DQ717533     1    24    24
browser |    24  100.0%          1     + 112192519 112192542              DQ717533     1    24    24
browser |    24  100.0%          1     - 112289961 112289984              DQ717533     1    24    24
browser |    24  100.0%          1     + 112492476 112492499              DQ717533     1    24    24
browser |    24  100.0%          1     + 117560414 117560437              DQ717533     1    24    24
browser |    22  100.0%          1     - 128818977 128818998              DQ717533     1    22    24
browser |    24  100.0%          1     + 136736207 136736230              DQ717533     1    24    24
browser |    24  100.0%          1     + 146158378 146158401              DQ717533     1    24    24
browser |    24  100.0%          1     - 161363163 161363186              DQ717533     1    24    24
browser |    24  100.0%          1     - 166411732 166411755              DQ717533     1    24    24
browser |    24  100.0%          1     - 195009293 195009316              DQ717533     1    24    24
browser |    24  100.0%         10     +   3266784   3266807              DQ717533     1    24    24
browser |    24  100.0%         10     -   7193530   7193553              DQ717533     1    24    24
browser |    24  100.0%         10     -   8481685   8481708              DQ717533     1    24    24
browser |    24  100.0%         10     -   8513109   8513132              DQ717533     1    24    24
browser |    24  100.0%         10     -   9727068   9727091              DQ717533     1    24    24
browser |    24  100.0%         10     -  11576663  11576686              DQ717533     1    24    24
browser |    24  100.0%         10     +  11776997  11777020              DQ717533     1    24    24
browser |    24  100.0%         10     -  18117043  18117066              DQ717533     1    24    24
browser |    24  100.0%         10     -  19676800  19676823              DQ717533     1    24    24
browser |    24  100.0%         10     +  22399561  22399584              DQ717533     1    24    24
browser |    24  100.0%         10     +  23747665  23747688              DQ717533     1    24    24
browser |    24  100.0%         10     -  32814700  32814723              DQ717533     1    24    24
browser |    24  100.0%         10     +  34615429  34615452              DQ717533     1    24    24
browser |    24  100.0%         10     -  38469387  38469410              DQ717533     1    24    24
browser |    24  100.0%         10     -  43755547  43755570              DQ717533     1    24    24
browser |    24  100.0%         10     +  47512483  47512506              DQ717533     1    24    24
browser |    24  100.0%         10     -  47550219  47550242              DQ717533     1    24    24
browser |    24  100.0%         10     +  47557216  47557239              DQ717533     1    24    24
browser |    24  100.0%         10     +  48868463  48868486              DQ717533     1    24    24
browser |    24  100.0%         10     -  74714787  74714810              DQ717533     1    24    24
browser |    24  100.0%         10     -  76759205  76759228              DQ717533     1    24    24
browser |    24  100.0%         10     +  81506821  81506844              DQ717533     1    24    24
browser |    24  100.0%         10     +  81665949  81665972              DQ717533     1    24    24
browser |    24  100.0%         10     +  82407692  82407715              DQ717533     1    24    24
browser |    24  100.0%         10     -  86981168  86981191              DQ717533     1    24    24
browser |    24  100.0%         10     -  88493471  88493494              DQ717533     1    24    24
browser |    24  100.0%         10     +  97156867  97156890              DQ717533     1    24    24
browser |    24  100.0%         10     - 100419162 100419185              DQ717533     1    24    24
browser |    24  100.0%         10     - 103911930 103911953              DQ717533     1    24    24
browser |    24  100.0%         10     - 110536222 110536245              DQ717533     1    24    24
browser |    24  100.0%         10     - 121979041 121979064              DQ717533     1    24    24
browser |    22  100.0%         10     - 122348320 122348341              DQ717533     1    22    24
browser |    24  100.0%         10     + 122669209 122669232              DQ717533     1    24    24
browser |    24  100.0%         11     -   6749684   6749707              DQ717533     1    24    24
browser |    24  100.0%         11     +   7526134   7526157              DQ717533     1    24    24
browser |    24  100.0%         11     +   9035237   9035260              DQ717533     1    24    24
browser |    24  100.0%         11     -  14521086  14521109              DQ717533     1    24    24
browser |    24  100.0%         11     +  14847091  14847114              DQ717533     1    24    24
browser |    24  100.0%         11     +  16154675  16154698              DQ717533     1    24    24
browser |    24  100.0%         11     -  16182203  16182226              DQ717533     1    24    24
browser |    24  100.0%         11     +  18756903  18756926              DQ717533     1    24    24
browser |    24  100.0%         11     +  19739172  19739195              DQ717533     1    24    24
browser |    24  100.0%         11     +  23193215  23193238              DQ717533     1    24    24
browser |    24  100.0%         11     -  27087663  27087686              DQ717533     1    24    24
browser |    24  100.0%         11     +  29114483  29114506              DQ717533     1    24    24
browser |    24  100.0%         11     -  29232575  29232598              DQ717533     1    24    24
browser |    24  100.0%         11     +  54467847  54467870              DQ717533     1    24    24
browser |    24  100.0%         11     +  70931648  70931671              DQ717533     1    24    24
browser |    24  100.0%         11     +  70957021  70957044              DQ717533     1    24    24
browser |    24  100.0%         11     +  73837534  73837557              DQ717533     1    24    24
browser |    24  100.0%         11     +  79632733  79632756              DQ717533     1    24    24
browser |    24  100.0%         11     -  79767437  79767460              DQ717533     1    24    24
browser |    24  100.0%         11     +  85330745  85330768              DQ717533     1    24    24
browser |    24  100.0%         11     -  90400759  90400782              DQ717533     1    24    24
browser |    24  100.0%         11     + 104750868 104750891              DQ717533     1    24    24
browser |    24  100.0%         12     +   3084163   3084186              DQ717533     1    24    24
browser |    24  100.0%         12     -   3112797   3112820              DQ717533     1    24    24
browser |    24  100.0%         12     -   6859685   6859708              DQ717533     1    24    24
browser |    24  100.0%         12     +  14644608  14644631              DQ717533     1    24    24
browser |    24  100.0%         12     -  18016468  18016491              DQ717533     1    24    24
browser |    22  100.0%         12     -  19831163  19831184              DQ717533     3    24    24
browser |    24  100.0%         12     +  19848802  19848825              DQ717533     1    24    24
browser |    24  100.0%         12     +  19864632  19864655              DQ717533     1    24    24
browser |    24  100.0%         12     -  21656472  21656495              DQ717533     1    24    24
browser |    24  100.0%         12     +  22425556  22425579              DQ717533     1    24    24
browser |    24  100.0%         12     +  23584568  23584591              DQ717533     1    24    24
browser |    24  100.0%         12     -  24745639  24745662              DQ717533     1    24    24
browser |    24  100.0%         12     +  26156917  26156940              DQ717533     1    24    24
browser |    24  100.0%         12     -  39485782  39485805              DQ717533     1    24    24
browser |    24  100.0%         12     +  52219988  52220011              DQ717533     1    24    24
browser |    24  100.0%         12     -  54407839  54407862              DQ717533     1    24    24
browser |    24  100.0%         12     +  60754130  60754153              DQ717533     1    24    24
browser |    24  100.0%         12     -  63338626  63338649              DQ717533     1    24    24
browser |    24  100.0%         12     -  74747348  74747371              DQ717533     1    24    24
browser |    24  100.0%         12     -  88482933  88482956              DQ717533     1    24    24
browser |    24  100.0%         12     -  90738022  90738045              DQ717533     1    24    24
browser |    24  100.0%         12     +  94235755  94235778              DQ717533     1    24    24
browser |    24  100.0%         12     -  96906705  96906728              DQ717533     1    24    24
browser |    24  100.0%         12     -  98328145  98328168              DQ717533     1    24    24
browser |    24  100.0%         12     + 109787499 109787522              DQ717533     1    24    24
browser |    22  100.0%         12     - 115365811 115365832              DQ717533     1    22    24
browser |    24  100.0%         13     -   3668377   3668400              DQ717533     1    24    24
browser |    24  100.0%         13     +   4510268   4510291              DQ717533     1    24    24
browser |    24  100.0%         13     +   4952149   4952172              DQ717533     1    24    24
browser |    24  100.0%         13     +   5295151   5295174              DQ717533     1    24    24
browser |    24  100.0%         13     +   8317710   8317733              DQ717533     1    24    24
browser |    24  100.0%         13     +   9903227   9903250              DQ717533     1    24    24
browser |    24  100.0%         13     -  12877981  12878004              DQ717533     1    24    24
browser |    24  100.0%         13     +  23823381  23823404              DQ717533     1    24    24
browser |    24  100.0%         13     -  27474259  27474282              DQ717533     1    24    24
browser |    24  100.0%         13     -  32489528  32489551              DQ717533     1    24    24
browser |    24  100.0%         13     -  32541185  32541208              DQ717533     1    24    24
browser |    24  100.0%         13     +  33958987  33959010              DQ717533     1    24    24
browser |    24  100.0%         13     +  50711573  50711596              DQ717533     1    24    24
browser |    24  100.0%         13     -  51189664  51189687              DQ717533     1    24    24
browser |    24  100.0%         13     -  54923222  54923245              DQ717533     1    24    24
browser |    24  100.0%         13     +  59269860  59269883              DQ717533     1    24    24
browser |    24  100.0%         13     +  61095333  61095356              DQ717533     1    24    24
browser |    24  100.0%         13     +  62807670  62807693              DQ717533     1    24    24
browser |    24  100.0%         13     +  64646863  64646886              DQ717533     1    24    24
browser |    24  100.0%         13     -  65668782  65668805              DQ717533     1    24    24
browser |    24  100.0%         13     -  68146444  68146467              DQ717533     1    24    24
browser |    24  100.0%         13     +  73291324  73291347              DQ717533     1    24    24
browser |    24  100.0%         13     +  81232315  81232338              DQ717533     1    24    24
browser |    24  100.0%         13     +  87212440  87212463              DQ717533     1    24    24
browser |    24  100.0%         13     +  88308787  88308810              DQ717533     1    24    24
browser |    24  100.0%         13     -  93674059  93674082              DQ717533     1    24    24
browser |    24  100.0%         13     - 102101165 102101188              DQ717533     1    24    24
browser |    24  100.0%         13     + 104084067 104084090              DQ717533     1    24    24
browser |    24  100.0%         13     - 106924249 106924272              DQ717533     1    24    24
browser |    24  100.0%         13     + 114675996 114676019              DQ717533     1    24    24
browser |    23  100.0%         13     - 118287977 118287999              DQ717533     1    23    24
browser |    24  100.0%         14     +   5088200   5088223              DQ717533     1    24    24
browser |    24  100.0%         14     +   7002743   7002766              DQ717533     1    24    24
browser |    24  100.0%         14     +   8129952   8129975              DQ717533     1    24    24
browser |    24  100.0%         14     +  11143936  11143959              DQ717533     1    24    24
browser |    24  100.0%         14     -  13342149  13342172              DQ717533     1    24    24
browser |    24  100.0%         14     +  23022219  23022242              DQ717533     1    24    24
browser |    24  100.0%         14     -  29487750  29487773              DQ717533     1    24    24
browser |    24  100.0%         14     +  31641709  31641732              DQ717533     1    24    24
browser |    24  100.0%         14     +  37223071  37223094              DQ717533     1    24    24
browser |    24  100.0%         14     -  37749445  37749468              DQ717533     1    24    24
browser |    24  100.0%         14     -  39458730  39458753              DQ717533     1    24    24
browser |    24  100.0%         14     -  51559600  51559623              DQ717533     1    24    24
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browser |    24  100.0%         14     -  66853945  66853968              DQ717533     1    24    24
browser |    24  100.0%         14     -  71459520  71459543              DQ717533     1    24    24
browser |    24  100.0%         14     -  72040938  72040961              DQ717533     1    24    24
browser |    24  100.0%         14     +  84468618  84468641              DQ717533     1    24    24
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browser |    24  100.0%         14     -  86373038  86373061              DQ717533     1    24    24
browser |    24  100.0%         14     +  98992788  98992811              DQ717533     1    24    24
browser |    24  100.0%         14     - 101821051 101821074              DQ717533     1    24    24
browser |    24  100.0%         14     + 107063598 107063621              DQ717533     1    24    24
browser |    24  100.0%         14     + 117316804 117316827              DQ717533     1    24    24
browser |    24  100.0%         14     + 117523605 117523628              DQ717533     1    24    24
browser |    24  100.0%         14     + 121244946 121244969              DQ717533     1    24    24
browser |    24  100.0%         15     -   3199324   3199347              DQ717533     1    24    24
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browser |    24  100.0%         15     -  14731354  14731377              DQ717533     1    24    24
browser |    24  100.0%         15     -  16186045  16186068              DQ717533     1    24    24
browser |    24  100.0%         15     -  17581140  17581163              DQ717533     1    24    24
browser |    24  100.0%         15     -  19053343  19053366              DQ717533     1    24    24
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browser |    24  100.0%         16     -  20927557  20927580              DQ717533     1    24    24
browser |    24  100.0%         16     -  22801377  22801400              DQ717533     1    24    24
browser |    24  100.0%         16     -  46944492  46944515              DQ717533     1    24    24
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browser |    24  100.0%         16     +  61133367  61133390              DQ717533     1    24    24
browser |    24  100.0%         16     +  61145007  61145030              DQ717533     1    24    24
browser |    23  100.0%         16     +  61151025  61151047              DQ717533     2    24    24
browser |    24  100.0%         16     +  62199270  62199293              DQ717533     1    24    24
browser |    24  100.0%         16     -  64790429  64790452              DQ717533     1    24    24
browser |    24  100.0%         16     -  69762394  69762417              DQ717533     1    24    24
browser |    24  100.0%         16     +  70068136  70068159              DQ717533     1    24    24
browser |    24  100.0%         16     +  71816731  71816754              DQ717533     1    24    24
browser |    24  100.0%         16     +  78242138  78242161              DQ717533     1    24    24
browser |    24  100.0%         16     +  79339738  79339761              DQ717533     1    24    24
browser |    24  100.0%         16     -  88946224  88946247              DQ717533     1    24    24
browser |    24  100.0%         16     -  97904262  97904285              DQ717533     1    24    24
browser |    22  100.0%         17     -  12506492  12506513              DQ717533     1    22    24
browser |    24  100.0%         17     -  15091328  15091351              DQ717533     1    24    24
browser |    24  100.0%         17     +  23338625  23338648              DQ717533     1    24    24
browser |    24  100.0%         17     -  34451455  34451478              DQ717533     1    24    24
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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