DQ710188
 

Information on mRNA DQ710188

Description: Mus musculus piRNA piR-125510, 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: DQ710188
Position: chr12:56796184-56796210

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 |    27  100.0%         12     -  56796184  56796210              DQ710188     1    27    27
browser |    27  100.0%          1     -   5878869   5878895              DQ710188     1    27    27
browser |    27  100.0%          1     -   6504898   6504924              DQ710188     1    27    27
browser |    27  100.0%          1     +   8066724   8066750              DQ710188     1    27    27
browser |    27  100.0%          1     +   8229165   8229191              DQ710188     1    27    27
browser |    27  100.0%          1     -  10804385  10804411              DQ710188     1    27    27
browser |    27  100.0%          1     +  13623589  13623615              DQ710188     1    27    27
browser |    27  100.0%          1     +  16811235  16811261              DQ710188     1    27    27
browser |    27  100.0%          1     +  18029829  18029855              DQ710188     1    27    27
browser |    27  100.0%          1     +  18589859  18589885              DQ710188     1    27    27
browser |    27  100.0%          1     +  19695443  19695469              DQ710188     1    27    27
browser |    27  100.0%          1     -  22069774  22069800              DQ710188     1    27    27
browser |    27  100.0%          1     +  26455851  26455877              DQ710188     1    27    27
browser |    27  100.0%          1     -  26512474  26512500              DQ710188     1    27    27
browser |    27  100.0%          1     +  27221999  27222025              DQ710188     1    27    27
browser |    27  100.0%          1     +  29696623  29696649              DQ710188     1    27    27
browser |    27  100.0%          1     -  29985604  29985630              DQ710188     1    27    27
browser |    27  100.0%          1     +  34389332  34389358              DQ710188     1    27    27
browser |    27  100.0%          1     -  48399659  48399685              DQ710188     1    27    27
browser |    27  100.0%          1     -  53171149  53171175              DQ710188     1    27    27
browser |    27  100.0%          1     -  58366824  58366850              DQ710188     1    27    27
browser |    27  100.0%          1     -  58855132  58855158              DQ710188     1    27    27
browser |    27  100.0%          1     -  60768318  60768344              DQ710188     1    27    27
browser |    27  100.0%          1     +  64425035  64425061              DQ710188     1    27    27
browser |    27  100.0%          1     -  66061087  66061113              DQ710188     1    27    27
browser |    27  100.0%          1     -  67794892  67794918              DQ710188     1    27    27
browser |    27  100.0%          1     +  70279017  70279043              DQ710188     1    27    27
browser |    27  100.0%          1     -  72169004  72169030              DQ710188     1    27    27
browser |    27  100.0%          1     -  74696900  74696926              DQ710188     1    27    27
browser |    27  100.0%          1     +  76594131  76594157              DQ710188     1    27    27
browser |    27  100.0%          1     +  79917542  79917568              DQ710188     1    27    27
browser |    27  100.0%          1     -  81546193  81546219              DQ710188     1    27    27
browser |    27  100.0%          1     +  82481578  82481604              DQ710188     1    27    27
browser |    27  100.0%          1     -  87065675  87065701              DQ710188     1    27    27
browser |    27  100.0%          1     +  87390655  87390681              DQ710188     1    27    27
browser |    27  100.0%          1     -  91403248  91403274              DQ710188     1    27    27
browser |    27  100.0%          1     +  93887065  93887091              DQ710188     1    27    27
browser |    27  100.0%          1     +  95625653  95625679              DQ710188     1    27    27
browser |    27  100.0%          1     - 101910183 101910209              DQ710188     1    27    27
browser |    27  100.0%          1     + 102962166 102962192              DQ710188     1    27    27
browser |    27  100.0%          1     - 103137212 103137238              DQ710188     1    27    27
browser |    27  100.0%          1     - 108340900 108340926              DQ710188     1    27    27
browser |    27  100.0%          1     + 109543908 109543934              DQ710188     1    27    27
browser |    27  100.0%          1     - 111185669 111185695              DQ710188     1    27    27
browser |    27  100.0%          1     + 111633876 111633902              DQ710188     1    27    27
browser |    27  100.0%          1     - 112196378 112196404              DQ710188     1    27    27
browser |    27  100.0%          1     + 112859985 112860011              DQ710188     1    27    27
browser |    27  100.0%          1     + 112946583 112946609              DQ710188     1    27    27
browser |    27  100.0%          1     - 116580317 116580343              DQ710188     1    27    27
browser |    27  100.0%          1     - 117633975 117634001              DQ710188     1    27    27
browser |    27  100.0%          1     - 125275418 125275444              DQ710188     1    27    27
browser |    27  100.0%          1     - 127490311 127490337              DQ710188     1    27    27
browser |    27  100.0%          1     - 127807110 127807136              DQ710188     1    27    27
browser |    27  100.0%          1     + 130464830 130464856              DQ710188     1    27    27
browser |    27  100.0%          1     - 137203217 137203243              DQ710188     1    27    27
browser |    27  100.0%          1     + 140747326 140747352              DQ710188     1    27    27
browser |    27  100.0%          1     + 140965924 140965950              DQ710188     1    27    27
browser |    27  100.0%          1     + 144262683 144262709              DQ710188     1    27    27
browser |    27  100.0%          1     + 145999450 145999476              DQ710188     1    27    27
browser |    27  100.0%          1     + 149271773 149271799              DQ710188     1    27    27
browser |    27  100.0%          1     + 149460084 149460110              DQ710188     1    27    27
browser |    27  100.0%          1     - 154779010 154779036              DQ710188     1    27    27
browser |    27  100.0%          1     - 159801643 159801669              DQ710188     1    27    27
browser |    27  100.0%          1     + 162670896 162670922              DQ710188     1    27    27
browser |    27  100.0%          1     + 166182534 166182560              DQ710188     1    27    27
browser |    27  100.0%          1     - 166594516 166594542              DQ710188     1    27    27
browser |    27  100.0%          1     + 169372143 169372169              DQ710188     1    27    27
browser |    27  100.0%          1     + 169946130 169946156              DQ710188     1    27    27
browser |    27  100.0%          1     - 174873048 174873074              DQ710188     1    27    27
browser |    27  100.0%          1     - 176374942 176374968              DQ710188     1    27    27
browser |    27  100.0%          1     + 177888395 177888421              DQ710188     1    27    27
browser |    27  100.0%          1     + 178004448 178004474              DQ710188     1    27    27
browser |    27  100.0%          1     + 179724343 179724369              DQ710188     1    27    27
browser |    27  100.0%          1     - 181095399 181095425              DQ710188     1    27    27
browser |    27  100.0%          1     + 181323237 181323263              DQ710188     1    27    27
browser |    27  100.0%          1     + 183299056 183299082              DQ710188     1    27    27
browser |    27  100.0%          1     + 195005432 195005458              DQ710188     1    27    27
browser |    27  100.0%         10     -   3555239   3555265              DQ710188     1    27    27
browser |    27  100.0%         10     +   8477821   8477847              DQ710188     1    27    27
browser |    27  100.0%         10     +  11572800  11572826              DQ710188     1    27    27
browser |    27  100.0%         10     -  19418952  19418978              DQ710188     1    27    27
browser |    27  100.0%         10     +  19675672  19675698              DQ710188     1    27    27
browser |    27  100.0%         10     -  19890679  19890705              DQ710188     1    27    27
browser |    27  100.0%         10     -  21522525  21522551              DQ710188     1    27    27
browser |    27  100.0%         10     -  22403416  22403442              DQ710188     1    27    27
browser |    27  100.0%         10     -  22563471  22563497              DQ710188     1    27    27
browser |    27  100.0%         10     -  23751526  23751552              DQ710188     1    27    27
browser |    27  100.0%         10     -  24979598  24979624              DQ710188     1    27    27
browser |    27  100.0%         10     +  25847093  25847119              DQ710188     1    27    27
browser |    27  100.0%         10     +  30692761  30692787              DQ710188     1    27    27
browser |    27  100.0%         10     +  30967446  30967472              DQ710188     1    27    27
browser |    27  100.0%         10     +  31361389  31361415              DQ710188     1    27    27
browser |    27  100.0%         10     -  34622129  34622155              DQ710188     1    27    27
browser |    27  100.0%         10     +  41719315  41719341              DQ710188     1    27    27
browser |    26  100.0%         10     -  43647402  43647427              DQ710188     1    26    27
browser |    27  100.0%         10     +  51761873  51761899              DQ710188     1    27    27
browser |    27  100.0%         10     +  56599621  56599647              DQ710188     1    27    27
browser |    27  100.0%         10     +  57016541  57016567              DQ710188     1    27    27
browser |    27  100.0%         10     +  62942543  62942569              DQ710188     1    27    27
browser |    27  100.0%         10     -  65477932  65477958              DQ710188     1    27    27
browser |    27  100.0%         10     -  66562547  66562573              DQ710188     1    27    27
browser |    27  100.0%         10     +  70630034  70630060              DQ710188     1    27    27
browser |    27  100.0%         10     +  71530027  71530053              DQ710188     1    27    27
browser |    27  100.0%         10     +  77789385  77789411              DQ710188     1    27    27
browser |    27  100.0%         10     -  78656096  78656122              DQ710188     1    27    27
browser |    27  100.0%         10     -  81510681  81510707              DQ710188     1    27    27
browser |    27  100.0%         10     -  81669809  81669835              DQ710188     1    27    27
browser |    27  100.0%         10     +  81806505  81806531              DQ710188     1    27    27
browser |    27  100.0%         10     -  83306037  83306063              DQ710188     1    27    27
browser |    27  100.0%         10     -  83511092  83511118              DQ710188     1    27    27
browser |    27  100.0%         10     +  85553839  85553865              DQ710188     1    27    27
browser |    27  100.0%         10     +  88489626  88489652              DQ710188     1    27    27
browser |    27  100.0%         10     -  94202240  94202266              DQ710188     1    27    27
browser |    27  100.0%         10     -  96032700  96032726              DQ710188     1    27    27
browser |    27  100.0%         10     -  97162619  97162645              DQ710188     1    27    27
browser |    27  100.0%         10     +  99177765  99177791              DQ710188     1    27    27
browser |    27  100.0%         10     + 104393992 104394018              DQ710188     1    27    27
browser |    27  100.0%         10     + 104674209 104674235              DQ710188     1    27    27
browser |    27  100.0%         10     + 105015728 105015754              DQ710188     1    27    27
browser |    27  100.0%         10     + 107838138 107838164              DQ710188     1    27    27
browser |    27  100.0%         10     - 109155386 109155412              DQ710188     1    27    27
browser |    27  100.0%         10     + 110534909 110534935              DQ710188     1    27    27
browser |    27  100.0%         10     - 113562912 113562938              DQ710188     1    27    27
browser |    27  100.0%         10     - 116446473 116446499              DQ710188     1    27    27
browser |    27  100.0%         10     + 117909332 117909358              DQ710188     1    27    27
browser |    27  100.0%         10     + 121003417 121003443              DQ710188     1    27    27
browser |    27  100.0%         10     - 122204082 122204108              DQ710188     1    27    27
browser |    27  100.0%         10     - 122672959 122672985              DQ710188     1    27    27
browser |    27  100.0%         10     + 123698029 123698055              DQ710188     1    27    27
browser |    27  100.0%         10     + 124415004 124415030              DQ710188     1    27    27
browser |    27  100.0%         10     - 124519153 124519179              DQ710188     1    27    27
browser |    27  100.0%         10     - 129228998 129229024              DQ710188     1    27    27
browser |    27  100.0%         10     + 129763952 129763978              DQ710188     1    27    27
browser |    27  100.0%         10     - 130399207 130399233              DQ710188     1    27    27
browser |    27  100.0%         11     -   6095800   6095826              DQ710188     1    27    27
browser |    27  100.0%         11     -   7529992   7530018              DQ710188     1    27    27
browser |    27  100.0%         11     -   9662291   9662317              DQ710188     1    27    27
browser |    27  100.0%         11     +  10713105  10713131              DQ710188     1    27    27
browser |    27  100.0%         11     +  12514715  12514741              DQ710188     1    27    27
browser |    27  100.0%         11     +  12748387  12748413              DQ710188     1    27    27
browser |    27  100.0%         11     +  15180485  15180511              DQ710188     1    27    27
browser |    27  100.0%         11     -  18760764  18760790              DQ710188     1    27    27
browser |    27  100.0%         11     -  19517733  19517759              DQ710188     1    27    27
browser |    27  100.0%         11     +  20469171  20469197              DQ710188     1    27    27
browser |    27  100.0%         11     -  23172891  23172917              DQ710188     1    27    27
browser |    27  100.0%         11     -  23194504  23194530              DQ710188     1    27    27
browser |    26  100.0%         11     +  27086392  27086417              DQ710188     1    26    27
browser |    27  100.0%         11     -  27904277  27904303              DQ710188     1    27    27
browser |    27  100.0%         11     +  28050088  28050114              DQ710188     1    27    27
browser |    27  100.0%         11     +  38375117  38375143              DQ710188     1    27    27
browser |    27  100.0%         11     -  39958860  39958886              DQ710188     1    27    27
browser |    27  100.0%         11     +  51331303  51331329              DQ710188     1    27    27
browser |    27  100.0%         11     -  54471708  54471734              DQ710188     1    27    27
browser |    27  100.0%         11     -  55136071  55136097              DQ710188     1    27    27
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browser |    27  100.0%         11     +  81439159  81439185              DQ710188     1    27    27
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browser |    27  100.0%         11     - 106185635 106185661              DQ710188     1    27    27
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browser |    27  100.0%         12     -  94007591  94007617              DQ710188     1    27    27
browser |    27  100.0%         12     -  94239113  94239139              DQ710188     1    27    27
browser |    27  100.0%         12     -  96198514  96198540              DQ710188     1    27    27
browser |    27  100.0%         12     +  98324281  98324307              DQ710188     1    27    27
browser |    27  100.0%         12     - 105270790 105270816              DQ710188     1    27    27
browser |    27  100.0%         12     + 109871142 109871168              DQ710188     1    27    27
browser |    27  100.0%         12     + 114599832 114599858              DQ710188     1    27    27
browser |    27  100.0%         12     + 115524640 115524666              DQ710188     1    27    27
browser |    26  100.0%         12     + 118320895 118320920              DQ710188     1    26    27
browser |    27  100.0%         12     + 119557314 119557340              DQ710188     1    27    27
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browser |    27  100.0%         13     +   5330818   5330844              DQ710188     1    27    27
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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