DQ544566
 

Information on mRNA DQ544566

Description: Mus musculus piRNA piR-12678, complete sequence.
Gene: n/a
Product: n/a
Author: Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
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: 2008-11-02
Version: 1
mRNA sequence: DQ544566
Position: chr12:56796290-56796320

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 |    31  100.0%         12     +  56796290  56796320              DQ544566     1    31    31
browser |    31  100.0%          1     +   5878975   5879005              DQ544566     1    31    31
browser |    31  100.0%          1     +   6505004   6505034              DQ544566     1    31    31
browser |    31  100.0%          1     -   8066614   8066644              DQ544566     1    31    31
browser |    31  100.0%          1     -   8229055   8229085              DQ544566     1    31    31
browser |    31  100.0%          1     -  13623479  13623509              DQ544566     1    31    31
browser |    31  100.0%          1     -  16811125  16811155              DQ544566     1    31    31
browser |    31  100.0%          1     -  18029719  18029749              DQ544566     1    31    31
browser |    31  100.0%          1     -  18589749  18589779              DQ544566     1    31    31
browser |    31  100.0%          1     -  19695333  19695363              DQ544566     1    31    31
browser |    31  100.0%          1     +  22069868  22069898              DQ544566     1    31    31
browser |    31  100.0%          1     -  26455741  26455771              DQ544566     1    31    31
browser |    31  100.0%          1     +  26512580  26512610              DQ544566     1    31    31
browser |    31  100.0%          1     -  27221889  27221919              DQ544566     1    31    31
browser |    31  100.0%          1     +  29985710  29985740              DQ544566     1    31    31
browser |    31  100.0%          1     -  34389222  34389252              DQ544566     1    31    31
browser |    31  100.0%          1     -  35830218  35830248              DQ544566     1    31    31
browser |    31  100.0%          1     -  40739735  40739765              DQ544566     1    31    31
browser |    31  100.0%          1     +  47264424  47264454              DQ544566     1    31    31
browser |    31  100.0%          1     +  48399765  48399795              DQ544566     1    31    31
browser |    31  100.0%          1     +  53171255  53171285              DQ544566     1    31    31
browser |    31  100.0%          1     +  58366930  58366960              DQ544566     1    31    31
browser |    31  100.0%          1     +  58855238  58855268              DQ544566     1    31    31
browser |    31  100.0%          1     +  60768424  60768454              DQ544566     1    31    31
browser |    31  100.0%          1     +  64221750  64221780              DQ544566     1    31    31
browser |    31  100.0%          1     -  64424925  64424955              DQ544566     1    31    31
browser |    31  100.0%          1     +  65003886  65003916              DQ544566     1    31    31
browser |    31  100.0%          1     +  67794998  67795028              DQ544566     1    31    31
browser |    31  100.0%          1     -  70278907  70278937              DQ544566     1    31    31
browser |    31  100.0%          1     +  74697006  74697036              DQ544566     1    31    31
browser |    31  100.0%          1     -  79917432  79917462              DQ544566     1    31    31
browser |    31  100.0%          1     +  81546299  81546329              DQ544566     1    31    31
browser |    31  100.0%          1     -  82481468  82481498              DQ544566     1    31    31
browser |    31  100.0%          1     +  87065781  87065811              DQ544566     1    31    31
browser |    31  100.0%          1     -  87390545  87390575              DQ544566     1    31    31
browser |    31  100.0%          1     +  91403354  91403384              DQ544566     1    31    31
browser |    31  100.0%          1     -  93886955  93886985              DQ544566     1    31    31
browser |    31  100.0%          1     -  95625543  95625573              DQ544566     1    31    31
browser |    31  100.0%          1     -  97103154  97103184              DQ544566     1    31    31
browser |    31  100.0%          1     + 101910289 101910319              DQ544566     1    31    31
browser |    31  100.0%          1     - 102962056 102962086              DQ544566     1    31    31
browser |    31  100.0%          1     + 103137318 103137348              DQ544566     1    31    31
browser |    31  100.0%          1     + 108341006 108341036              DQ544566     1    31    31
browser |    31  100.0%          1     - 109543798 109543828              DQ544566     1    31    31
browser |    31  100.0%          1     + 111185775 111185805              DQ544566     1    31    31
browser |    31  100.0%          1     - 111633766 111633796              DQ544566     1    31    31
browser |    31  100.0%          1     + 112196484 112196514              DQ544566     1    31    31
browser |    31  100.0%          1     - 112859875 112859905              DQ544566     1    31    31
browser |    31  100.0%          1     + 116580423 116580453              DQ544566     1    31    31
browser |    31  100.0%          1     + 117634081 117634111              DQ544566     1    31    31
browser |    31  100.0%          1     + 125275524 125275554              DQ544566     1    31    31
browser |    31  100.0%          1     + 127490417 127490447              DQ544566     1    31    31
browser |    31  100.0%          1     + 127807216 127807246              DQ544566     1    31    31
browser |    31  100.0%          1     - 130464720 130464750              DQ544566     1    31    31
browser |    31  100.0%          1     + 137203323 137203353              DQ544566     1    31    31
browser |    31  100.0%          1     - 140747216 140747246              DQ544566     1    31    31
browser |    31  100.0%          1     - 140965814 140965844              DQ544566     1    31    31
browser |    31  100.0%          1     - 144262573 144262603              DQ544566     1    31    31
browser |    31  100.0%          1     - 145999340 145999370              DQ544566     1    31    31
browser |    31  100.0%          1     - 149271663 149271693              DQ544566     1    31    31
browser |    31  100.0%          1     - 149459974 149460004              DQ544566     1    31    31
browser |    31  100.0%          1     + 154779116 154779146              DQ544566     1    31    31
browser |    31  100.0%          1     + 159801749 159801779              DQ544566     1    31    31
browser |    31  100.0%          1     - 162670786 162670816              DQ544566     1    31    31
browser |    31  100.0%          1     - 166182424 166182454              DQ544566     1    31    31
browser |    31  100.0%          1     - 169372033 169372063              DQ544566     1    31    31
browser |    31  100.0%          1     - 169946020 169946050              DQ544566     1    31    31
browser |    31  100.0%          1     + 174873154 174873184              DQ544566     1    31    31
browser |    31  100.0%          1     + 176375048 176375078              DQ544566     1    31    31
browser |    31  100.0%          1     - 177888285 177888315              DQ544566     1    31    31
browser |    31  100.0%          1     - 178004338 178004368              DQ544566     1    31    31
browser |    31  100.0%          1     - 179724233 179724263              DQ544566     1    31    31
browser |    31  100.0%          1     + 181095505 181095535              DQ544566     1    31    31
browser |    31  100.0%          1     - 181323127 181323157              DQ544566     1    31    31
browser |    31  100.0%          1     - 195005322 195005352              DQ544566     1    31    31
browser |    31  100.0%         10     +   3555345   3555375              DQ544566     1    31    31
browser |    31  100.0%         10     -   8477711   8477741              DQ544566     1    31    31
browser |    31  100.0%         10     -  11572690  11572720              DQ544566     1    31    31
browser |    31  100.0%         10     +  19419058  19419088              DQ544566     1    31    31
browser |    31  100.0%         10     -  19675562  19675592              DQ544566     1    31    31
browser |    31  100.0%         10     +  21522631  21522661              DQ544566     1    31    31
browser |    31  100.0%         10     +  22403522  22403552              DQ544566     1    31    31
browser |    31  100.0%         10     +  22563577  22563607              DQ544566     1    31    31
browser |    31  100.0%         10     +  23751632  23751662              DQ544566     1    31    31
browser |    31  100.0%         10     +  24979704  24979734              DQ544566     1    31    31
browser |    31  100.0%         10     -  25846983  25847013              DQ544566     1    31    31
browser |    31  100.0%         10     -  30692651  30692681              DQ544566     1    31    31
browser |    31  100.0%         10     -  30967336  30967366              DQ544566     1    31    31
browser |    31  100.0%         10     -  31361279  31361309              DQ544566     1    31    31
browser |    31  100.0%         10     +  34622235  34622265              DQ544566     1    31    31
browser |    31  100.0%         10     -  41719205  41719235              DQ544566     1    31    31
browser |    31  100.0%         10     +  43647507  43647537              DQ544566     1    31    31
browser |    31  100.0%         10     -  51761763  51761793              DQ544566     1    31    31
browser |    31  100.0%         10     -  56599511  56599541              DQ544566     1    31    31
browser |    31  100.0%         10     -  57016431  57016461              DQ544566     1    31    31
browser |    31  100.0%         10     -  62942433  62942463              DQ544566     1    31    31
browser |    31  100.0%         10     +  65478038  65478068              DQ544566     1    31    31
browser |    31  100.0%         10     +  66562653  66562683              DQ544566     1    31    31
browser |    31  100.0%         10     -  70629924  70629954              DQ544566     1    31    31
browser |    31  100.0%         10     -  71529917  71529947              DQ544566     1    31    31
browser |    31  100.0%         10     -  77789275  77789305              DQ544566     1    31    31
browser |    31  100.0%         10     +  78656202  78656232              DQ544566     1    31    31
browser |    28  100.0%         10     +  81510787  81510814              DQ544566     1    28    31
browser |    31  100.0%         10     +  81669915  81669945              DQ544566     1    31    31
browser |    31  100.0%         10     -  81806395  81806425              DQ544566     1    31    31
browser |    31  100.0%         10     +  83306143  83306173              DQ544566     1    31    31
browser |    31  100.0%         10     +  83511198  83511228              DQ544566     1    31    31
browser |    31  100.0%         10     -  85553729  85553759              DQ544566     1    31    31
browser |    31  100.0%         10     -  88489516  88489546              DQ544566     1    31    31
browser |    31  100.0%         10     +  94202346  94202376              DQ544566     1    31    31
browser |    31  100.0%         10     +  96032806  96032836              DQ544566     1    31    31
browser |    31  100.0%         10     +  97162725  97162755              DQ544566     1    31    31
browser |    31  100.0%         10     -  99177655  99177685              DQ544566     1    31    31
browser |    31  100.0%         10     - 104393882 104393912              DQ544566     1    31    31
browser |    31  100.0%         10     - 104674099 104674129              DQ544566     1    31    31
browser |    31  100.0%         10     - 105015618 105015648              DQ544566     1    31    31
browser |    31  100.0%         10     - 107838028 107838058              DQ544566     1    31    31
browser |    31  100.0%         10     + 109155492 109155522              DQ544566     1    31    31
browser |    31  100.0%         10     - 110534799 110534829              DQ544566     1    31    31
browser |    31  100.0%         10     + 113563018 113563048              DQ544566     1    31    31
browser |    31  100.0%         10     + 116446579 116446609              DQ544566     1    31    31
browser |    31  100.0%         10     - 117909222 117909252              DQ544566     1    31    31
browser |    31  100.0%         10     - 121003307 121003337              DQ544566     1    31    31
browser |    31  100.0%         10     + 122204188 122204218              DQ544566     1    31    31
browser |    31  100.0%         10     - 122344342 122344372              DQ544566     1    31    31
browser |    31  100.0%         10     + 122673065 122673095              DQ544566     1    31    31
browser |    31  100.0%         10     - 123697919 123697949              DQ544566     1    31    31
browser |    31  100.0%         10     - 124414894 124414924              DQ544566     1    31    31
browser |    31  100.0%         10     + 124519259 124519289              DQ544566     1    31    31
browser |    31  100.0%         10     + 129229104 129229134              DQ544566     1    31    31
browser |    31  100.0%         10     - 129763842 129763872              DQ544566     1    31    31
browser |    31  100.0%         10     + 130399313 130399343              DQ544566     1    31    31
browser |    31  100.0%         11     +   6095906   6095936              DQ544566     1    31    31
browser |    31  100.0%         11     +   7530098   7530128              DQ544566     1    31    31
browser |    31  100.0%         11     +   9662397   9662427              DQ544566     1    31    31
browser |    31  100.0%         11     -  10712995  10713025              DQ544566     1    31    31
browser |    31  100.0%         11     -  12514605  12514635              DQ544566     1    31    31
browser |    31  100.0%         11     -  12748277  12748307              DQ544566     1    31    31
browser |    31  100.0%         11     +  18760870  18760900              DQ544566     1    31    31
browser |    31  100.0%         11     +  19517839  19517869              DQ544566     1    31    31
browser |    31  100.0%         11     +  23172997  23173027              DQ544566     1    31    31
browser |    31  100.0%         11     +  23194610  23194640              DQ544566     1    31    31
browser |    31  100.0%         11     -  27086282  27086312              DQ544566     1    31    31
browser |    31  100.0%         11     +  27904383  27904413              DQ544566     1    31    31
browser |    31  100.0%         11     -  28049978  28050008              DQ544566     1    31    31
browser |    31  100.0%         11     -  38375007  38375037              DQ544566     1    31    31
browser |    31  100.0%         11     +  39958966  39958996              DQ544566     1    31    31
browser |    31  100.0%         11     -  51331193  51331223              DQ544566     1    31    31
browser |    31  100.0%         11     +  54471814  54471844              DQ544566     1    31    31
browser |    31  100.0%         11     +  55136177  55136207              DQ544566     1    31    31
browser |    31  100.0%         11     -  61313946  61313976              DQ544566     1    31    31
browser |    31  100.0%         11     -  63361235  63361265              DQ544566     1    31    31
browser |    31  100.0%         11     +  65347024  65347054              DQ544566     1    31    31
browser |    31  100.0%         11     +  66842483  66842513              DQ544566     1    31    31
browser |    31  100.0%         11     -  74022443  74022473              DQ544566     1    31    31
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browser |    31  100.0%         11     - 100556428 100556458              DQ544566     1    31    31
browser |    31  100.0%         11     + 106185741 106185771              DQ544566     1    31    31
browser |    31  100.0%         11     - 111076014 111076044              DQ544566     1    31    31
browser |    31  100.0%         11     + 111110886 111110916              DQ544566     1    31    31
browser |    31  100.0%         11     - 113805704 113805734              DQ544566     1    31    31
browser |    31  100.0%         11     + 115650140 115650170              DQ544566     1    31    31
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browser |    31  100.0%         11     - 117393366 117393396              DQ544566     1    31    31
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browser |    31  100.0%         12     - 109871032 109871062              DQ544566     1    31    31
browser |    31  100.0%         12     - 114599722 114599752              DQ544566     1    31    31
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browser |    31  100.0%         12     - 119557204 119557234              DQ544566     1    31    31
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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