DQ551039
 

Information on mRNA DQ551039

Description: Mus musculus piRNA piR-19151, 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: DQ551039
Position: chr12:56796292-56796323

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 |    32  100.0%         12     +  56796292  56796323              DQ551039     1    32    32
browser |    32  100.0%          1     +   5878977   5879008              DQ551039     1    32    32
browser |    32  100.0%          1     +   6505006   6505037              DQ551039     1    32    32
browser |    32  100.0%          1     -   8066611   8066642              DQ551039     1    32    32
browser |    32  100.0%          1     -   8229052   8229083              DQ551039     1    32    32
browser |    32  100.0%          1     -  13623476  13623507              DQ551039     1    32    32
browser |    32  100.0%          1     -  16811122  16811153              DQ551039     1    32    32
browser |    32  100.0%          1     -  18029716  18029747              DQ551039     1    32    32
browser |    32  100.0%          1     -  18589746  18589777              DQ551039     1    32    32
browser |    32  100.0%          1     -  19695330  19695361              DQ551039     1    32    32
browser |    32  100.0%          1     +  22069870  22069901              DQ551039     1    32    32
browser |    32  100.0%          1     -  26455738  26455769              DQ551039     1    32    32
browser |    32  100.0%          1     +  26512582  26512613              DQ551039     1    32    32
browser |    32  100.0%          1     -  27221886  27221917              DQ551039     1    32    32
browser |    32  100.0%          1     +  29985712  29985743              DQ551039     1    32    32
browser |    32  100.0%          1     -  34389219  34389250              DQ551039     1    32    32
browser |    32  100.0%          1     -  35830215  35830246              DQ551039     1    32    32
browser |    32  100.0%          1     -  40739732  40739763              DQ551039     1    32    32
browser |    32  100.0%          1     +  47264426  47264457              DQ551039     1    32    32
browser |    32  100.0%          1     +  48399767  48399798              DQ551039     1    32    32
browser |    32  100.0%          1     +  53171257  53171288              DQ551039     1    32    32
browser |    32  100.0%          1     +  58366932  58366963              DQ551039     1    32    32
browser |    32  100.0%          1     +  58855240  58855271              DQ551039     1    32    32
browser |    32  100.0%          1     +  60768426  60768457              DQ551039     1    32    32
browser |    32  100.0%          1     +  64221752  64221783              DQ551039     1    32    32
browser |    32  100.0%          1     -  64424922  64424953              DQ551039     1    32    32
browser |    32  100.0%          1     +  65003888  65003919              DQ551039     1    32    32
browser |    32  100.0%          1     +  67795000  67795031              DQ551039     1    32    32
browser |    32  100.0%          1     -  70278904  70278935              DQ551039     1    32    32
browser |    32  100.0%          1     +  74697008  74697039              DQ551039     1    32    32
browser |    32  100.0%          1     -  79917429  79917460              DQ551039     1    32    32
browser |    32  100.0%          1     +  81546301  81546332              DQ551039     1    32    32
browser |    32  100.0%          1     -  82481465  82481496              DQ551039     1    32    32
browser |    32  100.0%          1     +  87065783  87065814              DQ551039     1    32    32
browser |    32  100.0%          1     -  87390542  87390573              DQ551039     1    32    32
browser |    32  100.0%          1     +  91403356  91403387              DQ551039     1    32    32
browser |    32  100.0%          1     -  93886952  93886983              DQ551039     1    32    32
browser |    32  100.0%          1     -  95625540  95625571              DQ551039     1    32    32
browser |    32  100.0%          1     -  97103151  97103182              DQ551039     1    32    32
browser |    32  100.0%          1     + 101910291 101910322              DQ551039     1    32    32
browser |    32  100.0%          1     - 102962053 102962084              DQ551039     1    32    32
browser |    32  100.0%          1     + 103137320 103137351              DQ551039     1    32    32
browser |    32  100.0%          1     + 108341008 108341039              DQ551039     1    32    32
browser |    32  100.0%          1     - 109543795 109543826              DQ551039     1    32    32
browser |    32  100.0%          1     + 111185777 111185808              DQ551039     1    32    32
browser |    32  100.0%          1     - 111633763 111633794              DQ551039     1    32    32
browser |    32  100.0%          1     + 112196486 112196517              DQ551039     1    32    32
browser |    32  100.0%          1     - 112859872 112859903              DQ551039     1    32    32
browser |    32  100.0%          1     + 116580425 116580456              DQ551039     1    32    32
browser |    32  100.0%          1     + 117634083 117634114              DQ551039     1    32    32
browser |    32  100.0%          1     + 125275526 125275557              DQ551039     1    32    32
browser |    32  100.0%          1     + 127490419 127490450              DQ551039     1    32    32
browser |    32  100.0%          1     + 127807218 127807249              DQ551039     1    32    32
browser |    32  100.0%          1     - 130464717 130464748              DQ551039     1    32    32
browser |    32  100.0%          1     + 137203325 137203356              DQ551039     1    32    32
browser |    32  100.0%          1     - 140747213 140747244              DQ551039     1    32    32
browser |    32  100.0%          1     - 140965811 140965842              DQ551039     1    32    32
browser |    32  100.0%          1     - 144262570 144262601              DQ551039     1    32    32
browser |    32  100.0%          1     - 145999337 145999368              DQ551039     1    32    32
browser |    32  100.0%          1     - 149271660 149271691              DQ551039     1    32    32
browser |    32  100.0%          1     - 149459971 149460002              DQ551039     1    32    32
browser |    32  100.0%          1     + 154779118 154779149              DQ551039     1    32    32
browser |    32  100.0%          1     + 159801751 159801782              DQ551039     1    32    32
browser |    32  100.0%          1     - 162670783 162670814              DQ551039     1    32    32
browser |    32  100.0%          1     - 166182421 166182452              DQ551039     1    32    32
browser |    32  100.0%          1     - 169372030 169372061              DQ551039     1    32    32
browser |    32  100.0%          1     - 169946017 169946048              DQ551039     1    32    32
browser |    32  100.0%          1     + 174873156 174873187              DQ551039     1    32    32
browser |    32  100.0%          1     + 176375050 176375081              DQ551039     1    32    32
browser |    32  100.0%          1     - 177888282 177888313              DQ551039     1    32    32
browser |    32  100.0%          1     - 178004335 178004366              DQ551039     1    32    32
browser |    32  100.0%          1     - 179724230 179724261              DQ551039     1    32    32
browser |    32  100.0%          1     + 181095507 181095538              DQ551039     1    32    32
browser |    32  100.0%          1     - 181323124 181323155              DQ551039     1    32    32
browser |    32  100.0%          1     - 195005319 195005350              DQ551039     1    32    32
browser |    32  100.0%         10     +   3555347   3555378              DQ551039     1    32    32
browser |    32  100.0%         10     -   8477708   8477739              DQ551039     1    32    32
browser |    32  100.0%         10     -  11572687  11572718              DQ551039     1    32    32
browser |    32  100.0%         10     +  19419060  19419091              DQ551039     1    32    32
browser |    32  100.0%         10     -  19675559  19675590              DQ551039     1    32    32
browser |    32  100.0%         10     +  21522633  21522664              DQ551039     1    32    32
browser |    32  100.0%         10     +  22403524  22403555              DQ551039     1    32    32
browser |    32  100.0%         10     +  22563579  22563610              DQ551039     1    32    32
browser |    32  100.0%         10     +  23751634  23751665              DQ551039     1    32    32
browser |    32  100.0%         10     +  24979706  24979737              DQ551039     1    32    32
browser |    32  100.0%         10     -  25846980  25847011              DQ551039     1    32    32
browser |    32  100.0%         10     -  30692648  30692679              DQ551039     1    32    32
browser |    32  100.0%         10     -  30967333  30967364              DQ551039     1    32    32
browser |    32  100.0%         10     -  31361276  31361307              DQ551039     1    32    32
browser |    32  100.0%         10     +  34622237  34622268              DQ551039     1    32    32
browser |    32  100.0%         10     -  41719202  41719233              DQ551039     1    32    32
browser |    32  100.0%         10     +  43647509  43647540              DQ551039     1    32    32
browser |    32  100.0%         10     -  51761760  51761791              DQ551039     1    32    32
browser |    32  100.0%         10     -  56599508  56599539              DQ551039     1    32    32
browser |    32  100.0%         10     -  57016428  57016459              DQ551039     1    32    32
browser |    32  100.0%         10     -  62942430  62942461              DQ551039     1    32    32
browser |    32  100.0%         10     +  65478040  65478071              DQ551039     1    32    32
browser |    32  100.0%         10     +  66562655  66562686              DQ551039     1    32    32
browser |    32  100.0%         10     -  70629921  70629952              DQ551039     1    32    32
browser |    32  100.0%         10     -  71529914  71529945              DQ551039     1    32    32
browser |    32  100.0%         10     -  77789272  77789303              DQ551039     1    32    32
browser |    32  100.0%         10     +  78656204  78656235              DQ551039     1    32    32
browser |    32  100.0%         10     +  81669917  81669948              DQ551039     1    32    32
browser |    32  100.0%         10     -  81806392  81806423              DQ551039     1    32    32
browser |    32  100.0%         10     +  83306145  83306176              DQ551039     1    32    32
browser |    32  100.0%         10     +  83511200  83511231              DQ551039     1    32    32
browser |    32  100.0%         10     -  85553726  85553757              DQ551039     1    32    32
browser |    32  100.0%         10     -  88489513  88489544              DQ551039     1    32    32
browser |    32  100.0%         10     +  94202348  94202379              DQ551039     1    32    32
browser |    32  100.0%         10     +  96032808  96032839              DQ551039     1    32    32
browser |    32  100.0%         10     +  97162727  97162758              DQ551039     1    32    32
browser |    32  100.0%         10     -  99177652  99177683              DQ551039     1    32    32
browser |    32  100.0%         10     - 104393879 104393910              DQ551039     1    32    32
browser |    32  100.0%         10     - 104674096 104674127              DQ551039     1    32    32
browser |    32  100.0%         10     - 105015615 105015646              DQ551039     1    32    32
browser |    32  100.0%         10     - 107838025 107838056              DQ551039     1    32    32
browser |    32  100.0%         10     + 109155494 109155525              DQ551039     1    32    32
browser |    32  100.0%         10     - 110534796 110534827              DQ551039     1    32    32
browser |    32  100.0%         10     + 113563020 113563051              DQ551039     1    32    32
browser |    32  100.0%         10     + 116446581 116446612              DQ551039     1    32    32
browser |    32  100.0%         10     - 117909219 117909250              DQ551039     1    32    32
browser |    32  100.0%         10     - 121003304 121003335              DQ551039     1    32    32
browser |    32  100.0%         10     + 122204190 122204221              DQ551039     1    32    32
browser |    32  100.0%         10     - 122344339 122344370              DQ551039     1    32    32
browser |    32  100.0%         10     + 122673067 122673098              DQ551039     1    32    32
browser |    32  100.0%         10     - 123697916 123697947              DQ551039     1    32    32
browser |    32  100.0%         10     - 124414891 124414922              DQ551039     1    32    32
browser |    32  100.0%         10     + 124519261 124519292              DQ551039     1    32    32
browser |    32  100.0%         10     + 129229106 129229137              DQ551039     1    32    32
browser |    32  100.0%         10     - 129763839 129763870              DQ551039     1    32    32
browser |    32  100.0%         10     + 130399315 130399346              DQ551039     1    32    32
browser |    32  100.0%         11     +   6095908   6095939              DQ551039     1    32    32
browser |    32  100.0%         11     +   7530100   7530131              DQ551039     1    32    32
browser |    32  100.0%         11     +   9662399   9662430              DQ551039     1    32    32
browser |    32  100.0%         11     -  10712992  10713023              DQ551039     1    32    32
browser |    32  100.0%         11     -  12514602  12514633              DQ551039     1    32    32
browser |    32  100.0%         11     -  12748274  12748305              DQ551039     1    32    32
browser |    32  100.0%         11     +  18760872  18760903              DQ551039     1    32    32
browser |    32  100.0%         11     +  19517841  19517872              DQ551039     1    32    32
browser |    32  100.0%         11     +  23172999  23173030              DQ551039     1    32    32
browser |    32  100.0%         11     +  23194612  23194643              DQ551039     1    32    32
browser |    32  100.0%         11     -  27086279  27086310              DQ551039     1    32    32
browser |    32  100.0%         11     +  27904385  27904416              DQ551039     1    32    32
browser |    32  100.0%         11     -  28049975  28050006              DQ551039     1    32    32
browser |    32  100.0%         11     -  38375004  38375035              DQ551039     1    32    32
browser |    32  100.0%         11     +  39958968  39958999              DQ551039     1    32    32
browser |    32  100.0%         11     -  51331190  51331221              DQ551039     1    32    32
browser |    32  100.0%         11     +  54471816  54471847              DQ551039     1    32    32
browser |    32  100.0%         11     +  55136179  55136210              DQ551039     1    32    32
browser |    32  100.0%         11     -  61313943  61313974              DQ551039     1    32    32
browser |    32  100.0%         11     -  63361232  63361263              DQ551039     1    32    32
browser |    32  100.0%         11     +  65347026  65347057              DQ551039     1    32    32
browser |    32  100.0%         11     +  66842485  66842516              DQ551039     1    32    32
browser |    32  100.0%         11     -  74022440  74022471              DQ551039     1    32    32
browser |    32  100.0%         11     +  74114935  74114966              DQ551039     1    32    32
browser |    32  100.0%         11     -  74777902  74777933              DQ551039     1    32    32
browser |    32  100.0%         11     +  79634145  79634176              DQ551039     1    32    32
browser |    32  100.0%         11     -  81439046  81439077              DQ551039     1    32    32
browser |    32  100.0%         11     +  82226489  82226520              DQ551039     1    32    32
browser |    32  100.0%         11     +  85180812  85180843              DQ551039     1    32    32
browser |    32  100.0%         11     -  86739118  86739149              DQ551039     1    32    32
browser |    32  100.0%         11     +  88806199  88806230              DQ551039     1    32    32
browser |    32  100.0%         11     -  90795195  90795226              DQ551039     1    32    32
browser |    32  100.0%         11     +  90855416  90855447              DQ551039     1    32    32
browser |    32  100.0%         11     -  91992565  91992596              DQ551039     1    32    32
browser |    32  100.0%         11     -  98506769  98506800              DQ551039     1    32    32
browser |    32  100.0%         11     +  99605362  99605393              DQ551039     1    32    32
browser |    32  100.0%         11     - 100556425 100556456              DQ551039     1    32    32
browser |    32  100.0%         11     + 106185743 106185774              DQ551039     1    32    32
browser |    32  100.0%         11     - 111076011 111076042              DQ551039     1    32    32
browser |    32  100.0%         11     + 111110888 111110919              DQ551039     1    32    32
browser |    32  100.0%         11     - 113805701 113805732              DQ551039     1    32    32
browser |    32  100.0%         11     + 115650142 115650173              DQ551039     1    32    32
browser |    32  100.0%         11     - 116679068 116679099              DQ551039     1    32    32
browser |    32  100.0%         11     - 117393363 117393394              DQ551039     1    32    32
browser |    32  100.0%         11     - 120214662 120214693              DQ551039     1    32    32
browser |    32  100.0%         11     - 120963414 120963445              DQ551039     1    32    32
browser |    32  100.0%         12     -   3055049   3055080              DQ551039     1    32    32
browser |    32  100.0%         12     +   3085581   3085612              DQ551039     1    32    32
browser |    32  100.0%         12     +   3385225   3385256              DQ551039     1    32    32
browser |    32  100.0%         12     -   6569217   6569248              DQ551039     1    32    32
browser |    32  100.0%         12     -   6855708   6855739              DQ551039     1    32    32
browser |    32  100.0%         12     +  11158073  11158104              DQ551039     1    32    32
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browser |    32  100.0%         12     +  19312656  19312687              DQ551039     1    32    32
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browser |    32  100.0%         12     -  24448152  24448183              DQ551039     1    32    32
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browser |    32  100.0%         12     +  70712351  70712382              DQ551039     1    32    32
browser |    32  100.0%         12     +  70969200  70969231              DQ551039     1    32    32
browser |    32  100.0%         12     -  76794045  76794076              DQ551039     1    32    32
browser |    32  100.0%         12     +  79613030  79613061              DQ551039     1    32    32
browser |    32  100.0%         12     -  80466745  80466776              DQ551039     1    32    32
browser |    32  100.0%         12     +  85452212  85452243              DQ551039     1    32    32
browser |    32  100.0%         12     -  93479007  93479038              DQ551039     1    32    32
browser |    32  100.0%         12     +  94007699  94007730              DQ551039     1    32    32
browser |    32  100.0%         12     +  94239221  94239252              DQ551039     1    32    32
browser |    29  100.0%         12     +  96198622  96198650              DQ551039     1    29    32
browser |    32  100.0%         12     -  98324168  98324199              DQ551039     1    32    32
browser |    32  100.0%         12     + 105270898 105270929              DQ551039     1    32    32
browser |    32  100.0%         12     - 109871029 109871060              DQ551039     1    32    32
browser |    32  100.0%         12     - 114599719 114599750              DQ551039     1    32    32
browser |    32  100.0%         12     - 119557201 119557232              DQ551039     1    32    32
browser |    32  100.0%         13     -   4391126   4391157              DQ551039     1    32    32
browser |    32  100.0%         13     -   5330705   5330736              DQ551039     1    32    32
browser |    32  100.0%         13     +   8003593   8003624              DQ551039     1    32    32
browser |    32  100.0%         13     +   9487107   9487138              DQ551039     1    32    32
browser |    32  100.0%         13     +   9908405   9908436              DQ551039     1    32    32
browser |    32  100.0%         13     +  10943623  10943654              DQ551039     1    32    32
browser |    32  100.0%         13     -  11518638  11518669              DQ551039     1    32    32
browser |    32  100.0%         13     -  15608823  15608854              DQ551039     1    32    32
browser |    32  100.0%         13     +  19182452  19182483              DQ551039     1    32    32
browser |    32  100.0%         13     +  21818395  21818426              DQ551039     1    32    32
browser |    32  100.0%         13     -  22301841  22301872              DQ551039     1    32    32
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View details of parts of alignment within browser window.
Data schema/format description and download

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