DQ557916
 

Information on mRNA DQ557916

Description: Mus musculus piRNA piR-25028, 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: DQ557916
Position: chr12:56795055-56795084

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 |    30  100.0%         12     +  56795055  56795084              DQ557916     1    30    30
browser |    30  100.0%          1     +   5874988   5875017              DQ557916     1    30    30
browser |    30  100.0%          1     -   6242578   6242607              DQ557916     1    30    30
browser |    30  100.0%          1     +   6501018   6501047              DQ557916     1    30    30
browser |    30  100.0%          1     -   8070593   8070622              DQ557916     1    30    30
browser |    30  100.0%          1     +  10800514  10800543              DQ557916     1    30    30
browser |    30  100.0%          1     +  11957767  11957796              DQ557916     1    30    30
browser |    30  100.0%          1     -  16815106  16815135              DQ557916     1    30    30
browser |    30  100.0%          1     -  18033694  18033723              DQ557916     1    30    30
browser |    30  100.0%          1     -  18590979  18591008              DQ557916     1    30    30
browser |    30  100.0%          1     -  19699319  19699348              DQ557916     1    30    30
browser |    30  100.0%          1     -  21654686  21654715              DQ557916     1    30    30
browser |    30  100.0%          1     +  26388680  26388709              DQ557916     1    30    30
browser |    30  100.0%          1     -  26459721  26459750              DQ557916     1    30    30
browser |    30  100.0%          1     +  26509874  26509903              DQ557916     1    30    30
browser |    30  100.0%          1     -  27225869  27225898              DQ557916     1    30    30
browser |    30  100.0%          1     +  29982233  29982262              DQ557916     1    30    30
browser |    30  100.0%          1     -  34389992  34390021              DQ557916     1    30    30
browser |    30  100.0%          1     -  34957819  34957848              DQ557916     1    30    30
browser |    30  100.0%          1     -  35834205  35834234              DQ557916     1    30    30
browser |    30  100.0%          1     -  37817247  37817276              DQ557916     1    30    30
browser |    30  100.0%          1     -  38747580  38747609              DQ557916     1    30    30
browser |    30  100.0%          1     -  40741164  40741193              DQ557916     1    30    30
browser |    30  100.0%          1     -  45778055  45778084              DQ557916     1    30    30
browser |    30  100.0%          1     +  48393921  48393950              DQ557916     1    30    30
browser |    30  100.0%          1     +  48841448  48841477              DQ557916     1    30    30
browser |    30  100.0%          1     +  53169212  53169241              DQ557916     1    30    30
browser |    30  100.0%          1     +  58362951  58362980              DQ557916     1    30    30
browser |    30  100.0%          1     +  58851260  58851289              DQ557916     1    30    30
browser |    30  100.0%          1     +  60764438  60764467              DQ557916     1    30    30
browser |    30  100.0%          1     +  62573707  62573736              DQ557916     1    30    30
browser |    30  100.0%          1     +  64217773  64217802              DQ557916     1    30    30
browser |    30  100.0%          1     +  64999901  64999930              DQ557916     1    30    30
browser |    30  100.0%          1     +  81542314  81542343              DQ557916     1    30    30
browser |    30  100.0%          1     -  82483267  82483296              DQ557916     1    30    30
browser |    30  100.0%          1     +  84974032  84974061              DQ557916     1    30    30
browser |    30  100.0%          1     -  87394526  87394555              DQ557916     1    30    30
browser |    30  100.0%          1     -  89130488  89130517              DQ557916     1    30    30
browser |    30  100.0%          1     +  91399371  91399400              DQ557916     1    30    30
browser |    30  100.0%          1     -  93888575  93888604              DQ557916     1    30    30
browser |    30  100.0%          1     -  97108495  97108524              DQ557916     1    30    30
browser |    30  100.0%          1     + 101906306 101906335              DQ557916     1    30    30
browser |    30  100.0%          1     - 102966043 102966072              DQ557916     1    30    30
browser |    30  100.0%          1     + 103133339 103133368              DQ557916     1    30    30
browser |    30  100.0%          1     - 103521301 103521330              DQ557916     1    30    30
browser |    30  100.0%          1     + 104217729 104217758              DQ557916     1    30    30
browser |    30  100.0%          1     + 107966961 107966990              DQ557916     1    30    30
browser |    30  100.0%          1     + 108337026 108337055              DQ557916     1    30    30
browser |    30  100.0%          1     + 109056835 109056864              DQ557916     1    30    30
browser |    30  100.0%          1     - 109547775 109547804              DQ557916     1    30    30
browser |    30  100.0%          1     - 110261547 110261576              DQ557916     1    30    30
browser |    30  100.0%          1     + 110865768 110865797              DQ557916     1    30    30
browser |    30  100.0%          1     + 111181793 111181822              DQ557916     1    30    30
browser |    30  100.0%          1     - 112950454 112950483              DQ557916     1    30    30
browser |    30  100.0%          1     - 114117763 114117792              DQ557916     1    30    30
browser |    30  100.0%          1     + 115813534 115813563              DQ557916     1    30    30
browser |    30  100.0%          1     + 116576437 116576466              DQ557916     1    30    30
browser |    30  100.0%          1     + 117630095 117630124              DQ557916     1    30    30
browser |    30  100.0%          1     + 120499015 120499044              DQ557916     1    30    30
browser |    30  100.0%          1     + 121705553 121705582              DQ557916     1    30    30
browser |    30  100.0%          1     - 125251238 125251267              DQ557916     1    30    30
browser |    30  100.0%          1     - 126356939 126356968              DQ557916     1    30    30
browser |    30  100.0%          1     - 126871659 126871688              DQ557916     1    30    30
browser |    30  100.0%          1     - 130466518 130466547              DQ557916     1    30    30
browser |    30  100.0%          1     - 139657357 139657386              DQ557916     1    30    30
browser |    30  100.0%          1     + 159797769 159797798              DQ557916     1    30    30
browser |    30  100.0%          1     + 160643882 160643911              DQ557916     1    30    30
browser |    30  100.0%          1     - 162674767 162674796              DQ557916     1    30    30
browser |    30  100.0%          1     + 163296498 163296527              DQ557916     1    30    30
browser |    30  100.0%          1     - 169376017 169376046              DQ557916     1    30    30
browser |    30  100.0%          1     - 169950008 169950037              DQ557916     1    30    30
browser |    30  100.0%          1     + 174869981 174870010              DQ557916     1    30    30
browser |    30  100.0%          1     + 176371063 176371092              DQ557916     1    30    30
browser |    30  100.0%          1     - 177892236 177892265              DQ557916     1    30    30
browser |    30  100.0%          1     - 178008325 178008354              DQ557916     1    30    30
browser |    30  100.0%          1     - 179728212 179728241              DQ557916     1    30    30
browser |    30  100.0%          1     - 180443512 180443541              DQ557916     1    30    30
browser |    30  100.0%          1     + 181091519 181091548              DQ557916     1    30    30
browser |    30  100.0%          1     - 181326605 181326634              DQ557916     1    30    30
browser |    30  100.0%         10     +   3551358   3551387              DQ557916     1    30    30
browser |    30  100.0%         10     +  19415073  19415102              DQ557916     1    30    30
browser |    30  100.0%         10     -  21091999  21092028              DQ557916     1    30    30
browser |    30  100.0%         10     +  21518646  21518675              DQ557916     1    30    30
browser |    30  100.0%         10     +  22559592  22559621              DQ557916     1    30    30
browser |    30  100.0%         10     -  24567023  24567052              DQ557916     1    30    30
browser |    30  100.0%         10     +  24977877  24977906              DQ557916     1    30    30
browser |    30  100.0%         10     -  25848741  25848770              DQ557916     1    30    30
browser |    30  100.0%         10     -  30696636  30696665              DQ557916     1    30    30
browser |    30  100.0%         10     -  30971318  30971347              DQ557916     1    30    30
browser |    30  100.0%         10     -  31365268  31365297              DQ557916     1    30    30
browser |    30  100.0%         10     -  31630411  31630440              DQ557916     1    30    30
browser |    30  100.0%         10     -  33766583  33766612              DQ557916     1    30    30
browser |    30  100.0%         10     +  34618250  34618279              DQ557916     1    30    30
browser |    30  100.0%         10     -  41723189  41723218              DQ557916     1    30    30
browser |    30  100.0%         10     +  45431428  45431457              DQ557916     1    30    30
browser |    30  100.0%         10     -  50371110  50371139              DQ557916     1    30    30
browser |    30  100.0%         10     -  51763560  51763589              DQ557916     1    30    30
browser |    30  100.0%         10     -  54469147  54469176              DQ557916     1    30    30
browser |    30  100.0%         10     +  55592060  55592089              DQ557916     1    30    30
browser |    30  100.0%         10     -  56603498  56603527              DQ557916     1    30    30
browser |    30  100.0%         10     -  57020417  57020446              DQ557916     1    30    30
browser |    30  100.0%         10     -  59222408  59222437              DQ557916     1    30    30
browser |    30  100.0%         10     -  62448543  62448572              DQ557916     1    30    30
browser |    30  100.0%         10     +  65475126  65475155              DQ557916     1    30    30
browser |    30  100.0%         10     +  65787025  65787054              DQ557916     1    30    30
browser |    30  100.0%         10     +  66558676  66558705              DQ557916     1    30    30
browser |    30  100.0%         10     +  75216877  75216906              DQ557916     1    30    30
browser |    30  100.0%         10     +  78652719  78652748              DQ557916     1    30    30
browser |    30  100.0%         10     -  80816229  80816258              DQ557916     1    30    30
browser |    30  100.0%         10     -  81810378  81810407              DQ557916     1    30    30
browser |    30  100.0%         10     +  83507213  83507242              DQ557916     1    30    30
browser |    30  100.0%         10     -  83628004  83628033              DQ557916     1    30    30
browser |    30  100.0%         10     -  84585295  84585324              DQ557916     1    30    30
browser |    30  100.0%         10     -  85556097  85556126              DQ557916     1    30    30
browser |    30  100.0%         10     +  85604724  85604753              DQ557916     1    30    30
browser |    30  100.0%         10     -  88803598  88803627              DQ557916     1    30    30
browser |    30  100.0%         10     +  90160903  90160932              DQ557916     1    30    30
browser |    30  100.0%         10     +  94198864  94198893              DQ557916     1    30    30
browser |    30  100.0%         10     +  95993535  95993564              DQ557916     1    30    30
browser |    30  100.0%         10     +  96028826  96028855              DQ557916     1    30    30
browser |    30  100.0%         10     +  98934486  98934515              DQ557916     1    30    30
browser |    30  100.0%         10     -  99181638  99181667              DQ557916     1    30    30
browser |    30  100.0%         10     - 104397860 104397889              DQ557916     1    30    30
browser |    30  100.0%         10     + 104655779 104655808              DQ557916     1    30    30
browser |    30  100.0%         10     - 104678087 104678116              DQ557916     1    30    30
browser |    30  100.0%         10     - 105017212 105017241              DQ557916     1    30    30
browser |    30  100.0%         10     + 105508944 105508973              DQ557916     1    30    30
browser |    30  100.0%         10     - 107842014 107842043              DQ557916     1    30    30
browser |    30  100.0%         10     + 109151505 109151534              DQ557916     1    30    30
browser |    30  100.0%         10     - 111893810 111893839              DQ557916     1    30    30
browser |    30  100.0%         10     + 113559042 113559071              DQ557916     1    30    30
browser |    30  100.0%         10     + 116442594 116442623              DQ557916     1    30    30
browser |    30  100.0%         10     - 117911930 117911959              DQ557916     1    30    30
browser |    30  100.0%         10     + 122139969 122139998              DQ557916     1    30    30
browser |    30  100.0%         10     - 124418882 124418911              DQ557916     1    30    30
browser |    30  100.0%         10     - 124446382 124446411              DQ557916     1    30    30
browser |    30  100.0%         10     + 124516781 124516810              DQ557916     1    30    30
browser |    30  100.0%         10     + 129225125 129225154              DQ557916     1    30    30
browser |    30  100.0%         10     - 129765078 129765107              DQ557916     1    30    30
browser |    30  100.0%         10     + 130396437 130396466              DQ557916     1    30    30
browser |    30  100.0%         11     -   5312508   5312537              DQ557916     1    30    30
browser |    30  100.0%         11     -   6485335   6485364              DQ557916     1    30    30
browser |    30  100.0%         11     +   9658414   9658443              DQ557916     1    30    30
browser |    30  100.0%         11     -  10716975  10717004              DQ557916     1    30    30
browser |    30  100.0%         11     +  12457723  12457752              DQ557916     1    30    30
browser |    30  100.0%         11     +  12904450  12904479              DQ557916     1    30    30
browser |    30  100.0%         11     -  15184361  15184390              DQ557916     1    30    30
browser |    30  100.0%         11     -  15837359  15837388              DQ557916     1    30    30
browser |    30  100.0%         11     +  19516610  19516639              DQ557916     1    30    30
browser |    30  100.0%         11     -  20470701  20470730              DQ557916     1    30    30
browser |    30  100.0%         11     +  22285687  22285716              DQ557916     1    30    30
browser |    30  100.0%         11     -  22532546  22532575              DQ557916     1    30    30
browser |    30  100.0%         11     +  23169011  23169040              DQ557916     1    30    30
browser |    30  100.0%         11     -  26510295  26510324              DQ557916     1    30    30
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browser |    30  100.0%         11     -  28053961  28053990              DQ557916     1    30    30
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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